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from collections import defaultdict
d = "./"
mgiID2MRK_ENSE = {}
enseID2mgiID = {}
with open(d + "inputs/MRK_ENSEMBL.rpt") as f:
for line in f:
items = line[:-1].split("\t")
mgiID = items[0]
mgiID2MRK_ENSE[mgiID] = items
enseID = items[5]
enseID2mgiID[enseID] = mgiID
enseID2MGI_GMC = {}
with open(d + "inputs/MGI_Gene_Model_Coord.rpt") as f:
MGI_GMC_headers = f.readline()[:-1].split("\t")
for line in f:
items = line[:-1].split("\t")
enseID = items[10]
enseID2MGI_GMC[enseID] = items
mgiID2MRK_Seq = {}
with open(d + "inputs/MRK_Sequence.rpt") as f:
MRK_Seq_headers = f.readline()[:-1].split("\t")
for line in f:
items = line[:-1].split("\t")
mgiID = items[0]
mgiID2MRK_Seq[mgiID] = items
enseID2mart = {}
with open(d + "inputs/mart_export.txt") as f:
mart_headers = f.readline()[:-1].split("\t")
for line in f:
items = line[:-1].split("\t")
enseID = items[0]
enseID2mart[enseID] = items
geneSymbol2TF = {}
with open(d + "inputs/TF_TcoF-DB.tsv") as f:
TF_headers = f.readline()[:-1].split("\t")
for line in f:
items = line[:-1].split("\t")
geneSymbol = items[0]
geneSymbol2TF[geneSymbol] = items
geneSymbol2Regulated = defaultdict(list)
with open(d + "inputs/trrust_rawdata.mouse.tsv") as f:
for line in f:
items = line[:-1].split("\t")
TFSymbol = items[0]
geneSymbol2Regulated[TFSymbol].append(items[1])
with open(d + "gencode.vM23.metadata.tab", "w") as fout:
fout.write("\t".join([
"Accession",
"AccessionVersion",
"Gene",
"FullName",
"GeneType",
"HgncID",
"Chromosome",
"Strand",
"ChromosomeStart",
"ChromosomeEnd",
"LocusGroup",
"LocusType",
"Location",
"LocationSortable",
"Aliases",
"VegaID",
"UcscID",
"RefseqID",
"CcdsID",
"UniprotID",
"PubmedID",
"MgdID",
"RgdID",
"CosmicID",
"OmimID",
"MirBaseID",
"IsTFi (TcoF-DB)",
"DnaBindingDomain",
"Regulates (TRRUST)"
]))
fout.write("\n")
with open(d + "inputs/gencode.vM23.primary_assembly.annotation.gtf") as f:
for line in f:
if line.startswith("##"):
continue
items = line[:-1].split("\t")
if items[2] != "gene":
continue
extra = {x.strip().split(" ")[0]: x.strip().split(" ")[1].strip('"') for x in items[8].split(";")[:-1]}
enseID = extra["gene_id"].split(".")[0]
geneSymbol = extra.get("gene_name", "")
fout.write("\t".join([
enseID,
extra["gene_id"],
geneSymbol,
enseID2MGI_GMC[enseID][3] if enseID in enseID2MGI_GMC else "", # full name
extra["gene_type"], # gene type from gencode
"", # HGNC id
items[0], # Chromosome
items[6],
items[3], # Start
items[4], # End
"", # Locus group
mgiID2MRK_ENSE[mgiID][8], # Locus type
"", # Location
"", # Location, sortable
"", # Aliases
enseID2mart[enseID][5] if enseID in enseID2mart else "", # VEGA id
enseID2mart[enseID][4] if enseID in enseID2mart else "", # UCSC id
mgiID2MRK_Seq[mgiID][12], # Refseq id
enseID2mart[enseID][6] if enseID in enseID2mart else "", # CCDS id
mgiID2MRK_Seq[mgiID][14], # Uniprot id
"", # Pubmed id
"", # MGD id
"", # RGD id
"", # COSMIC id
"", # OMIM id
"", # MIRbase id
"True" if (geneSymbol in geneSymbol2TF) else "False", # IsTF?
"", # DBD
",".join(geneSymbol2Regulated[geneSymbol]) # TF regulated genes
]))
fout.write("\n")
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