Module:Infobox gene
"یَمہٕ ماڈیوٗلُک دَستاویز ییٚہِ Module:Infobox gene/دَستاویز جاے بَناونہٕ"
local p = {}
local localSeparatorStr = "،" -- **lclz** Kashmiri comma
local localNotApplicableStr = "دٔستِیاب کِہیٖن" -- **lclz** n/a
local root
--define Global Color Scheme
local rowBGcolor = 'light-dark(#eee, #27292d) !important' --'var(--background-color-neutral)'
local titleBGcolor = 'light-dark(#ddd, #404244) !important'
local sideTitleBGcolor = 'light-dark(#c3fdb8, #003500) !important'
-- wrapped "protected call", return "value error" with error info on error
local function check_values(f,args)
local exist, val = pcall(f, unpack(args))
if exist and val ~= nil then
return(val)
else
return("'''VALUE_ERROR''' (" .. tostring(val) .. ")")
end
end
local function trim(s)
return (s:gsub("^%s*(.-)%s*$", "%1"))
end
function p.getTemplateData(frame)
local root_qid = mw.text.trim(frame.args['QID'] or "")
local mm_qid = ""
local collapse_orthologs = mw.text.trim(frame.args['collapse_orthologs'] or '')
local entity = {}
local entity_protein = {}
local entity_mouse = {}
local entity_mouse_protein = {}
local checkOrtholog = 0 -- fixed type
local mouse_propertyID = "P684"
local protein_propertyID = "P688"
if root_qid == "" then
entity = mw.wikibase.getEntity()
if entity then root_qid = entity.id else root_qid = "" end
else
entity = mw.wikibase.getEntity(root_qid)
end
local subclass = p.getValue(entity, "P31") or ""
if string.find(subclass, 'protein') or string.find(subclass, 'پرٛوٹیٖن') then -- **lclz**
local claims
if entity.claims then
claims = entity.claims["P702"]
end
if claims then
entity = {}
if (claims[1] and claims[1].mainsnak.snaktype == "value" and claims[1].mainsnak.datavalue.type == "wikibase-entityid") then
for k, v in pairs(claims) do
local itemID = "Q" .. claims[#entity + 1].mainsnak.datavalue.value["numeric-id"]
entity[#entity + 1] = mw.wikibase.getEntity(itemID)
root_qid = itemID
end
end
end
entity = mw.wikibase.getEntity(root_qid)
end
if entity then
local claims
if entity.claims then
claims = entity.claims[protein_propertyID]
end
if claims then
if (claims[1] and claims[1].mainsnak.snaktype == "value" and claims[1].mainsnak.datavalue.type == "wikibase-entityid") then
for k, v in pairs(claims) do
local protein_itemID = "Q" .. claims[#entity_protein + 1].mainsnak.datavalue.value["numeric-id"]
entity_protein[#entity_protein + 1] = mw.wikibase.getEntity(protein_itemID)
end
end
end
if entity.claims then
claims = entity.claims[mouse_propertyID]
end
local qualifierID = "P703"
local mouse_qual = "Q83310"
if claims then
if (claims[1] and claims[1].mainsnak.snaktype == "value" and claims[1].mainsnak.datavalue.type == "wikibase-entityid") then
for k, v in pairs(claims) do
if checkOrtholog == 1 then
break
end
local mouse_itemID = "Q" .. v.mainsnak.datavalue.value["numeric-id"]
local quals
if v.qualifiers then
quals = v.qualifiers.P703
end
if quals then
for qk, qv in pairs(quals) do
local qual_obj_id = "Q"..qv.datavalue.value["numeric-id"]
if qual_obj_id == mouse_qual then
mm_qid = mouse_itemID
entity_mouse = mw.wikibase.getEntity(mouse_itemID)
checkOrtholog = 1
break
end
end
end
end
end
else
checkOrtholog = 0
end
if entity_mouse and entity_mouse.claims then
claims = entity_mouse.claims[protein_propertyID]
end
if claims then
if (claims[1] and claims[1].mainsnak.snaktype == "value" and claims[1].mainsnak.datavalue.type == "wikibase-entityid") then
for k, v in pairs(claims) do
local protein_itemID = "Q" .. claims[#entity_mouse_protein + 1].mainsnak.datavalue.value["numeric-id"]
entity_mouse_protein[#entity_mouse_protein + 1] = mw.wikibase.getEntity(protein_itemID)
end
end
end
end
if entity then
local name = check_values(p.getLabel,{entity})
local bgee_wikidata_id = 'Q54985720'
local expressed_in_tissues = check_values(p.getValue, {entity, "P5572", localNotApplicableStr, localSeparatorStr, bgee_wikidata_id})
local expressed_in_mouse_tissues = check_values(p.getValue, {entity_mouse, "P5572", localNotApplicableStr, localSeparatorStr, bgee_wikidata_id})
local entrez_gene = check_values(p.getValue, {entity, "P351", localNotApplicableStr} )
local entrez_gene_mm = check_values(p.getValue, {entity_mouse, "P351", localNotApplicableStr})
local image = check_values( p.getImage, {entity, "P18", " ", "250px"})
local uniprotID_hs = check_values(p.getValueProtein, {entity_protein, "P352", localNotApplicableStr})
local uniprotID_mm = check_values(p.getValueProtein, {entity_mouse_protein, "P352", localNotApplicableStr})
local pdbIDs = check_values(p.getPDB, {entity_protein})
local aliases = check_values(p.getAliases, {entity})
local gene_symbol = check_values(p.getValue, {entity, "P353"})
local hgnc_id = check_values(p.getValue, {entity, "P354"})
local homologene_id = check_values(p.getValue, {entity, "P593"})
local omim_id = check_values(p.getValue, {entity, "P492"})
local mgi_id = check_values(p.getValue, {entity_mouse, "P671"})
local ChEMBL_id = check_values(p.getValue, {entity_protein, "P592"})
local IUPHAR_id = check_values(p.getValue, {entity_protein, "P595"})
local ec_no = check_values(p.getValueProtein, {entity_protein, "P591"})
local mol_funct = check_values(p.getGO, {entity_protein, "P680"})
local cell_comp = check_values(p.getGO, {entity_protein, "P681"})
local bio_process = check_values(p.getGO, {entity_protein, "P682"})
local expression_images = check_values(p.getImage, {entity,"P692","<br><br>","250px"})
local ensembl = check_values(p.getValue, {entity, "P594", localNotApplicableStr})
local ensembl_mm = check_values(p.getValue, {entity_mouse, "P594", localNotApplicableStr})
local refseq_mRNA = check_values(p.getRefseq_mRNA, {entity, "P639", localNotApplicableStr})
local refseq_mRNA_mm = check_values(p.getRefseq_mRNA, {entity_mouse, "P639", localNotApplicableStr})
local refseq_prot = check_values(p.getRefseq_protein, {entity_protein, "P637", localNotApplicableStr})
local refseq_prot_mm = check_values(p.getRefseq_protein, {entity_mouse_protein, "P637", localNotApplicableStr})
local gstart = check_values(p.getChromosomeLoc, {entity, "P644", "hg"})
local gend = check_values(p.getChromosomeLoc, {entity, "P645", "hg"})
local chr = check_values(p.trimChromosome, {entity})
local cytoband = check_values(p.getValue, {entity, "P4196", localNotApplicableStr})
local db = check_values(p.getAliasFromGenomeAssembly, {entity,"hg"})
local gstart_mm = check_values(p.getChromosomeLoc, {entity_mouse, "P644", "mm"})
local gend_mm = check_values(p.getChromosomeLoc, {entity_mouse, "P645", "mm"})
local chr_mm = check_values( p.trimChromosome, {entity_mouse})
local db_mm = check_values(p.getAliasFromGenomeAssembly, {entity_mouse,"mm"})
local cytoband_mm = check_values(p.getValue, {entity_mouse, "P4196", localNotApplicableStr})
local disease, dis_ref = p.getDisease(entity, "P2293")
local drug, drug_ref, drug_pqid, drug_pname = p.getDrug(entity_protein, "P129")
p.createTable()
p.renderUpperTitle(name)
p.renderImage(image)
p.renderAvailableStructures(uniprotID_hs, uniprotID_mm, checkOrtholog, pdbIDs)
p.renderIdentifiers(aliases, hgnc_id, gene_symbol, homologene_id, omim_id, mgi_id, ChEMBL_id, IUPHAR_id, ec_no, entrez_gene, ensembl)
if (chr ~= "" and gstart ~= "" and gend ~= "") or (chr_mm ~= "" and gstart_mm ~= "" and gend_mm ~= "") then
p.renderGeneLocation(frame, chr, gstart, gend, db, cytoband, ensembl, chr_mm, gstart_mm, gend_mm, db_mm, cytoband_mm, ensembl_mm, name)
end
if expression_images ~= "" or expressed_in_tissues ~= localNotApplicableStr then
p.renderRNAexpression(expression_images, entrez_gene, ensembl, expressed_in_tissues, ensembl_mm, expressed_in_mouse_tissues)
end
if (mol_funct ~= "" and cell_comp ~= "" and bio_process ~= "") then
p.renderGeneOntology(mol_funct, cell_comp, bio_process, uniprotID_hs)
end
p.renderOrthologs(frame, entrez_gene, entrez_gene_mm, ensembl, ensembl_mm, uniprotID_hs, uniprotID_mm, refseq_mRNA, refseq_mRNA_mm, refseq_prot, refseq_prot_mm, db, chr, gstart, gend, db_mm, chr_mm, gstart_mm, gend_mm, collapse_orthologs)
p.renderFooter(root_qid, mm_qid)
return tostring(root)
else
return "An Error has occurred retrieving Wikidata item for infobox"
end
end
function p.createTable(subbox)
if subbox == 'sub' then
root
:tag('table')
:css('padding', '0')
:css('border', 'none')
:css('margin', '0')
:css('width', 'auto')
:css('min-width', '100%')
:css('font-size', '100%')
:css('clear', 'none')
:css('float', 'none')
else
root = mw.html.create('table')
root
:addClass('infobox')
:css('width', '26.4em')
end
end
function p.renderUpperTitle(name)
local title = name
if not title then return "error: failed to get label"; end
root
:tag('tr')
:tag('th')
:attr('colspan', 4)
:css('text-align', 'center')
:css('font-size', '125%')
:css('font-weight', 'bold')
:wikitext(title)
:done()
end
function p.renderCaption(entity)
--caption
end
function p.renderImage(image)
root
:tag('tr')
:tag('td')
:attr('colspan', 4)
:css('text-align', 'center')
:wikitext(image)
:done()
end
function p.renderAvailableStructures(uniprotID_hs, uniprotID_mm, checkOrtholog, pdbIDs)
local title = 'دٔستِیاب ڈانٛچہٕ' -- **lclz** Available structures
local pdb_link = "[[Protein_Data_Bank|PDB]]"
local searchTitle = ""
local listTitle = "پی ڈی بی (PDB) کوڈَن ہُنٛد فِہرِست" -- **lclz** List of PDB id codes
local PDBe_base = 'https://www.ebi.ac.uk/pdbe/searchResults.html?display=both&term='
local RCSB_base = 'https://www.rcsb.org/search?q='
..'rcsb_polymer_entity_container_identifiers.reference_sequence_identifiers.database_name:UniProt%20AND%20'
..'rcsb_polymer_entity_container_identifiers.reference_sequence_identifiers.database_accession:'
local url_uniprot = " "
if checkOrtholog == 1 and uniprotID_mm ~= 'n/a' then
searchTitle = 'آرتھولاگ تَلاش: ' -- **lclz** Ortholog search
url_uniprot = uniprotID_mm..','..uniprotID_hs
else
searchTitle = 'اِنسٲنی UniProt تَلاش: ' -- **lclz** Human UniProt search
url_uniprot = uniprotID_hs
end
local PDBe_list = " "
if url_uniprot:match("([^,]+),") then
PDBe_list = string.gsub(url_uniprot, ",", "%%20or%%20")
else
PDBe_list = url_uniprot
end
local PDBe = "["..PDBe_base..PDBe_list.." PDBe] "
local RCSB = "["..RCSB_base..url_uniprot.." RCSB] "
if string.match(pdbIDs, '%w+') then
root
:tag('tr')
:tag('td')
:attr('colspan', 4)
:css('text-align', 'center')
:css('background-color', rowBGcolor)
:css('color', 'inherit')
:tag('table')
:css('padding', '0')
:css('border', 'none')
:css('margin', '0')
:css('width', '100%')
:css('text-align', 'left')
:tag('tr')
:tag('th')
:attr('colspan', '4')
:css('text-align', 'center')
:css('background-color', titleBGcolor)
:css('color', 'inherit')
:wikitext(title)
:done()
:done()
:tag('tr')
:tag('th')
:attr('rowspan', '2')
:css('background-color', sideTitleBGcolor)
:css('color', 'inherit')
:css('width', '43px')
:wikitext(pdb_link)
:done()
:tag('td')
:attr('colspan', '2')
:css('background-color', rowBGcolor)
:css('color', 'inherit')
:wikitext(searchTitle)
:tag('span')
:attr('class', 'plainlinks')
:wikitext(PDBe)
:wikitext(RCSB)
:done()
:done()
:done()
:tag('tr')
:tag('td')
:tag('table')
:attr('class', 'collapsible collapsed')
:css('padding', '0')
:css('border', 'none')
:css('margin', '0')
:css('width', '100%')
:css('text-align', 'left')
:tag('tr')
:css('text-align', 'center')
:tag('th')
:css('background-color', titleBGcolor)
:css('color', 'inherit')
:attr('colspan', '2')
:wikitext(listTitle)
:done()
:done()
:tag('tr')
:tag('td')
:attr('colspan', '2')
:css('background-color', rowBGcolor)
:css('color', 'inherit')
:tag('p')
:tag('span')
:attr('class', 'plainlinks')
:wikitext(pdbIDs)
:done()
:done()
:done()
:done()
:done()
:done()
:done()
:done()
:done()
:done()
else
return ""
end
end
function p.renderIdentifiers(aliases, hgnc_id, gene_symbol, homologene_id, omim_id, mgi_id, ChEMBL_id, IUPHAR_id, ec_no, entrez_gene, ensembl)
local title = "شِناخَتھ کَرَن وٲلؠ" -- **lclz** Identifiers
local label_aliases = "[[Gene nomenclature|عُرف]]" -- **lclz** Aliases
local symbol_url
if gene_symbol == "" or gene_symbol == nil then
symbol_url = ""
else
if hgnc_id == "" or hgnc_id == nil then
symbol_url = gene_symbol
else
symbol_url = "[https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/"..hgnc_id.." "..gene_symbol.."]"
