Open file handle for sequences filtered by length

Author: johnne

tango/search.py

@@ -46,10 +46,11 @@ def filter_seqs_by_len(infile, outfile, minlen):
 
     from Bio.SeqIO import parse, write
     i = 0
-    for record in tqdm.tqdm(parse(infile, 'fasta'), unit=" sequences", ncols=100, desc="Filtering sequences"):
-        if len(record) >= minlen:
-            write(record, outfile, "fasta")
-            i += 1
+    with open(outfile, 'w') as fh:
+        for record in tqdm.tqdm(parse(infile, 'fasta'), unit=" sequences", ncols=100, desc="Filtering sequences"):
+            if len(record) >= minlen:
+                write(record, fh, "fasta")
+                i += 1
     sys.stderr.write("{} sequences longer than {} written to {}\n".format(i, minlen, outfile))