Deactivated sequence retrieval from DAS if no network connection.

ggirelli · Feb 7, 2019 · 1a8f91d · 1a8f91d
1 parent c2c32c1
commit 1a8f91d
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Showing 2 changed files with 4 additions and 3 deletions.
diff --git 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
@@ -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)