end
end
aliases = string.gsub(aliases, '، '..gene_symbol..'$', '')
aliases = string.gsub(aliases, gene_symbol..'، ', '')
aliases = string.gsub(aliases, '، '..gene_symbol..'،', '،')
aliases = string.gsub(aliases, "، ،", "،")
aliases = string.gsub(aliases, "، $", "")
local label_ext_id = "نؠبرِم شِناخَتھ" -- **lclz** External IDs
omim_id = string.gsub(omim_id, "%s", "")
local omim_list = mw.text.split(omim_id, localSeparatorStr)
local omim = ""
if (omim_id ~= nil and omim_id ~= "") then
omim = "[[Mendelian_Inheritance_in_Man|OMIM]]"..": "
end
for i, v in ipairs(omim_list) do
if string.match(v, '%w+') then
omim = omim.."[https://omim.org/entry/"..v.." "..v.."]، "
end
end
omim = trim(string.gsub(omim, "، $",""))
homologene_id = string.gsub(homologene_id, "%s", "")
local homolo_list = mw.text.split(homologene_id, localSeparatorStr)
local homolo =""
if (homologene_id ~= nil and homologene_id ~= "") then
homolo = "[[HomoloGene]]"..": "
end
for i, v in ipairs(homolo_list) do
if string.match(v, '%w+') then
homolo = homolo.."[https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=homologene&dopt=HomoloGene&list_uids="..v.." "..v.."] "
end
end
homolo = trim(string.gsub(homolo, "، $",""))
local genecards = "[[GeneCards]]"..": "
genecards = genecards.."[https://www.genecards.org/cgi-bin/carddisp.pl?gene="..gene_symbol.." "..gene_symbol.."]"
mgi_id = string.gsub(mgi_id, "%s", "")
local mgi_list = mw.text.split(mgi_id, localSeparatorStr)
local mgi = ""
if (mgi_id ~= nil and mgi_id ~= "") then
mgi = "[[Mouse_Genome_Informatics|MGI]]"..": "
end
for i, v in ipairs(mgi_list) do
if string.match(v, '%w+') then
local mgi_number = string.sub(mgi_id, 5)
mgi = mgi.."[http://www.informatics.jax.org/marker/"..mgi_id.." "..mgi_number.."] "
end
end
mgi = trim(string.gsub(mgi, "، $",""))
local ChEMBL = ""
if string.match(ChEMBL_id, '%w+') then
ChEMBL = "[[ChEMBL]]"..": ".."[https://www.ebi.ac.uk/chembldb/index.php/target/inspect/CHEMBL"..ChEMBL_id.." "..ChEMBL_id.."] "
end
local IUPHAR = ""
if string.match(IUPHAR_id, '%w+') then
IUPHAR = "[[International_Union_of_Basic_and_Clinical_Pharmacology|IUPHAR]]"..": ".."[http://www.guidetopharmacology.org/GRAC/ObjectDisplayForward?objectId="..IUPHAR_id.." "..IUPHAR_id.."]"
end
local label_EC = "[[Enzyme_Commission_number|ای سی (EC) نَمبَر]]" -- **lclz** EC number
ec_no = string.gsub(ec_no, "%d%.%d+%.%d+%.%-,", "")
ec_no = string.gsub(ec_no, "%d%.%d+%.%d+%.%-", "")
local link_ec_no = string.gsub(ec_no, "،" ,"+")
local EC = "[https://www.genome.jp/dbget-bin/www_bget?enzyme+" .. link_ec_no .. " " .. ec_no .. "]"
local oma = "[[Orthologous_MAtrix|OMA]]:"
oma = oma.."[https://omabrowser.org/oma/vps/"..mw.text.split(ensembl,"،")[1].." "..gene_symbol.." - orthologs]"
local external_id_table = {omim, mgi, homolo, ChEMBL, IUPHAR, genecards, oma}
local external_id_processed_table = {}
for i, v in ipairs(external_id_table) do
if (v ~= "") then
external_id_processed_table[#external_id_processed_table + 1] = v
end
end
local external_ids = tostring(table.concat(external_id_processed_table, "؛ "))
root
:tag('tr')
:tag('th')
:attr('colspan', '4')
:css('text-align', 'center')
:css('background-color', titleBGcolor)
:css('color', 'inherit')
:wikitext(title)
:done()
:tag('tr')
:tag('th')
:attr('scope', 'row')
:css('background-color', sideTitleBGcolor)
:css('color', 'inherit')
:tag('span')
:attr('class', 'plainlinks')
:wikitext(label_aliases)
:done()
:done()
:tag('td')
:attr('colspan','3')
:css('background', rowBGcolor)
:css('color', 'inherit')
:tag('span')
:attr('class', 'plainlinks')
:wikitext(symbol_url)
:done()
:wikitext(mw.text.nowiki(aliases))
:done()
:done()
:tag('tr')
:tag('th')
:attr('scope', 'row')
:css('background-color', sideTitleBGcolor)
:css('color', 'inherit')
:wikitext(label_ext_id)
:done()
:tag('td')
:attr('colspan', '3')
:css('background-color', rowBGcolor)
:css('color', 'inherit')
:tag('span')
:attr('class', 'plainlinks')
:wikitext(external_ids)
:done()
:done()
:done()
if ec_no ~= "" then
root
:tag('tr')
:tag('th')
:attr('scope', 'row')
:css('background-color', sideTitleBGcolor)
:css('color', 'inherit')
:wikitext(label_EC)
:done()
:tag('td')
:attr('colspan', '3')
:css('background-color', rowBGcolor)
:css('color', 'inherit')
:tag('span')
:attr('class', 'plainlinks')
:wikitext(EC)
:done()
:done()
:done()
end
end
function p.renderDiseases(frame, disease, dis_ref, name, qid)
local title = "جِنیٲتی بؠمٲرؠ" -- **lclz**
local ref_flag_all = false
local disease_name = ''
for index,value in ipairs(disease) do
if (dis_ref[index] ~= nil and dis_ref[index] ~= '') then
if disease_name == '' then
disease_name = value
else
disease_name = disease_name.."، "..value
end
ref_flag_all = true
end
end
if ref_flag_all then
root
:tag('tr')
:tag('td')
:attr('colspan', 4)
:css('text-align', 'center')
:css('background-color', rowBGcolor)
:css('color', 'inherit')
:tag('tr')
:tag('th')
:attr('colspan', '3')
:css('text-align', 'center')
:css('background-color', titleBGcolor)
:css('color', 'inherit')
:wikitext(title)
:done()
:done()
:done()
:done()
local ref_url = "https://www.wikidata.org/wiki/"..qid.."#P2293"
local title = "یِم بؠمٲرؠ یِم جِنیٲتی طور پٲٹھؠ " .. name .. " سٟتؠ وابَستہٕ چھِ، وِکیٖڈیٹا پؠٹھ وُچھِو/اؠڈِٹ کٔرِو" -- **lclz**
local ref_link = disease_name..frame:extensionTag("ref",frame:expandTemplate{ title = 'cite_web', args = { title = title, url = ref_url} })
root
:tag('tr')
:attr('colspan', 4)
:css('text-align', 'center')
:css('background-color', rowBGcolor)
:css('color', 'inherit')
:tag('td')
:css('background-color', rowBGcolor)
:css('color', 'inherit')
:attr('scope', 'row')
:attr('colspan', '3')
:wikitext(ref_link)
:done()
:done()
end
end
function p.renderDrug(frame,drug, drug_ref, drug_pqid, drug_pname)
local title = "دَواہُک مقصد" -- **lclz** Targeted by drug
local ref_flag_all = false
local drug_list_per_protein = {}
for index,value in ipairs(drug) do
if (drug_ref[index] ~= nil and drug_ref[index] ~= '') then
local protein_qid = drug_pqid[index]
if drug_list_per_protein[protein_qid] == '' or drug_list_per_protein[protein_qid] == nil then
drug_list_per_protein[protein_qid] = value
else
drug_list_per_protein[protein_qid] = drug_list_per_protein[protein_qid]..'، '..value
end
ref_flag_all = true
end
end
if ref_flag_all then
root
:tag('tr')
:tag('td')
:attr('colspan', 4)
:css('text-align', 'center')
:css('background-color', rowBGcolor)
:css('color', 'inherit')
:tag('tr')
:tag('th')
:attr('colspan', '3')
:css('text-align', 'center')
:css('background-color', titleBGcolor)
:css('color', 'inherit')
:wikitext(title)
:done()
:done()
:done()
:done()
for k,v in pairs(drug_list_per_protein) do
local drug_name = v
local ref_url = "https://www.wikidata.org/wiki/"..k.."#P129"
local title = "یِم دَوا یِم جِسمٲنی طور پٲٹھؠ " .. drug_pname[k] .. " سٟتؠ رَلان چھِ، وِکیٖڈیٹا پؠٹھ وُچھِو/اؠڈِٹ کٔرِو" -- **lclz**
local ref_link = drug_name..frame:extensionTag("ref",frame:expandTemplate{ title = 'cite_web', args = { title = title, url = ref_url} })
root
:tag('tr')
:attr('colspan', 4)
:css('text-align', 'center')
:css('background-color', rowBGcolor)
:css('color', 'inherit')
:tag('td')
:css('background-color', rowBGcolor)
:css('color', 'inherit')
:attr('scope', 'row')
:attr('colspan', '3')
:wikitext(ref_link)
:done()
:done()
end
end
end
function p.renderGeneLocation(frame, chr, gstart, gend, db, cytoband, ensembl, chr_mm, gstart_mm, gend_mm, db_mm, cytoband_mm, ensembl_mm, name)
local titleHuman = "جیٖنٕچ جاے ([[Human genome|اِنسان]])" -- **lclz**
local titleMouse = "جیٖنٕچ جاے ([[Laboratory mouse|گَگُر]])" -- **lclz**
local label_chr = "[[Chromosome|کرٛوموزوم]]" -- **lclz**
local label_locus = "[[Locus (genetics)|بؠنٛڈ]]" -- **lclz**
local label_gstart = "شُروٗع" -- **lclz**
local label_gend = "خَتٕم" -- **lclz**
local tooltip_arrowSign = "یَتھ خٲطرٕ جینومِک جاے "..name -- **lclz**
local arrowSign_width = 14
if chr ~= "" and gstart ~= "" and gend ~= "" then
local chrLengthTable = {}
chrLengthTable["1"] = 248956422
chrLengthTable["2"] = 242193529
chrLengthTable["3"] = 198295559
chrLengthTable["4"] = 190214555
chrLengthTable["5"] = 181538259
chrLengthTable["6"] = 170805979
chrLengthTable["7"] = 159345973
chrLengthTable["8"] = 145138636
chrLengthTable["9"] = 138394717
chrLengthTable["10"] = 133797422
chrLengthTable["11"] = 135086622
chrLengthTable["12"] = 133275309
chrLengthTable["13"] = 114364328
chrLengthTable["14"] = 107043718
chrLengthTable["15"] = 101991189
chrLengthTable["16"] = 90338345
chrLengthTable["17"] = 83257441
chrLengthTable["18"] = 80373285
chrLengthTable["19"] = 58617616
chrLengthTable["20"] = 64444167
chrLengthTable["21"] = 46709983
chrLengthTable["22"] = 50818468
chrLengthTable["X"] = 156040895
chrLengthTable["Y"] = 57227415
chrLengthTable["MT"] = 16569
local chrLength = chrLengthTable[chr]
local chrTextTable = {}
chrTextTable["1"] = "کرٛوموزوم 1 (اِنسان)"
chrTextTable["2"] = "کرٛوموزوم 2 (اِنسان)"
chrTextTable["3"] = "کرٛوموزوم 3 (اِنسان)"
chrTextTable["4"] = "کرٛوموزوم 4 (اِنسان)"
chrTextTable["5"] = "کرٛوموزوم 5 (اِنسان)"
chrTextTable["6"] = "کرٛوموزوم 6 (اِنسان)"
chrTextTable["7"] = "کرٛوموزوم 7 (اِنسان)"
chrTextTable["8"] = "کرٛوموزوم 8 (اِنسان)"
chrTextTable["9"] = "کرٛوموزوم 9 (اِنسان)"
