Minor bug fixes related to last update

kevlar-dev · Nov 10, 2018 · 3f9d0e3 · 3f9d0e3
1 parent ffdeb21
commit 3f9d0e3
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Showing 4 changed files with 11 additions and 7 deletions.
diff --git a/kevlar/cli/alac.py b/kevlar/cli/alac.py
@@ -44,10 +44,10 @@ def subparser(subparsers):
                             'length of the longest contig; each bin specifies '
                             'a reference target sequence against which '
                             'assembled contigs will be aligned')
-    local_args.add_argument('--include', metavar='REGEX', type=re.escape,
+    local_args.add_argument('--include', metavar='REGEX', type=str,
                             help='discard alignments to any chromosomes whose '
                             'sequence IDs do not match the given pattern')
-    local_args.add_argument('--exclude', metavar='REGEX', type=re.escape,
+    local_args.add_argument('--exclude', metavar='REGEX', type=str,
                             help='discard alignments to any chromosomes whose '
                             'sequence IDs match the given pattern')
 

diff --git a/kevlar/cli/cutout.py b/kevlar/cli/cutout.py
@@ -36,10 +36,10 @@ def subparser(subparsers):
                            'reference targets if the distance between two '
                            'seed matches is > X; by default, X is 3 times the '
                            'length of the longest contig')
-    subparser.add_argument('--include', metavar='REGEX', type=re.escape,
+    subparser.add_argument('--include', metavar='REGEX', type=str,
                            help='discard alignments to any chromosomes whose '
                            'sequence IDs do not match the given pattern')
-    subparser.add_argument('--exclude', metavar='REGEX', type=re.escape,
+    subparser.add_argument('--exclude', metavar='REGEX', type=str,
                            help='discard alignments to any chromosomes whose '
                            'sequence IDs match the given pattern')
     subparser.add_argument('contigs', help='assembled reads in Fasta format')

diff --git a/kevlar/cli/localize.py b/kevlar/cli/localize.py
@@ -34,10 +34,10 @@ def subparser(subparsers):
                            'reference targets if the distance between two '
                            'seed matches is > X; by default, X is 3 times the '
                            'length of the longest contig')
-    subparser.add_argument('--include', metavar='REGEX', type=re.escape,
+    subparser.add_argument('--include', metavar='REGEX', type=str,
                            help='discard alignments to any chromosomes whose '
                            'sequence IDs do not match the given pattern')
-    subparser.add_argument('--exclude', metavar='REGEX', type=re.escape,
+    subparser.add_argument('--exclude', metavar='REGEX', type=str,
                            help='discard alignments to any chromosomes whose '
                            'sequence IDs match the given pattern')
     subparser.add_argument('contigs', help='assembled reads in Fasta format')

diff --git a/kevlar/cutout.py b/kevlar/cutout.py
@@ -44,6 +44,8 @@ def contigs_2_seeds(partstream, seedstream, seedsize=51, logstream=sys.stdout):
     for n, seed in enumerate(sorted(seeds)):
         print('>seed{}\n{}'.format(n, seed), file=seedstream)
     seedstream.flush()
+    message = 'contigs decomposed into {} seeds'.format(n)
+    print('[kevlar::cutout]', message, file=logstream)
 
 
 def get_seed_matches(seedfile, refrfile, seedsize=51, logstream=sys.stdout):
@@ -56,6 +58,8 @@ def get_seed_matches(seedfile, refrfile, seedsize=51, logstream=sys.stdout):
     seed_index = dict()
     for seqid, start, end, seq in bwa_align(bwa_args, seqfilename=seedfile):
         seed_index[seq] = (seqid, start)
+    message = 'found positions for {} seeds'.format(len(seed_index))
+    print('[kevlar::cutout]', message, file=logstream)
     return seed_index
 
 
@@ -123,7 +127,7 @@ def cutout(partstream, refrfile, seedsize=51, delta=50, maxdiff=None,
         cutter = localize(
             contiglist, refrseqs, seed_matches, seedsize=seedsize, delta=delta,
             maxdiff=maxdiff, inclpattern=inclpattern, exclpattern=exclpattern,
-            debug=True, logstream=logstream
+            debug=False, logstream=logstream
         )
         for gdna in cutter:
             yield partid, gdna