FIX : Cope with lowercase fasta files. Fixes #24.

labgem · Nov 14, 2019 · 043f96c · 043f96c
1 parent 42a1556
commit 043f96c
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Showing 2 changed files with 3 additions and 3 deletions.
diff --git a/VERSION b/VERSION
@@ -1 +1 @@
-1.0.0
+1.0.4
diff --git a/ppanggolin/annotate/synta.py b/ppanggolin/annotate/synta.py
@@ -160,14 +160,14 @@ def read_fasta(org, fnaFile):
     for line in fnaFile:
         if line.startswith('>'):
             if contig_seq != "":
-                contigs[contig.name] = contig_seq
+                contigs[contig.name] = contig_seq.upper()
             contig_seq = ""
             contig = org.getOrAddContig(line.split()[0][1:])
         else:
             contig_seq += line.strip()
     # processing the last contig
     if contig_seq != "":
-        contigs[contig.name] = contig_seq
+        contigs[contig.name] = contig_seq.upper()
     return contigs
 
 def write_tmp_fasta(contigs, tmpdir ):