chrTextTable["10"] = "کرٛوموزوم 10 (اِنسان)"
chrTextTable["11"] = "کرٛوموزوم 11 (اِنسان)"
chrTextTable["12"] = "کرٛوموزوم 12 (اِنسان)"
chrTextTable["13"] = "کرٛوموزوم 13 (اِنسان)"
chrTextTable["14"] = "کرٛوموزوم 14 (اِنسان)"
chrTextTable["15"] = "کرٛوموزوم 15 (اِنسان)"
chrTextTable["16"] = "کرٛوموزوم 16 (اِنسان)"
chrTextTable["17"] = "کرٛوموزوم 17 (اِنسان)"
chrTextTable["18"] = "کرٛوموزوم 18 (اِنسان)"
chrTextTable["19"] = "کرٛوموزوم 19 (اِنسان)"
chrTextTable["20"] = "کرٛوموزوم 20 (اِنسان)"
chrTextTable["21"] = "کرٛوموزوم 21 (اِنسان)"
chrTextTable["22"] = "کرٛوموزوم 22 (اِنسان)"
chrTextTable["X"] = "X کرٛوموزوم (اِنسان)"
chrTextTable["Y"] = "Y کرٛوموزوم (اِنسان)"
chrTextTable["MT"] = "مایٹوکانٛڈرِیَل ڈی این اے (اِنسان)"
local chrText = chrTextTable[chr]
local markerWidth = ((gend - gstart) * 294.133 )/ chrLength
if markerWidth < 2 then
markerWidth = 2
else
markerWidth = math.ceil(markerWidth)
end
local markerLocation = (147.0666 * (gstart + gend) / chrLength ) + 1.6 - (markerWidth / 2)
local arrowSignLocation = markerLocation + (markerWidth / 2) - (arrowSign_width / 2)
markerLocation = math.floor( markerLocation * 10 + 0.5 ) / 10
local source_link_chr, source_link_gstart, source_link_gend
if( db == "hg38" ) then
source_link_chr = frame:extensionTag("ref", "[http://May2017.archive.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g="..ensembl.." GRCh38: Ensembl release 89: "..ensembl.."] – [[Ensembl genome database project|Ensembl]], May 2017", {name = "refGRCh38Ensembl"})
source_link_gstart = frame:extensionTag("ref", "", {name = "refGRCh38Ensembl"})
source_link_gend = frame:extensionTag("ref", "", {name = "refGRCh38Ensembl"})
elseif( db == "hg37") then
source_link_chr = frame:extensionTag("ref", "[http://grch37.ensembl.org/Homo_sapiens/Gene/Summary?db=core;&g="..ensembl.." GRCh37: Ensembl release 89: "..ensembl.."] – [[Ensembl genome database project|Ensembl]], May 2017", {name = "refGRCh37Ensembl"})
source_link_gstart = frame:extensionTag("ref", "", {name = "refGRCh37Ensembl"})
source_link_gend = frame:extensionTag("ref", "", {name = "refGRCh37Ensembl"})
else
source_link_chr = ""
source_link_gstart = ""
source_link_gend = ""
end
local wikitext_for_ideogram_image = ""
if chr == "MT" then
else
wikitext_for_ideogram_image = wikitext_for_ideogram_image.."<div align=\"center\">"
wikitext_for_ideogram_image = wikitext_for_ideogram_image.."<div style=\"position: relative; width: 300px;\">"
wikitext_for_ideogram_image = wikitext_for_ideogram_image.."[[File:Human chromosome "..chr.." ideogram.svg|300px|"..chrText.."]]"
wikitext_for_ideogram_image = wikitext_for_ideogram_image.."<div style=\"position: absolute; left: "..arrowSignLocation.."px; top: 2px; padding: 0;\">"
wikitext_for_ideogram_image = wikitext_for_ideogram_image.."[[File:HSR 1996 II 3.5e.svg|"..arrowSign_width.."px|"..tooltip_arrowSign.."]]</div>"
wikitext_for_ideogram_image = wikitext_for_ideogram_image.."<div style=\"position: absolute; left: "..markerLocation.."px; top: 19px; padding: 0;\">[[File:Red rectangle "..markerWidth.."x18.png|"..markerWidth.."px|"..tooltip_arrowSign.."]]</div>"
wikitext_for_ideogram_image = wikitext_for_ideogram_image.."</div>"
wikitext_for_ideogram_image = wikitext_for_ideogram_image.."</div>"
end
root
:tag('tr')
:tag('td')
:attr('colspan', 4)
:css('text-align', 'center')
:css('background-color', rowBGcolor)
:css('color', 'inherit')
:tag('table')
:attr('class', 'collapsible collapsed')
:css('padding', '0')
:css('border', 'none')
:css('margin', '0')
:css('width', '100%')
:css('text-align', 'left')
:tag('tr')
:tag('th')
:attr('colspan', '4')
:css('text-align', 'center')
:css('background-color', titleBGcolor)
:css('color', 'inherit')
:wikitext(titleHuman)
:done()
:done()
:tag('tr')
:tag('td')
:attr('colspan', '4')
:css('text-align', 'center')
:css('background-color', rowBGcolor)
:css('color', 'inherit')
:wikitext("[[File:Ideogram human chromosome "..chr..".svg|300px|"..chrText.."]]")
:done()
:done()
:tag('tr')
:tag('th')
:attr('scope', 'row')
:attr('width', '15%')
:css('background-color', sideTitleBGcolor)
:css('color', 'inherit')
:wikitext(label_chr)
:done()
:tag('td')
:attr('colspan', '3')
:attr('width', '85%')
:css('background-color', rowBGcolor)
:css('color', 'inherit')
:tag('span')
:attr('class', 'plainlinks')
:wikitext("[["..chrText.."]]"..source_link_chr)
:done()
:done()
:done()
:tag('tr')
:tag('td')
:attr('colspan', '4')
:css('text-align', 'center')
:css('background-color', rowBGcolor)
:css('color', 'inherit')
:wikitext(wikitext_for_ideogram_image)
:done()
:done()
:tag('tr')
:tag('th')
:attr('scope', 'row')
:attr('rowspan', '2')
:attr('width', '15%')
:css('background-color', sideTitleBGcolor)
:css('color', 'inherit')
:wikitext(label_locus)
:done()
:tag('td')
:attr('rowspan', '2')
:attr('width', '35%')
:css('background-color', rowBGcolor)
:css('color', 'inherit')
:tag('span')
:attr('class', 'plainlinks')
:wikitext(cytoband)
:done()
:done()
:tag('th')
:attr('scope', 'row')
:css('background-color', sideTitleBGcolor)
:css('color', 'inherit')
:wikitext(label_gstart)
:done()
:tag('td')
:css('background-color', rowBGcolor)
:css('color', 'inherit')
:tag('span')
:attr('class', 'plainlinks')
:wikitext(p.separateWithComma(gstart).." [[Base pair|بی پی (bp)]]"..source_link_gstart)
:done()
:done()
:done()
:tag('tr')
:tag('th')
:attr('scope', 'row')
:css('background-color', sideTitleBGcolor)
:css('color', 'inherit')
:wikitext(label_gend)
:done()
:tag('td')
:css('background-color', rowBGcolor)
:css('color', 'inherit')
:tag('span')
:attr('class', 'plainlinks')
:wikitext(p.separateWithComma(gend).." [[Base pair|بی پی (bp)]]"..source_link_gend)
:done()
:done()
:done()
:done()
:done()
:done()
end
if chr_mm ~= "" and gstart_mm ~= "" and gend_mm ~= "" then
local chrLengthTable_mm = {}
chrLengthTable_mm["1"] = 195471971
chrLengthTable_mm["2"] = 182113224
chrLengthTable_mm["3"] = 160039680
chrLengthTable_mm["4"] = 156508116
chrLengthTable_mm["5"] = 151834684
chrLengthTable_mm["6"] = 149736546
chrLengthTable_mm["7"] = 145441459
chrLengthTable_mm["8"] = 129401213
chrLengthTable_mm["9"] = 124595110
chrLengthTable_mm["10"] = 130694993
chrLengthTable_mm["11"] = 122082543
chrLengthTable_mm["12"] = 120129022
chrLengthTable_mm["13"] = 120421639
chrLengthTable_mm["14"] = 124902244
chrLengthTable_mm["15"] = 104043685
chrLengthTable_mm["16"] = 98207768
chrLengthTable_mm["17"] = 94987271
chrLengthTable_mm["18"] = 90702639
chrLengthTable_mm["19"] = 61431566
chrLengthTable_mm["X"] = 171031299
chrLengthTable_mm["Y"] = 91744698
chrLengthTable_mm["MT"] = 16299
local chrLength_mm = chrLengthTable_mm[chr_mm]
local chrTextTable_mm = {}
chrTextTable_mm["1"] = "کرٛوموزوم 1 (گَگُر)"
chrTextTable_mm["2"] = "کرٛوموزوم 2 (گَگُر)"
chrTextTable_mm["3"] = "کرٛوموزوم 3 (گَگُر)"
chrTextTable_mm["4"] = "کرٛوموزوم 4 (گَگُر)"
chrTextTable_mm["5"] = "کرٛوموزوم 5 (گَگُر)"
chrTextTable_mm["6"] = "کرٛوموزوم 6 (گَگُر)"
chrTextTable_mm["7"] = "کرٛوموزوم 7 (گَگُر)"
chrTextTable_mm["8"] = "کرٛوموزوم 8 (گَگُر)"
chrTextTable_mm["9"] = "کرٛوموزوم 9 (گَگُر)"
chrTextTable_mm["10"] = "کرٛوموزوم 10 (گَگُر)"
chrTextTable_mm["11"] = "کرٛوموزوم 11 (گَگُر)"
chrTextTable_mm["12"] = "کرٛوموزوم 12 (گَگُر)"
chrTextTable_mm["13"] = "کرٛوموزوم 13 (گَگُر)"
chrTextTable_mm["14"] = "کرٛوموزوم 14 (گَگُر)"
chrTextTable_mm["15"] = "کرٛوموزوم 15 (گَگُر)"
chrTextTable_mm["16"] = "کرٛوموزوم 16 (گَگُر)"
chrTextTable_mm["17"] = "کرٛوموزوم 17 (گَگُر)"
chrTextTable_mm["18"] = "کرٛوموزوم 18 (گَگُر)"
chrTextTable_mm["19"] = "کرٛوموزوم 19 (گَگُر)"
chrTextTable_mm["X"] = "X کرٛوموزوم (گَگُر)"
chrTextTable_mm["Y"] = "Y کرٛوموزوم (گَگُر)"
chrTextTable_mm["MT"] = "مایٹوکانٛڈرِیَل ڈی این اے (گَگُر)"
local chrText_mm = chrTextTable_mm[chr_mm]
local markerWidth_mm = ((gend_mm - gstart_mm) * 294.133 )/ chrLength_mm
if markerWidth_mm < 2 then
markerWidth_mm = 2
else
markerWidth_mm = math.ceil(markerWidth_mm)
end
local markerLocation_mm = (147.0666 * (gstart_mm + gend_mm) / chrLength_mm ) + 1.6 - (markerWidth_mm / 2)
local arrowSignLocation_mm = markerLocation_mm + (markerWidth_mm / 2) - (arrowSign_width / 2)
markerLocation_mm = math.floor( markerLocation_mm * 10 + 0.5 ) / 10
local source_link_chr_mm = ""
local source_link_gstart_mm = ""
local source_link_gend_mm = ""
if( db_mm == "mm10" or db_mm == "mm0") then
source_link_chr_mm = frame:extensionTag("ref", "[http://May2017.archive.ensembl.org/Mus_musculus/Gene/Summary?db=core;g="..ensembl_mm.." GRCm38: Ensembl release 89: "..ensembl_mm.."] – [[Ensembl genome database project|Ensembl]], May 2017", {name = "refGRCm38Ensembl"})
source_link_gstart_mm = frame:extensionTag("ref", "", {name = "refGRCm38Ensembl"})
source_link_gend_mm = frame:extensionTag("ref", "", {name = "refGRCm38Ensembl"})
else
source_link_chr_mm = ""
source_link_gstart_mm = ""
source_link_gend_mm = ""
end
local wikitext_for_ideogram_image_mm = ""
if chr_mm == "MT" then
else
wikitext_for_ideogram_image_mm = wikitext_for_ideogram_image_mm.."<div align=\"center\">"
wikitext_for_ideogram_image_mm = wikitext_for_ideogram_image_mm.."<div style=\"position: relative; width: 300px;\">"
wikitext_for_ideogram_image_mm = wikitext_for_ideogram_image_mm.."[[File:Ideogram of house mouse chromosome "..chr_mm..".svg|300px|"..chrText_mm.."]]"
