pickles_dir)
# Use GENCODE datasource to get list of all possible genes
gencode_ds_loc = expanduser(args.gencode_ds)
gencode_ds = DatasourceFactory.createDatasource(
configFilename=gencode_ds_loc, leafDir=os.path.dirname(gencode_ds_loc))
# Use simple_uniprot TSV to get the uniprot_entry_names
# Create the transcript to uniprot info mappings. But take less RAM. Given a gene, get the uniprot record.
uniprotDS = GenericTranscriptDatasource(src_file=uniprot_tsv,
title="UniProt",
version="2014_12",
geneColumnName="gene")
# key is the uniprot_entry_name from the uniprotDS
muts = generateTranscriptMuts(gencode_ds, uniprotDS)
swissKeys = swiss_data.keys()
tremblKeys = trembl_data.keys()
featureTypeToAnnotation = {
"SITE": "site",
"VARIANT": "natural_variation",
"COMPBIAS": "region",
"REGION": "region",
"DOMAIN": "region",
"CONFLICT": "experimental_info"
}
featureTypes = featureTypeToAnnotation.keys()
ctr = 0
numTranscriptsNotInUniprot = 0
# TODO: Remove hardcoded paths
# TODO: Reduce code duplication
swiss_data = parseWithShove(uniprot_swiss_fname, parse_uniprot_data, "/bulk/pickles/")
trembl_data = parseWithShove(uniprot_trembl_fname, parse_uniprot_data, "/bulk/pickles/")
# Use GAF datasource to get list of all possible genes
gafDS = Gaf(gaf_file, gaf_transcript_file)
# Use simple_uniprot TSV to get the uniprot_entry_names
# Create the gene to uniprot info mappings. But take less RAM. Given a gene, get the uniprot record.
uniprotDS = Generic_Gene_DataSource(src_file=uniprot_tsv, title="UniProt", version="2011_09", geneColumnName="gene")
# key is the uniprot_entry_name from the uniprotDS
muts = generateTranscriptMuts(gafDS, uniprotDS)
swissKeys = swiss_data.keys()
tremblKeys = trembl_data.keys()
featureTypeToAnnotation = {"SITE":"site", "VARIANT":"natural_variation", "COMPBIAS":"region" , "REGION":"region", "DOMAIN":"region", "CONFLICT":"experimental_info"}
featureTypes = featureTypeToAnnotation.keys()
ctr = 0
numTranscriptsNotInUniprot = 0
uniprotEntryNameKey = 'UniProt_uniprot_entry_name'
for m in muts:
ctr += 1
if (ctr % 1000) == 0:
print(str(ctr))
if m[uniprotEntryNameKey] in swissKeys:
# TODO: Reduce code duplication
swiss_data = parse_with_shove(uniprot_swiss_fname, parse_uniprot_data, pickles_dir)
trembl_data = parse_with_shove(uniprot_trembl_fname, parse_uniprot_data, pickles_dir)
# Use GENCODE datasource to get list of all possible genes
gencode_ds_loc = expanduser(args.gencode_ds)
gencode_ds = DatasourceFactory.createDatasource(configFilename=gencode_ds_loc, leafDir=os.path.dirname(gencode_ds_loc))
# Use simple_uniprot TSV to get the uniprot_entry_names
# Create the transcript to uniprot info mappings. But take less RAM. Given a gene, get the uniprot record.
uniprotDS = GenericTranscriptDatasource(src_file=uniprot_tsv, title="UniProt", version="2014_12", geneColumnName="gene")
# key is the uniprot_entry_name from the uniprotDS
muts = generateTranscriptMuts(gencode_ds, uniprotDS)
swissKeys = swiss_data.keys()
tremblKeys = trembl_data.keys()
featureTypeToAnnotation = {"SITE":"site", "VARIANT":"natural_variation", "COMPBIAS":"region" , "REGION":"region", "DOMAIN":"region", "CONFLICT":"experimental_info"}
featureTypes = featureTypeToAnnotation.keys()
ctr = 0
numTranscriptsNotInUniprot = 0
uniprotEntryNameKey = 'UniProt_uniprot_entry_name'
txs_already_processed = set()
records_already_processed = set()
num_txs_with_same_data = 0
for m in muts:
if m['transcript_id'] in txs_already_processed:
continue
