From 1a8f91d8090189f3710e3f2371dcedbecf8e9237 Mon Sep 17 00:00:00 2001 From: Gabriele Girelli Date: Thu, 7 Feb 2019 07:39:03 +0100 Subject: [PATCH] Deactivated sequence retrieval from DAS if no network connection. --- bin/ifpd_mkdb | 3 ++- ifpd/bioext.py | 4 ++-- 2 files changed, 4 insertions(+), 3 deletions(-) diff --git a/bin/ifpd_mkdb b/bin/ifpd_mkdb index 86b04ae..ce157b2 100755 --- a/bin/ifpd_mkdb +++ b/bin/ifpd_mkdb @@ -174,7 +174,8 @@ bed = UCSCbed(args.bedFile, oligoGenerator = bed.buffer(False, args.enforceBED3) if args.retainSequences: logging.info("Enabled sequence retrieval from UCSC...") - oligoGenerator = UCSCbed.add_sequence_to_raw_record(oligoGenerator) + oligoGenerator = UCSCbed.add_sequence_to_raw_record( + oligoGenerator, args.hasNetwork) logging.info("Writing database...") chromList = set() diff --git a/ifpd/bioext.py b/ifpd/bioext.py index 9ba26ed..4141f46 100644 --- a/ifpd/bioext.py +++ b/ifpd/bioext.py @@ -105,7 +105,7 @@ def parse_bed_line(line, enforceBED3 = False, incrementChromEnd = False): return(lineDF) @staticmethod - def add_sequence_to_raw_record(bedRecords): + def add_sequence_to_raw_record(bedRecords, hasNetwork = False): for record in bedRecords: assert type("") == type(record) record = record.strip().split("\t") @@ -114,7 +114,7 @@ def add_sequence_to_raw_record(bedRecords): assert_msg += f" {len(record)} found." assert 3 <= len(record), assert_msg - if 4 > len(record): + if 4 > len(record) and hasNetwork: oligoSequence = fp.web.get_sequence_from_UCSC( (record[0], int(record[1]), int(record[2])), args.refGenome) record.append(oligoSequence)