wikitext_for_ideogram_image_mm = wikitext_for_ideogram_image_mm.."<div style=\"position: absolute; left: "..arrowSignLocation_mm.."px; top: 2px; padding: 0;\">"
wikitext_for_ideogram_image_mm = wikitext_for_ideogram_image_mm.."[[File:HSR 1996 II 3.5e.svg|"..arrowSign_width.."px|"..tooltip_arrowSign.."]]</div>"
wikitext_for_ideogram_image_mm = wikitext_for_ideogram_image_mm.."<div style=\"position: absolute; left: "..markerLocation_mm.."px; top: 19px; padding: 0;\">[[File:Red rectangle "..markerWidth_mm.."x18.png|"..markerWidth_mm.."px|"..tooltip_arrowSign.."]]</div>"
wikitext_for_ideogram_image_mm = wikitext_for_ideogram_image_mm.."</div>"
wikitext_for_ideogram_image_mm = wikitext_for_ideogram_image_mm.."</div>"
end
root
:tag('tr')
:tag('td')
:attr('colspan', 4)
:css('text-align', 'center')
:css('background-color', rowBGcolor)
:css('color', 'inherit')
:tag('table')
:attr('class', 'collapsible collapsed')
:css('padding', '0')
:css('border', 'none')
:css('margin', '0')
:css('width', '100%')
:css('text-align', 'left')
:tag('tr')
:tag('th')
:attr('colspan', '4')
:css('text-align', 'center')
:css('background-color', titleBGcolor)
:css('color', 'inherit')
:wikitext(titleMouse)
:done()
:done()
:tag('tr')
:tag('td')
:attr('colspan', '4')
:css('text-align', 'center')
:css('background-color', rowBGcolor)
:css('color', 'inherit')
:wikitext("[[File:Ideogram house mouse chromosome "..chr_mm..".svg|260px|"..chrText_mm.."]]")
:done()
:done()
:tag('tr')
:tag('th')
:attr('scope', 'row')
:attr('width', '15%')
:css('background-color', sideTitleBGcolor)
:css('color', 'inherit')
:wikitext(label_chr)
:done()
:tag('td')
:attr('colspan', '3')
:attr('width', '85%')
:css('background-color', rowBGcolor)
:css('color', 'inherit')
:tag('span')
:attr('class', 'plainlinks')
:wikitext(chrText_mm..source_link_chr_mm)
:done()
:done()
:done()
:tag('tr')
:tag('td')
:attr('colspan', '4')
:css('text-align', 'center')
:css('background-color', rowBGcolor)
:css('color', 'inherit')
:wikitext(wikitext_for_ideogram_image_mm)
:done()
:done()
:tag('tr')
:tag('th')
:attr('scope', 'row')
:attr('rowspan', '2')
:attr('width', '15%')
:css('background-color', sideTitleBGcolor)
:css('color', 'inherit')
:wikitext(label_locus)
:done()
:tag('td')
:attr('rowspan', '2')
:attr('width', '35%')
:css('background-color', rowBGcolor)
:css('color', 'inherit')
:tag('span')
:attr('class', 'plainlinks')
:wikitext(cytoband_mm)
:done()
:done()
:tag('th')
:attr('scope', 'row')
:css('background-color', sideTitleBGcolor)
:css('color', 'inherit')
:wikitext(label_gstart)
:done()
:tag('td')
:css('background-color', rowBGcolor)
:css('color', 'inherit')
:tag('span')
:attr('class', 'plainlinks')
:wikitext(p.separateWithComma(gstart_mm).." [[Base pair|بی پی (bp)]]"..source_link_gstart_mm)
:done()
:done()
:done()
:tag('tr')
:tag('th')
:attr('scope', 'row')
:css('background-color', sideTitleBGcolor)
:css('color', 'inherit')
:wikitext(label_gend)
:done()
:tag('td')
:css('background-color', rowBGcolor)
:css('color', 'inherit')
:tag('span')
:attr('class', 'plainlinks')
:wikitext(p.separateWithComma(gend_mm).." [[Base pair|بی پی (bp)]]"..source_link_gend_mm)
:done()
:done()
:done()
:done()
:done()
:done()
end
end
function p.renderExpressionList(expressed_in_tissues, default_text)
if default_text == nil then default_text = "" end
local anatomic_entity_labels = localNotApplicableStr
local collapse = "none"
local split_values = mw.text.split(expressed_in_tissues, localSeparatorStr)
local anatomic_entity_list = {}
local anatomic_entities = {}
local results
for k,v in ipairs(split_values) do
if string.match(v, '%w+') and v ~= localNotApplicableStr then
anatomic_entity_list[#anatomic_entity_list+1] = "<li style='line-height: 137%;'>"..v.."</li>"
anatomic_entities[#anatomic_entities+1] = v
end
end
if #anatomic_entity_list < 11 then
if #anatomic_entity_list == 0 then
anatomic_entity_labels = localNotApplicableStr
default_text = ""
end
else
collapse = "collapsible collapsed"
default_text = default_text .. '<br>' .. table.remove(anatomic_entities, 1) .. '<br>' .. table.remove(anatomic_entities, 1) .. '<br>' ..table.remove(anatomic_entities, 1) .. '<br>' .. table.remove(anatomic_entities, 1) .. '<br>' .. table.remove(anatomic_entities, 1) .. '<br>'
end
if anatomic_entity_list[#anatomic_entity_list] then
anatomic_entity_labels = table.concat(anatomic_entity_list, "<br>")
end
results = {collapse, default_text, anatomic_entity_labels}
return results
end
function p.renderRNAexpression(expression_images, entrez_gene,
ensembl, bgee_expression, ensembl_mouse, bgee_expression_mouse)
local bgee_gene_page = "https://www.bgee.org/gene/"
local title = "[[Gene expression|آر این اے ظٲہِر گَژھنُک طٔریٖقہٕ]]" -- **lclz**
local biogps_link = ""
local biogps_title = "BioGPS"
biogps_title = "[http://biogps.org/ " .. biogps_title .. "]"
if expression_images ~= "" then
biogps_link = "[http://biogps.org/gene/"..entrez_gene.."/ More reference expression data]"
else
expression_images = localNotApplicableStr
end
local ensembl_id = string.match(ensembl,"%a+%d+") or ""
local ensembl_id_mouse = string.match(ensembl_mouse,"%a+%d+") or ""
local bgee_title = "Bgee"
bgee_title = "[https://www.bgee.org/ " .. bgee_title .. "]"
local bgee_default = "["..bgee_gene_page..ensembl_id.." Top expressed in]"
bgee_expression = p.renderExpressionList(bgee_expression, bgee_default)
local bgee_collapse = bgee_expression[1]
bgee_default = bgee_expression[2]
local bgee_tissues = bgee_expression[3]
local bgee_default_mm = "["..bgee_gene_page..ensembl_id_mouse.." Top expressed in]"
bgee_expression_mouse = p.renderExpressionList(bgee_expression_mouse, bgee_default_mm)
local bgee_collapse_mm = bgee_expression_mouse[1]
bgee_default_mm = bgee_expression_mouse[2]
local bgee_tissues_mm = bgee_expression_mouse[3]
local bgee_more_link = ""
if bgee_tissues ~= localNotApplicableStr then
bgee_more_link = "["..bgee_gene_page..ensembl_id.." More reference expression data]"
end
root
:tag('tr')
:tag('td')
:attr('colspan', 4)
:css('text-align', 'center')
:css('background-color', rowBGcolor)
:css('color', 'inherit')
:tag('table')
:attr('class', 'collapsible collapsed')
:css('padding', '0')
:css('border', 'none')
:css('margin', '0')
:css('width', '100%')
:css('text-align', 'left')
:tag('tr')
:tag('th')
:attr('colspan', '4')
:css('text-align', 'center')
:css('background-color', titleBGcolor)
:css('color', 'inherit')
:wikitext(title)
:done()
:done()
:tag('tr')
:tag('th')
:attr('scope', 'row')
:css('background-color', sideTitleBGcolor)
:css('color', 'inherit')
:wikitext(bgee_title)
:done()
:tag('td')
:tag('table')
:attr('class', 'none')
:css('padding', '0')
:css('border', 'none')
:css('margin', '0')
:css('width', '100%')
:css('text-align', 'left')
:tag('tr')
:tag('th')
:wikitext("'''[[Human genome|اِنسان]]'''") -- **lclz**
:done()
:tag('th')
:wikitext("'''[[Laboratory mouse|گَگُر]] (آرتھولاگ)'''") -- **lclz**
:done()
:done()
:tag('tr')
:tag('td')
:tag('table')
:attr('class', bgee_collapse)
:css('padding', '0')
:css('border', 'none')
:css('margin', '0')
:css('width', '100%')
:css('text-align', 'center')
:tag('tr')
:tag('td')
:attr('colspan', '1')
:tag('span')
:attr('class', 'plainlinks')
:css('margin', '-3px')
:wikitext(bgee_default)
:done()
:done()
:done()
:tag('tr')
:tag('td')
:attr('colspan', '1')
:tag('div')
:css('margin', '-12px 0px -10px 0px')
:attr('class', 'plainlinks')
:tag('ul')
:css('line-height', '15%')
:css('margin', '9px')
:wikitext(bgee_tissues)
:done()
:done()
:done()
:done()
:done()
:done()
:tag('td')
:tag('table')
:attr('class', bgee_collapse_mm)
:css('padding', '0')
:css('border', 'none')
:css('margin', '0')
:css('width', '100%')
:css('text-align', 'center')
:tag('tr')
:tag('td')
:attr('colspan', '1')
:tag('span')
:attr('class', 'plainlinks')
:css('margin', '-3px')
:wikitext(bgee_default_mm)
:done()
:done()
:done()
:tag('tr')
:tag('td')
:attr('colspan', '1')
:tag('div')
:css('margin', '-12px 0px -10px 0px')
:attr('class', 'plainlinks')
:tag('ul')
:css('line-height', '15%')
:css('margin', '9px')
:wikitext(bgee_tissues_mm)
:done()
:done()
:done()
:done()
:done()
:done()
:done()
:tag('tr')
:tag('td')
:attr('colspan', '4')
:css('text-align', 'center')
:css('background-color', rowBGcolor)
:css('color', 'inherit')
:tag('span')
:attr('class', 'plainlinks')
:wikitext(bgee_more_link)
:done()
:done()
:done()
:done()
:done()
:done()
:tag('tr')
:tag('th')
:attr('scope', 'row')
:css('background-color', sideTitleBGcolor)
:css('color', 'inherit')
:wikitext(biogps_title)
:done()
:tag('td')
:tag('table')
:attr('class', bgee_collapse)
:css('padding', '0')
:css('border', 'none')
:css('margin', '0')
:css('width', '100%')
:css('text-align', 'left')
:tag('tr')
:tag('td')
:attr('colspan', '4')
:css('text-align', 'center')
:css('background-color', rowBGcolor)
:css('color', 'inherit')
:wikitext(expression_images)
:done()
:done()
:tag('tr')
:tag('td')
:attr('colspan', '4')
:css('text-align', 'center')
:css('background-color', rowBGcolor)
:css('color', 'inherit')
:tag('span')
:attr('class', 'plainlinks')
:wikitext(biogps_link)
:done()
:done()
:done()
:done()
:done()
:done()
:done()
:done()
:done()
end
function p.renderGeneOntology(mol_funct, cell_comp, bio_process, uniprotID)
local title = "[[Gene ontology|جیٖن آنٹولوجی]]" -- **lclz**
local mol_funct_title = "مالیکیولَر کٲم" -- **lclz**
local cell_comp_title = "سؠلُک حِصہٕ" -- **lclz**
local bio_process_title = "حیٲتِیٲتی عَمَل" -- **lclz**
local amigo_link = "[http://amigo.geneontology.org/" .. " Amigo]"
local quickGO_link = "[https://www.ebi.ac.uk/QuickGO/" .. " QuickGO]"
root
:tag('tr')
:tag('td')
:attr('colspan', 4)
:css('text-align', 'center')
:css('background-color', rowBGcolor)
:css('color', 'inherit')
:tag('table')
:attr('class', 'collapsible collapsed')
:css('padding', '0')
:css('border', 'none')
:css('margin', '0')
:css('width', '100%')
:css('text-align', 'left')
:tag('tr')
:tag('th')
:attr('colspan', '4')
:css('text-align', 'center')
:css('background-color', titleBGcolor)
:css('color', 'inherit')
:wikitext(title)
:done()
:done()
:tag('tr')
:tag('td')
:css('background-color', sideTitleBGcolor)
:css('color', 'inherit')
:css('font-weight', 'bold')
:wikitext(mol_funct_title)
:done()
:tag('td')
:css('background-color', rowBGcolor)
:css('color', 'inherit')
:tag('div')
:attr('class', 'plainlinks')
:wikitext(mol_funct)
:wikitext( '\n' )
:done()
:done()
:done()
:tag('tr')
:tag('td')
:css('background-color', sideTitleBGcolor)
:css('color', 'inherit')
:css('font-weight', 'bold')
:wikitext(cell_comp_title)
:done()
:tag('td')
:css('background-color', rowBGcolor)
:css('color', 'inherit')
:tag('div')
:attr('class', 'plainlinks')
:wikitext(cell_comp)
:wikitext( '\n' )
:done()
:done()
:done()
:tag('tr')
:tag('td')
:css('background-color', sideTitleBGcolor)
:css('color', 'inherit')
:css('font-weight', 'bold')
:wikitext(bio_process_title)
:done()
:tag('td')
:css('background-color', rowBGcolor)
:css('color', 'inherit')
:tag('div')
:attr('class', 'plainlinks')
:wikitext(bio_process)
:wikitext( '\n' )
:done()
:done()
:done()
:tag('tr')
:tag('td')
:css('background-color', rowBGcolor)
:css('color', 'inherit')
:css('text-align', 'center')
:attr('colspan', '4')
:wikitext("ذَرایَع:") -- **lclz** Sources
:wikitext(amigo_link)
:wikitext(" / ")
:wikitext(quickGO_link)
:done()
:done()
:done()
:done()
:done()
end
function p.renderOrthologs(frame, entrez_gene, entrez_gene_mm, ensembl, ensembl_mm, uniprot, uniprot_mm, refseq_mRNA, refseq_mRNA_mm, refseq_prot, refseq_prot_mm, db, chr, gstart, gend, db_mm, chr_mm, gstart_mm, gend_mm, collapse_orthologs)
local title = "[[Orthologs|آرتھولاگ]]" -- **lclz**
local ortholog_class = collapse_orthologs ~= '' and 'collapsible collapsed' or 'collapsible'
local category_chromosome = '[[Category:اِنسٲنی کرٛوموزوم '..chr..' پؠٹھ جیٖن]]'
if chr == "MT" then
category_chromosome = '[[Category:اِنسٲنی مایٹوکانٛڈرِیَل جیٖن]]'
end
if chr == "" then
category_chromosome = '[[Category:اِنسٲنی جیٖن]]'
end
if mw.title.getCurrentTitle().namespace ~= 0 then
category_chromosome = ""
end
local entrezTitle = "[[Entrez]]"
entrez_gene = string.gsub(entrez_gene, "%s", "")
local entrez_link = localNotApplicableStr
local entrez_collapse
local entrez_default = ""
local split_entrez = mw.text.split(entrez_gene, localSeparatorStr)
local entrez_link_list = {}
for k,v in ipairs(split_entrez) do
if string.match(v, '%w+') and v ~= localNotApplicableStr then
entrez_link_list[#entrez_link_list+1] = "[https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=retrieve&dopt=default&list_uids="..entrez_gene.."&rn=1 "..entrez_gene.."]"
end
end
if #entrez_link_list < 5 then
entrez_collapse = "none"
if entrez_default == nil and #entrez_link_list == 0 then entrez_link = localNotApplicableStr end
else
entrez_collapse = "collapsible collapsed"
entrez_default = table.remove(entrez_link_list, 1) .. '<br>' .. table.remove(entrez_link_list, 1) .. '<br>' ..table.remove(entrez_link_list, 1) .. '<br>' .. table.remove(entrez_link_list, 1) .. '<br>' .. table.remove(entrez_link_list, 1) .. '<br>'
end
if entrez_link_list[#entrez_link_list] then
entrez_link = table.concat(entrez_link_list, "<br>")
end
entrez_gene_mm = string.gsub(entrez_gene_mm, "%s", "")
local entrez_mm_link = localNotApplicableStr
local entrez_mm_collapse
local entrez_mm_default = ""
local split_entrez_mm = mw.text.split(entrez_gene_mm, localSeparatorStr)
local entrez_mm_link_list = {}
for k,v in ipairs(split_entrez_mm) do
if string.match(v, '%w+') and v ~= localNotApplicableStr then
entrez_mm_link_list[#entrez_mm_link_list+1] = "[https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=retrieve&dopt=default&list_uids="..v.."&rn=1 "..v.."]"
end
end
if #entrez_mm_link_list < 5 then
entrez_mm_collapse = "none"
if entrez_mm_default == nil and #entrez_mm_link_list == 0 then entrez_mm_link = localNotApplicableStr end
else
entrez_mm_collapse = "collapsible collapsed"
entrez_mm_default = table.remove(entrez_mm_link_list, 1) .. '<br>' .. table.remove(entrez_mm_link_list, 1) .. '<br>' ..table.remove(entrez_mm_link_list, 1) .. '<br>' .. table.remove(entrez_mm_link_list, 1) .. '<br>' .. table.remove(entrez_mm_link_list, 1) .. '<br>'
end
if entrez_mm_link_list[#entrez_mm_link_list] then
entrez_mm_link = table.concat(entrez_mm_link_list, "<br>")
end
local ensemblTitle = "[[Ensembl]]"
ensembl = string.gsub(ensembl, "%s", "")
local ensembl_link = localNotApplicableStr
local ensembl_collapse
local ensembl_default = ""
local split_ensembl = mw.text.split(ensembl, localSeparatorStr)
local ensembl_link_list = {}
for k,v in ipairs(split_ensembl) do
if string.match(v, '%w+') and v ~= localNotApplicableStr then
ensembl_link_list[#ensembl_link_list+1] = "[http://www.ensembl.org/Homo_sapiens/geneview?gene="..v..";db=core".." "..v.."]"
end
end
if #ensembl_link_list < 5 then
ensembl_collapse = "none"
if ensembl_default == nil and #ensembl_link_list == 0 then ensembl_link = localNotApplicableStr end
else
ensembl_collapse = "collapsible collapsed"
ensembl_default = table.remove(ensembl_link_list, 1) .. '<br>' .. table.remove(ensembl_link_list, 1) .. '<br>' ..table.remove(ensembl_link_list, 1) .. '<br>' .. table.remove(ensembl_link_list, 1) .. '<br>' .. table.remove(ensembl_link_list, 1) .. '<br>'
end
if ensembl_link_list[#ensembl_link_list] then
ensembl_link = table.concat(ensembl_link_list, "<br>")
end
ensembl_mm = string.gsub(ensembl_mm, "%s", "")
local ensembl_mm_link = localNotApplicableStr
local ensembl_mm_collapse
local ensembl_mm_default = ""
local split_ensembl_mm = mw.text.split(ensembl_mm, localSeparatorStr)
local ensembl_mm_link_list = {}
for k,v in ipairs(split_ensembl_mm) do
if string.match(v, '%w+') and v ~= localNotApplicableStr then
ensembl_mm_link_list[#ensembl_mm_link_list+1] = "[http://www.ensembl.org/Mus_musculus/geneview?gene="..v..";db=core".." "..v.."]"
end
end
if #ensembl_mm_link_list < 5 then
ensembl_mm_collapse = "none"
if ensembl_mm_default == nil and #ensembl_mm_link_list == 0 then ensembl_mm_link = localNotApplicableStr end
else
ensembl_mm_collapse = "collapsible collapsed"
ensembl_mm_default = table.remove(ensembl_mm_link_list, 1) .. '<br>' .. table.remove(ensembl_mm_link_list, 1) .. '<br>' ..table.remove(ensembl_mm_link_list, 1) .. '<br>' .. table.remove(ensembl_mm_link_list, 1) .. '<br>' .. table.remove(ensembl_mm_link_list, 1) .. '<br>'
end
if ensembl_mm_link_list[#ensembl_mm_link_list] then
ensembl_mm_link = table.concat(ensembl_mm_link_list, "<br>")
end
local uniprotTitle = "[[UniProt]]"
local uniprot_url = "https://www.uniprot.org/uniprot/"
local uniprot_link = localNotApplicableStr
local uniprot_collapse
local uniprot_default = ""
local split_uniprot = mw.text.split(uniprot, '%p')
local uniprot_link_list = {}
local uniprot_first = {}
local uniprot_alternate = {}
local hash = {}
for k,v in ipairs(split_uniprot) do
if not hash[v] then
local label = mw.text.trim(v)
local concat_uniprot_link = uniprot_url .. label
if string.match(v, '%w+') and v ~= localNotApplicableStr then
if string.match(v, '^O') or string.match(v,'^P') or string.match(v, '^Q') then
uniprot_first[#uniprot_first+1] = "[" .. concat_uniprot_link .. " " ..label .. "]"
else
uniprot_alternate[#uniprot_alternate+1] = "[" .. concat_uniprot_link .. " " ..label .. "]"
end
end
hash[v] = true
end
end
if #uniprot_first > 0 then
uniprot_link_list = uniprot_first
else
uniprot_link_list = uniprot_alternate
end
if #uniprot_link_list < 5 then
uniprot_collapse = "none"
if uniprot_default == nil and #uniprot_link_list == 0 then uniprot_link = localNotApplicableStr end
else
uniprot_collapse = "collapsible collapsed"
uniprot_default = table.remove(uniprot_link_list, 1) .. '<br>' .. table.remove(uniprot_link_list, 1) .. '<br>' ..table.remove(uniprot_link_list, 1) .. '<br>' .. table.remove(uniprot_link_list, 1) .. '<br>' .. table.remove(uniprot_link_list, 1) .. '<br>'
end
if uniprot_link_list[#uniprot_link_list] then
uniprot_link = table.concat(uniprot_link_list, "<br>")
end
local uniprot_mm_link = localNotApplicableStr
local uniprot_mm_collapse
local uniprot_mm_default = ""
local split_uniprot_mm = mw.text.split(uniprot_mm, localSeparatorStr)
local uniprot_mm_link_list = {}
local uniprot_mm_first = {}
local uniprot_mm_alternate = {}
local hash2 = {}
for k,v in ipairs(split_uniprot_mm) do
if not hash2[v] then
local label = mw.text.trim(v)
local concat_uniprot_link = uniprot_url .. label
if string.match(v, '%w+') and v ~= localNotApplicableStr then
if string.match(v, '^O') or string.match(v,'^P') or string.match(v, '^Q') then
uniprot_mm_first[#uniprot_mm_first+1] = "[" .. concat_uniprot_link .. " " ..label .. "]"
else
uniprot_mm_alternate[#uniprot_mm_alternate+1] = "[" .. concat_uniprot_link .. " " ..label .. "]"
end
end
hash2[v] = true
end
end
if #uniprot_mm_first > 0 then
uniprot_mm_link_list = uniprot_mm_first
else
uniprot_mm_link_list = uniprot_mm_alternate
end
if #uniprot_mm_link_list < 5 then
uniprot_mm_collapse = "none"
if uniprot_mm_default == nil and #uniprot_mm_link_list == 0 then uniprot_mm_link = localNotApplicableStr end
else
uniprot_mm_collapse = "collapsible collapsed"
uniprot_mm_default = table.remove(uniprot_mm_link_list, 1) .. '<br>' .. table.remove(uniprot_mm_link_list, 1) .. '<br>' ..table.remove(uniprot_mm_link_list, 1) .. '<br>' .. table.remove(uniprot_mm_link_list, 1) .. '<br>' .. table.remove(uniprot_mm_link_list, 1) .. '<br>'
end
if uniprot_mm_link_list[#uniprot_mm_link_list] then
uniprot_mm_link = table.concat(uniprot_mm_link_list, "<br>")
end
local ncbi_link = "https://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val="
local refseq_mRNATitle = "RefSeq (mRNA)"
local refseq_mRNA_link = localNotApplicableStr
local refseq_mRNA_collapse
local refseq_mRNA_default = ""
local split_refseq_mRNA = mw.text.split(refseq_mRNA, localSeparatorStr)
local link_list_first_mRNA = {}
local link_list_alternate_mRNA = {}
local link_list = {}
for k,v in ipairs(split_refseq_mRNA) do
local label = mw.text.trim(v)
local concat_ncbi_link = ncbi_link .. label
if string.match(v, '%w+') and v ~= localNotApplicableStr then
if string.match(v, 'NM') or string.match(v, 'NP') then
link_list_first_mRNA[#link_list_first_mRNA+1] = "[" .. concat_ncbi_link .. " " ..label .. "]"
elseif string.match(v, 'XM') or string.match(v, 'XP') then
link_list_alternate_mRNA[#link_list_alternate_mRNA+1] = "[" .. concat_ncbi_link .. " " ..label .. "]"
end
end
end
if #link_list_first_mRNA > 0 then
link_list = link_list_first_mRNA
else
link_list = link_list_alternate_mRNA
end
if #link_list < 6 then
refseq_mRNA_collapse = "none"
if refseq_mRNA_default == nil and #link_list == 0 then refseq_mRNA_link = localNotApplicableStr end
else
refseq_mRNA_collapse = "collapsible collapsed"
refseq_mRNA_default = table.remove(link_list, 1) .. '<br>' .. table.remove(link_list, 1) .. '<br>' ..table.remove(link_list, 1) .. '<br>' .. table.remove(link_list, 1) .. '<br>' .. table.remove(link_list, 1) .. '<br>'
end
if link_list[#link_list] then
refseq_mRNA_link = table.concat(link_list, "<br>")
end
local refseq_mRNA_mm_link = localNotApplicableStr
local refseq_mRNA_mm_collapse
local refseq_mRNA_mm_default = ""
local split_refseq_mRNA_mm = mw.text.split(refseq_mRNA_mm, localSeparatorStr)
local link_list_mm = {}
local link_list_first_mRNA_mm = {}
local link_list_alternate_mRNA_mm = {}
for k,v in ipairs(split_refseq_mRNA_mm) do
local label = mw.text.trim(v)
local concat_ncbi_link = ncbi_link .. label
if string.match(v, '%w+') and v ~= localNotApplicableStr then
if string.match(v, 'NM') or string.match(v, 'NP') then
link_list_first_mRNA_mm[#link_list_first_mRNA_mm+1] = "[" .. concat_ncbi_link .. " " ..label .. "]"
elseif string.match(v, 'XM') or string.match(v, 'XP') then
link_list_alternate_mRNA_mm[#link_list_alternate_mRNA_mm+1] = "[" .. concat_ncbi_link .. " " ..label .. "]"
end
end
end
if #link_list_first_mRNA_mm > 0 then
link_list_mm = link_list_first_mRNA_mm
else
link_list_mm = link_list_alternate_mRNA_mm
end
if #link_list_mm < 6 then
refseq_mRNA_mm_collapse = "none"
if refseq_mRNA_mm_default == nil and #link_list_mm == 0 then refseq_mRNA_mm_link = localNotApplicableStr end
else
refseq_mRNA_mm_collapse = "collapsible collapsed"
refseq_mRNA_mm_default = table.remove(link_list_mm, 1) .. '<br>' .. table.remove(link_list_mm, 1) .. '<br>' ..table.remove(link_list_mm, 1) .. '<br>' .. table.remove(link_list_mm, 1) .. '<br>' .. table.remove(link_list_mm, 1) .. '<br>'
end
if link_list_mm[#link_list_mm] then
refseq_mRNA_mm_link = table.concat(link_list_mm, "<br>")
end
local refseq_protTitle = "RefSeq (protein)"
local refseq_prot_link = localNotApplicableStr
local refseq_prot_collapse
local refseq_prot_default = ""
local split_refseq_prot = mw.text.split(refseq_prot, localSeparatorStr)
local link_list_prot = {}
local link_list_first_prot = {}
local link_list_alternate_prot = {}
for k,v in ipairs(split_refseq_prot) do
local label = mw.text.trim(v)
local concat_ncbi_link = ncbi_link .. label
if string.match(v, '%w+') and v ~= localNotApplicableStr then
if string.match(v, 'NM') or string.match(v, 'NP') then
link_list_first_prot[#link_list_first_prot+1] = "[" .. concat_ncbi_link .. " " ..label .. "]"
elseif string.match(v, 'XM') or string.match(v, 'XP') then
link_list_alternate_prot[#link_list_alternate_prot+1] = "[" .. concat_ncbi_link .. " " ..label .. "]"
end
end
end
if #link_list_first_prot > 0 then
link_list_prot = link_list_first_prot
else
link_list_prot = link_list_alternate_prot
end
if #link_list_prot < 6 then
refseq_prot_collapse = "none"
if refseq_prot_default == nil and #link_list_prot == 0 then refseq_prot_link = localNotApplicableStr end
else
refseq_prot_collapse = "collapsible collapsed"
refseq_prot_default = table.remove(link_list_prot, 1) .. '<br>' .. table.remove(link_list_prot, 1) .. '<br>' ..table.remove(link_list_prot, 1) .. '<br>' .. table.remove(link_list_prot, 1) .. '<br>' .. table.remove(link_list_prot, 1) .. '<br>'
end
if link_list_prot[#link_list_prot] then
refseq_prot_link = table.concat(link_list_prot, "<br>")
end
local refseq_prot_mm_link = localNotApplicableStr
local refseq_prot_mm_collapse
local refseq_prot_mm_default = ""
local split_refseq_prot_mm = mw.text.split(refseq_prot_mm, localSeparatorStr)
local link_list_prot_mm = {}
local link_list_first_prot_mm = {}
local link_list_alternate_prot_mm = {}
for k,v in ipairs(split_refseq_prot_mm) do
local label = mw.text.trim(v)
local concat_ncbi_link = ncbi_link .. label
if string.match(v, '%w+') and v ~= localNotApplicableStr then
if string.match(v, 'NM') or string.match(v, 'NP') then
link_list_first_prot_mm[#link_list_first_prot_mm+1] = "[" .. concat_ncbi_link .. " " ..label .. "]"
elseif string.match(v, 'XM') or string.match(v, 'XP') then
link_list_alternate_prot_mm[#link_list_alternate_prot_mm+1] = "[" .. concat_ncbi_link .. " " ..label .. "]"
end
end
end
if #link_list_first_prot_mm > 0 then
link_list_prot_mm = link_list_first_prot_mm
else
link_list_prot_mm = link_list_alternate_prot_mm
end
if #link_list_prot_mm < 6 then
refseq_prot_mm_collapse = "none"
if refseq_prot_mm_default == nil and #link_list_prot_mm == 0 then refseq_prot_mm_link = localNotApplicableStr end
else
refseq_prot_mm_collapse = "collapsible collapsed"
refseq_prot_mm_default = table.remove(link_list_prot_mm, 1) .. '<br>' .. table.remove(link_list_prot_mm, 1) .. '<br>' ..table.remove(link_list_prot_mm, 1) .. '<br>' .. table.remove(link_list_prot_mm, 1) .. '<br>' .. table.remove(link_list_prot_mm, 1) .. '<br>'
end
if link_list_prot_mm[#link_list_prot_mm] then
refseq_prot_mm_link = table.concat(link_list_prot_mm, "<br>")
end
local locTitle = "Location (UCSC)"
local gstart_mb = p.locToMb(gstart, 2)
local gend_mb = p.locToMb(gend, 2)
local chr_loc_link = ""
if (string.match(db, '%w+') and string.match(chr, '%w+') and string.match(gstart, '%w+') and string.match(gend, '%w+') )then
local chr_ucsc
if chr == "MT" then
chr_ucsc = "M"
else
chr_ucsc = chr
end
chr_loc_link = "[https://genome.ucsc.edu/cgi-bin/hgTracks?org=Human&db="..db.."&position=chr"..chr_ucsc..":"..gstart.."-"..gend.." ".."Chr "..chr_ucsc..": "..gstart_mb.." – "..gend_mb.." Mb]"
else
chr_loc_link = localNotApplicableStr
end
local gstart_mm_mb = p.locToMb(gstart_mm, 2)
local gend_mm_mb = p.locToMb(gend_mm, 2)
local chr_loc_mm_link = ""
if (string.match(db_mm, '%w+') and string.match(chr_mm, '%w+') and string.match(gstart_mm, '%w+') and string.match(gend_mm, '%w+') )then
local chr_mm_ucsc
if chr_mm == "MT" then
chr_mm_ucsc = "M"
else
chr_mm_ucsc = chr_mm
end
chr_loc_mm_link = "[https://genome.ucsc.edu/cgi-bin/hgTracks?org=Mouse&db="..db_mm.."&position=chr"..chr_mm_ucsc..":"..gstart_mm.."-"..gend_mm.." ".."Chr "..chr_mm_ucsc..": "..gstart_mm_mb.." – "..gend_mm_mb.." Mb]"
else
chr_loc_mm_link = localNotApplicableStr
end
local pubmedTitle = "[[PubMed]] search"
local pubmed_link = entrez_gene
if string.match(entrez_gene, '%w+') and entrez_gene ~= localNotApplicableStr then
pubmed_link = frame:extensionTag("ref",frame:expandTemplate{ title = 'cite_web', args = { title ="Human PubMed Reference:" , url = "https://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=Link&LinkName=gene_pubmed&from_uid="..entrez_gene, website = "National Center for Biotechnology Information, U.S. National Library of Medicine" } } )
end
local pubmed_mm_link = entrez_gene_mm
if string.match(entrez_gene_mm, '%w+') and entrez_gene_mm ~= localNotApplicableStr then
pubmed_mm_link = frame:extensionTag("ref",frame:expandTemplate{ title = 'cite_web', args = { title ="Mouse PubMed Reference:" , url ="https://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=Link&LinkName=gene_pubmed&from_uid="..entrez_gene_mm, website = "National Center for Biotechnology Information, U.S. National Library of Medicine" } } )
end
root
:tag('tr')
:tag('td')
:attr('colspan', 4)
:css('text-align', 'center')
:css('background-color', rowBGcolor)
:css('color', 'inherit')
:tag('table')
:attr('class', ortholog_class)
:css('padding', '0')
:css('border', 'none')
:css('margin', '0')
:css('width', '100%')
:css('text-align', 'left')
:tag('tr')
:tag('th')
:attr('colspan', '4')
:css('text-align', 'center')
:css('background-color', titleBGcolor)
:css('color', 'inherit')
:wikitext(title)
:done()
:done()
:tag('tr')
:tag('th')
:attr('scope', 'row')
:css('background-color', sideTitleBGcolor)
:css('color', 'inherit')
:wikitext("زاتھ") -- **lclz**
:done()
:tag('td')
:wikitext("'''اِنسان'''") -- **lclz**
:done()
:tag('td')
:wikitext("'''گَگُر'''") -- **lclz**
:done()
:done()
:tag('tr')
:tag('th')
:attr('scope', 'row')
:css('background-color', sideTitleBGcolor)
:css('color', 'inherit')
:wikitext(entrezTitle)
:done()
:tag('td')
:tag('table')
:attr('class', entrez_collapse)
:css('padding', '0')
:css('border', 'none')
:css('margin', '0')
:css('width', '100%')
:css('text-align', 'right')
:tag('tr')
:tag('th')
:attr('colspan', '1')
:tag('span')
:attr('class', 'plainlinks')
:wikitext(entrez_default)
:done()
:done()
:done()
:tag('tr')
:tag('td')
:attr('colspan', '1')
:tag('p')
:attr('class', 'plainlinks')
:wikitext(entrez_link)
:done()
:done()
:done()
:done()
:done()
:tag('td')
:tag('table')
:attr('class', entrez_mm_collapse)
:css('padding', '0')
:css('border', 'none')
:css('margin', '0')
:css('width', '100%')
:css('text-align', 'right')
:tag('tr')
:tag('th')
:attr('colspan', '1')
:tag('span')
:attr('class', 'plainlinks')
:wikitext(entrez_mm_default)
:done()
:done()
:done()
:tag('tr')
:tag('td')
:attr('colspan', '1')
:tag('p')
:attr('class', 'plainlinks')
:wikitext(entrez_mm_link)
:done()
:done()
:done()
:done()
:done()
:done()
:tag('tr')
:tag('th')
:attr('scope', 'row')
:css('background-color', sideTitleBGcolor)
:css('color', 'inherit')
:wikitext(ensemblTitle)
:done()
:tag('td')
:tag('table')
:attr('class', ensembl_collapse)
:css('padding', '0')
:css('border', 'none')
:css('margin', '0')
:css('width', '100%')
:css('text-align', 'right')
:tag('tr')
:tag('th')
:attr('colspan', '1')
:tag('span')
:attr('class', 'plainlinks')
:wikitext(ensembl_default)
:done()
:done()
:done()
:tag('tr')
:tag('td')
:attr('colspan', '1')
:tag('p')
:attr('class', 'plainlinks')
:wikitext(ensembl_link)
:done()
:done()
:done()
:done()
:done()
:tag('td')
:tag('table')
:attr('class', ensembl_mm_collapse)
:css('padding', '0')
:css('border', 'none')
:css('margin', '0')
:css('width', '100%')
:css('text-align', 'right')
:tag('tr')
:tag('th')
:attr('colspan', '1')
:tag('span')
:attr('class', 'plainlinks')
:wikitext(ensembl_mm_default)
:done()
:done()
:done()
:tag('tr')
:tag('td')
:attr('colspan', '1')
:tag('p')
:attr('class', 'plainlinks')
:wikitext(ensembl_mm_link)
:done()
:done()
:done()
:done()
:done()
:done()
:tag('tr')
:tag('th')
:attr('scope', 'row')
:css('background-color', sideTitleBGcolor)
:css('color', 'inherit')
:wikitext(uniprotTitle)
:done()
:tag('td')
:tag('table')
:attr('class', uniprot_collapse)
:css('padding', '0')
:css('border', 'none')
:css('margin', '0')
:css('width', '100%')
:css('text-align', 'right')
:tag('tr')
:tag('th')
:attr('colspan', '1')
:tag('span')
:attr('class', 'plainlinks')
:wikitext(uniprot_default)
:done()
:done()
:done()
:tag('tr')
:tag('td')
:attr('colspan', '1')
:tag('p')
:attr('class', 'plainlinks')
:wikitext(uniprot_link)
:done()
:done()
:done()
:done()
:done()
:tag('td')
:tag('table')
:attr('class', uniprot_mm_collapse)
:css('padding', '0')
:css('border', 'none')
:css('margin', '0')
:css('width', '100%')
:css('text-align', 'right')
:tag('tr')
:tag('th')
:attr('colspan', '1')
:tag('span')
:attr('class', 'plainlinks')
:wikitext(uniprot_mm_default)
:done()
:done()
:done()
:tag('tr')
:tag('td')
:attr('colspan', '1')
:tag('p')
:attr('class', 'plainlinks')
:wikitext(uniprot_mm_link)
:done()
:done()
:done()
:done()
:done()
:done()
:tag('tr')
:tag('th')
:attr('scope', 'row')
:css('background-color', sideTitleBGcolor)
:css('color', 'inherit')
:wikitext(refseq_mRNATitle)
:done()
:tag('td')
:tag('table')
:attr('class', refseq_mRNA_collapse)
:css('padding', '0')
:css('border', 'none')
:css('margin', '0')
:css('width', '100%')
:css('text-align', 'right')
:tag('tr')
:tag('th')
:attr('colspan', '1')
:attr('class', 'plainlinks')
:wikitext(refseq_mRNA_default)
:done()
:done()
:tag('tr')
:tag('td')
:attr('colspan', '1')
:tag('p')
:tag('span')
:attr('class', 'plainlinks')
:wikitext(refseq_mRNA_link)
:done()
:done()
:done()
:done()
:done()
:done()
:tag('td')
:tag('table')
:attr('class', refseq_mRNA_mm_collapse)
:css('padding', '0')
:css('border', 'none')
:css('margin', '0')
:css('width', '100%')
:css('text-align', 'right')
:tag('tr')
:tag('th')
:attr('colspan', '1')
:attr('class', 'plainlinks')
:wikitext(refseq_mRNA_mm_default)
:done()
:done()
:tag('tr')
:tag('td')
:attr('colspan', '1')
:tag('p')
:tag('span')
:attr('class', 'plainlinks')
:wikitext(refseq_mRNA_mm_link)
:done()
:done()
:done()
:done()
:done()
:done()
:done()
:tag('tr')
:tag('th')
:attr('scope', 'row')
:css('background-color', sideTitleBGcolor)
:css('color', 'inherit')
:wikitext(refseq_protTitle)
:done()
:tag('td')
:tag('table')
:attr('class', refseq_prot_collapse)
:css('padding', '0')
:css('border', 'none')
:css('margin', '0')
:css('width', '100%')
:css('text-align', 'right')
:tag('tr')
:tag('th')
:attr('colspan', '1')
:attr('class', 'plainlinks')
:wikitext(refseq_prot_default)
:done()
:done()
:tag('tr')
:tag('td')
:attr('colspan', '1')
:tag('p')
:tag('span')
:attr('class', 'plainlinks')
:wikitext(refseq_prot_link)
:done()
:done()
:done()
:done()
:done()
:done()
:tag('td')
:tag('table')
:attr('class', refseq_prot_mm_collapse)
:css('padding', '0')
:css('border', 'none')
:css('margin', '0')
:css('width', '100%')
:css('text-align', 'right')
:tag('tr')
:tag('th')
:attr('colspan', '1')
:attr('class', 'plainlinks')
:wikitext(refseq_prot_mm_default)
:done()
:done()
:tag('tr')
:tag('td')
:attr('colspan', '1')
:tag('p')
:tag('span')
:attr('class', 'plainlinks')
:wikitext(refseq_prot_mm_link)
:done()
:done()
:done()
:done()
:done()
:done()
:done()
:tag('tr')
:tag('th')
:attr('scope', 'row')
:css('background-color', sideTitleBGcolor)
:css('color', 'inherit')
:wikitext(locTitle)
:done()
:tag('td')
:tag('span')
:attr('class', 'plainlinks')
:wikitext(chr_loc_link)
:done()
:done()
:tag('td')
:tag('span')
:attr('class', 'plainlinks')
:wikitext(chr_loc_mm_link)
:done()
:done()
:done()
:tag('tr')
:tag('th')
:attr('scope', 'row')
:css('background-color', sideTitleBGcolor)
:css('color', 'inherit')
:wikitext(pubmedTitle)
:done()
:tag('td')
:tag('span')
:attr('class', 'plainlinks')
:wikitext(pubmed_link)
:done()
:done()
:tag('td')
:tag('span')
:attr('class', 'plainlinks')
:wikitext(pubmed_mm_link)
:done()
:wikitext(category_chromosome)
:done()
:done()
:done()
:done()
:done()
end
function p.formatRow(title)
root
:tag('tr')
:tag('td')
:attr('colspan', '4')
:css('text-align', 'center')
:css('background-color', rowBGcolor)
:css('color', 'inherit')
:tag('table')
:css('padding', '0')
:css('border', 'none')
:css('margin', '0')
:css('width', '100%')
:css('text-align', 'left')
:tag('tr')
:css('background-color', titleBGcolor)
:css('color', 'inherit')
:css('text-align', 'center')
:tag('th')
:attr('colspan',"2")
:wikitext(title)
:done()
:done()
:done()
:done()
:done()
end
function p.renderFooter(Qid, Qid_mm)
local text = "[[Wikidata]]"
local hs_link = "[[d:"..Qid.."|اِنسان وُچھِو/اؠڈِٹ کٔرِو]]" -- **lclz**
local mm_link = ""
local link_no_hs
local link_no_mm
if Qid_mm == "" then
link_no_mm = 0
link_no_hs = 4
else
link_no_mm = 2
link_no_hs = 2
mm_link = "[[d:"..Qid_mm.."|گَگُر وُچھِو/اؠڈِٹ کٔرِو]]" -- **lclz**
end
root
:tag('tr')
:tag('td')
:attr('colspan', '4')
:css('text-align', 'center')
:css('background-color', rowBGcolor)
:css('color', 'inherit')
:wikitext(text)
:done()
:tag('tr')
:tag('td')
:attr('colspan', '4')
:css('text-align', 'center')
:css('background-color', rowBGcolor)
:css('color', 'inherit')
:tag('table')
:css('padding', '0')
:css('border', 'none')
:css('margin', '0')
:css('width', '100%')
:css('text-align', 'center')
:tag('tr')
:tag('td')
:attr('colspan', link_no_hs)
:css('background-color', rowBGcolor)
:css('color', 'inherit')
:css('text-align', 'center')
:wikitext(hs_link)
:done()
:tag('td')
:attr('colspan', link_no_mm)
:css('background-color', rowBGcolor)
:css('color', 'inherit')
:css('text-align', 'center')
:wikitext(mm_link)
:done()
:done()
:done()
:done()
root:done()
end
function p.rowLabel(label)
root
:tag('tr')
:tag('th')
:attr('rowspan', '2')
:css('background-color', sideTitleBGcolor)
:css('color', 'inherit')
:css('width', '43px')
:wikitext(label)
end
function p.getLabel(entity)
local data = entity
local f = {'labels','ks','value'} -- **lclz** Attempt to pull Kashmiri first if set
local i = 1
while true do
local index = f[i]
if not index then
if type(data) == "table" then
return mw.text.jsonEncode(data, mw.text.JSON_PRESERVE_KEYS + mw.text.JSON_PRETTY)
else
return tostring(data)
end
end
data = data[index] or data[tonumber(index)]
if not data then
return p.getLabelFallback(entity) -- fallback mechanism
end
i = i + 1
end
end
-- Fallback to EN if KS label is missing
function p.getLabelFallback(entity)
local data = entity
local f = {'labels','en','value'}
local i = 1
while true do
local index = f[i]
if not index then
if type(data) == "table" then
return mw.text.jsonEncode(data, mw.text.JSON_PRESERVE_KEYS + mw.text.JSON_PRETTY)
else
return tostring(data)
end
end
data = data[index] or data[tonumber(index)]
if not data then
return
end
i = i + 1
end
end
function p.getValue(entity, propertyID, return_val, sep, stated_in)
local claims
if return_val == nil then return_val = "" end
if sep == nil then sep = " " end
if entity and entity.claims then
claims = entity.claims[propertyID]
end
if claims then
if (claims[1] and claims[1].mainsnak.snaktype == "value" and claims[1].mainsnak.datavalue.type == "wikibase-entityid") then
local out = {}
for k, v in pairs(claims) do
local datav = mw.wikibase.label(v.mainsnak.datavalue.value["id"])
if datav == nil then datav = " " end
local is_from_given_source = true
if stated_in ~= nil then
is_from_given_source = false
if v.references then
for rk, rv in pairs(v.references) do
local ref_val = rv.snaks.P248
if ref_val then
for stated_k, stated_v in pairs(ref_val) do
if (stated_v and stated_v.snaktype == "value" and stated_v.datavalue.type == "wikibase-entityid") then
local ref_stated_in_val = stated_v.datavalue.value["id"]
if ref_stated_in_val == stated_in then is_from_given_source = true end
end
end
end
end
end
end
if is_from_given_source then
out[#out + 1] = datav
end
end
return table.concat(out, sep)
else
return entity:formatPropertyValues(propertyID).value
end
else
return return_val
end
end
function p.getValueProtein(protein_entities, propertyID, return_val)
if return_val == nil then return_val = "" end
local sep = "،" -- **lclz**
local overall_results = {}
for key, val in pairs(protein_entities) do
local claims
local entity = val
if entity and entity.claims then
claims = entity.claims[propertyID]
end
if claims then
local results
if (claims[1] and claims[1].mainsnak.snaktype == "value" and claims[1].mainsnak.datavalue.type == "wikibase-entityid") then
local out = {}
for k, v in pairs(claims) do
local datav = mw.wikibase.getLabel("Q" .. v.mainsnak.datavalue.value["numeric-id"])
if datav == nil then datav = " " end
out[#out + 1] = datav
end
results = table.concat(out, sep)
else
results = entity:formatPropertyValues(propertyID).value
end
overall_results[#overall_results+1] = results
end
end
local str_overall_results = table.concat(overall_results, sep)
if string.match(str_overall_results, '%w+') then
return str_overall_results
else
return return_val
end
end
function p.getQid(entity)
local Qid
if entity and entity.id then
Qid = entity.id
return Qid
else
return ""
end
end
function p.getRefseq_mRNA(entity, propertyID, return_val)
if return_val == nil then return_val = "" end
local input_rank = "RANK_PREFERRED"
local claims
if entity.claims then
claims = entity.claims[propertyID]
end
if claims then
if (claims[1] and claims[1].mainsnak.snaktype == "value" and claims[1].mainsnak.datavalue.type == "wikibase-entityid" ) then
local out = {}
for k, v in pairs(claims) do
local sitelink = mw.wikibase.getSitelink("Q" .. v.mainsnak.datavalue.value["numeric-id"])
local label = mw.wikibase.getLabel("Q" .. v.mainsnak.datavalue.value["numeric-id"])
if label == nil then label = "Q" .. v.mainsnak.datavalue.value["numeric-id"] end
if sitelink then
out[#out + 1] = "[[" .. sitelink .. "|" .. label .. "]]"
else
out[#out + 1] = "[[:d:Q" .. v.mainsnak.datavalue.value["numeric-id"] .. "|" .. label .. "]]"
end
end
return table.concat(out, "، ") -- **lclz**
else
local results = entity:formatPropertyValues(propertyID, mw.wikibase.entity.claimRanks).value
return results
end
else
return return_val
end
end
function p.getRefseq_protein(protein_entities, propertyID, return_val)
local sep = localSeparatorStr
local overall_results = {}
for key, val in pairs(protein_entities) do
local claims
local entity = val
if entity.claims then
claims = entity.claims[propertyID]
end
if claims then
local results
if (claims[1] and claims[1].mainsnak.snaktype == "value" and claims[1].mainsnak.datavalue.type == "wikibase-entityid" ) then
local out = {}
for k, v in pairs(claims) do
local datav = mw.wikibase.getLabel("Q" .. v.mainsnak.datavalue.value["numeric-id"])
if datav == nil then datav = " " end
out[#out + 1] = datav
end
results = table.concat(out, sep)
else
results = entity:formatPropertyValues(propertyID, mw.wikibase.entity.claimRanks).value
end
overall_results[#overall_results+1] = results
end
end
local str_overall_results = table.concat(overall_results, sep)
return str_overall_results
end
function p.getImage(entity, propertyID, sep, imgsize)
local claims
if entity and entity.claims then
claims = entity.claims[propertyID]
end
if claims then
if (claims[1] and claims[1].mainsnak.datatype == "commonsMedia") then
local out = {}
for k, v in pairs(claims) do
local filename = v.mainsnak.datavalue.value
out[#out + 1] = "[[File:" .. filename .. "|" .. imgsize .. "]]"
end
return table.concat(out, sep)
else
return ""
end
else
return ""
end
end
function p.getPDB(protein_entities)
local pdb_propertyID = "P638"
local overall_results = {}
for key, val in pairs(protein_entities) do
local claims
local entity = val
if entity and entity.claims then
claims = entity.claims[pdb_propertyID]
end
local sitelink = "https://www.rcsb.org/structure/"
if claims then
local results
if (claims[1] and claims[1].mainsnak.snaktype == "value") then
local out = {}
for k, v in pairs(claims) do
local label = mw.wikibase.getLabel(v.mainsnak.datavalue.value)
if label == nil then label = v.mainsnak.datavalue.value end
if sitelink then
out[#out + 1] = "[" .. sitelink .. label .. " " ..label .. "]"
else
out[#out + 1] = "[[:d:Q" .. v.mainsnak.datavalue.value .. "|" .. label .. "]]"
end
end
results = table.concat(out, "، ") -- **lclz**
else
results = entity:formatPropertyValues(pdb_propertyID, mw.wikibase.entity.claimRanks).value
end
overall_results[#overall_results+1] = results
end
end
return table.concat(overall_results, "،%%s") -- **lclz**
end
function p.getAliases(entity)
if entity['aliases'] ~= nil then
local test = entity['aliases']['ks'] -- **lclz** Attempt to pull Kashmiri first
if not test then test = entity['aliases']['en'] end
if test then
local a = ''
for key, value in ipairs(test) do
a = a .. '، ' .. value['value'] -- **lclz**
end
return a
else
return ""
end
else
return ""
end
end
function p.getChromosomeLoc(entity, propertyID, prefix)
local output = ""
local sep = " "
local qualifierID = "P659"
local newest_build = "0"
local claims
if entity and entity.claims then
claims = entity.claims[propertyID]
end
if claims then
if (claims[1] ) then
for k, v in pairs(claims) do
local location = v.mainsnak.datavalue.value
local quals
if v.qualifiers then
quals = v.qualifiers.P659
end
if quals then
for qk, qv in pairs(quals) do
local qual_obj_id = "Q"..qv.datavalue.value["numeric-id"]
local qual_obj = mw.wikibase.getEntity(qual_obj_id)
local alias = ""
if qual_obj["aliases"] ~= nil then
local test = qual_obj["aliases"]["en"]
if test then
for key, value in ipairs(test) do
if string.match(value['value'], prefix) then
alias = value['value']
local build_no = alias:gsub(prefix,"")
if build_no > newest_build then
output = location
newest_build = build_no
end
end
end
end
end
end
else
output = location
end
end
return output
else
return ""
end
else
return ""
end
end
function p.getAliasFromGenomeAssembly(entity, prefix)
local output = ""
local sep = " "
local propertyID = "P644"
local qualifierID = "P659"
local newest_build = "0"
local claims
if entity.claims then
claims = entity.claims[propertyID]
end
if claims then
if (claims[1] ) then
for k, v in pairs(claims) do
local location = ''
local quals
if v.qualifiers then
quals = v.qualifiers.P659
end
if quals then
for qk, qv in pairs(quals) do
local qual_obj_id = "Q"..qv.datavalue.value["numeric-id"]
local qual_obj = mw.wikibase.getEntity(qual_obj_id)
local alias = ""
if qual_obj["aliases"] ~= nil then
local test = qual_obj["aliases"]["en"]
if test then
for key, value in ipairs(test) do
if string.match(value['value'], prefix) then
alias = value['value']
local build_no = alias:gsub(prefix,"")
if build_no > newest_build then
newest_build = build_no
end
end
end
end
end
end
else
output = location
end
end
return prefix .. newest_build
else
return ""
end
else
return ""
end
end
function p.trimChromosome(entity)
local string_to_trim = p.getValue(entity, "P1057")
local out = ''
if string.find(string_to_trim, 'chromosome MT') or string.find(string_to_trim, 'mitochondri') then
out = "MT"
elseif string.find(string_to_trim, 'chromosome') then
out = string.match(string_to_trim, "%d+")
if out == nil then
out = string.match(string_to_trim, "X") or string.match(string_to_trim, "Y")
end
end
return out
end
function p.locToMb(num, idp)
num = tonumber(num)
if num == nil then
return ""
else
local mb = num/1000000
local mult = 10^(idp or 0)
return math.floor(mb * mult + 0.5) / mult
end
end
function p.isempty(s)
return s == nil or s == ''
end
function p.getGO(protein_entities, propertyID)
local overall_results = {}
local results = ""
for key, val in pairs(protein_entities) do
local claims
local entity = val
if entity.claims then
claims = entity.claims[propertyID]
end
local propertyID_child = "P686"
if claims then
if (claims[1] and claims[1].mainsnak.snaktype == "value" and claims[1].mainsnak.datavalue.type == "wikibase-entityid") then
for k, v in pairs(claims) do
local itemID_child = "Q" .. v.mainsnak.datavalue.value["numeric-id"]
local entity = mw.wikibase.getEntity(itemID_child)
local claims
local result_GOID = ''
if entity and entity.claims then claims = entity.claims[propertyID_child] end
if claims then
result_GOID = entity:formatPropertyValues(propertyID_child, {mw.wikibase.entity.claimRanks.RANK_NORMAL}).value
else
result_GOID = nil
end
local sitelink = "http://amigo.geneontology.org/amigo/term/"
local label = mw.wikibase.getLabel("Q" .. v.mainsnak.datavalue.value["numeric-id"])
if label == nil then label = "Q" .. v.mainsnak.datavalue.value["numeric-id"] end
local wiki_link = ""
if sitelink and result_GOID ~= nil then
wiki_link = "\n* [" .. sitelink .. result_GOID .. " " .. label .."]"
else
wiki_link = "\n* [[:d:Q" .. v.mainsnak.datavalue.value["numeric-id"] .. "|" .. label .. "]]"
end
overall_results[#overall_results+1] = wiki_link
end
else
results = entity:formatPropertyValues(propertyID, mw.wikibase.entity.claimRanks).value
end
end
end
local hash = {}
local res = {}
for _,v in ipairs(overall_results) do
if (not hash[v]) then
res[#res+1] = v
hash[v] = true
end
end
return table.concat(res, "")
end
local function getReference(qID, entity, property_id, ref_index)
local f = {"claims",property_id, ref_index, "references"}
local id = qID
local data = entity
if not data then
return nil
end
local i = 1
while true do
local index = f[i]
if not index then
if type(data) == "table" then
return mw.text.jsonEncode(data, mw.text.JSON_PRESERVE_KEYS + mw.text.JSON_PRETTY)
else
return tostring(data)
end
end
data = data[index] or data[tonumber(index)]
if not data then
return ""
end
i = i + 1
end
end
function p.getDisease(entity, propertyID)
local claims
local return_val = ""
if entity and entity.claims then
claims = entity.claims[propertyID]
end
if claims then
if (claims[1] and claims[1].mainsnak.snaktype == "value" and claims[1].mainsnak.datavalue.type == "wikibase-entityid") then
local out = {}
local datasource = {}
for k, v in pairs(claims) do
local datav = mw.wikibase.getLabel("Q" .. v.mainsnak.datavalue.value["numeric-id"])
if datav == nil then datav = " " end
local id = "Q" .. v.mainsnak.datavalue.value["numeric-id"]
local linkTarget = mw.wikibase.getSitelink(id)
local refLink = ""
local ref = ""
ref = getReference("", entity, "P2293", k)
if (ref ~= nil and ref ~= '') then
refLink = ref
end
if linkTarget then
out[#out + 1] = "[["..linkTarget.."|"..datav.."]]"
else
out[#out + 1] = "[[:d:" .. id .. "|" .. datav .. "]]"
end
datasource[#out] = refLink
end
return out, datasource
else
return return_val, return_val
end
else
return return_val
end
return return_val
end
function p.getDrug(protein_entities, propertyID)
local out = {}
local datasource = {}
local pname = {}
local pqid = {}
for key, val in pairs(protein_entities) do
local claims
local entity = val
local name = check_values(p.getLabel,{entity})
if entity.claims then
claims = entity.claims[propertyID]
end
local protein_id
if entity then protein_id = entity.id else protein_id = "" end
if claims then
if (claims[1] and claims[1].mainsnak.snaktype == "value" and claims[1].mainsnak.datavalue.type == "wikibase-entityid") then
for k, v in pairs(claims) do
local datav = mw.wikibase.getLabel("Q" .. v.mainsnak.datavalue.value["numeric-id"])
if datav == nil then datav = "" end
local id = "Q" .. v.mainsnak.datavalue.value["numeric-id"]
local linkTarget = mw.wikibase.getSitelink(id)
local refLink = ""
local ref = getReference(protein_id, entity, "P129",k)
if (ref ~= nil and ref ~= '') then
refLink = ref
end
if linkTarget then
out[#out + 1] = "[["..linkTarget.."|"..datav.."]]"
else
out[#out + 1] = "[[:d:" .. id .. "|" .. datav .. "]]"
end
pname[protein_id] = name
pqid[#out] = protein_id
datasource[#out] = refLink
end
end
end
end
return out, datasource, pqid, pname
end
function p.separateWithComma(bp)
local commaSeparated = bp
while true do
local k
commaSeparated, k = string.gsub(commaSeparated, "^(-?%d+)(%d%d%d)", '%1،%2') -- **lclz**
if k == 0 then
break
end
end
return commaSeparated
end
return p