Mercurial > repos > peterjc > seq_select_by_id
changeset 20:6c5822581e41 draft
planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_select_by_id commit 5fb6ee31f33e8e24c1ae5d56c93ac3e0157dad72-dirty
| author | peterjc |
|---|---|
| date | Thu, 09 Feb 2017 11:28:17 -0500 |
| parents | d66a0766f13e |
| children | 3dc9fd2ad70c |
| files | tools/seq_select_by_id/seq_select_by_id.py |
| diffstat | 1 files changed, 2 insertions(+), 0 deletions(-) [+] |
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--- a/tools/seq_select_by_id/seq_select_by_id.py Wed Feb 01 10:51:12 2017 -0500 +++ b/tools/seq_select_by_id/seq_select_by_id.py Thu Feb 09 11:28:17 2017 -0500 @@ -80,6 +80,7 @@ if warn: sys.stderr.write(warn) + # Index the sequence file. # If very big, could use SeqIO.index_db() to avoid memory bottleneck... records = SeqIO.index(in_file, seq_format) @@ -110,6 +111,7 @@ count = 0 # This does have the overhead of parsing into SeqRecord objects, # but doing the header and index at the low level is too fidly. + name = None # We want the variable to leak from the iterator's scope... iterator = (records[name] for name in parse_ids(tabular_file, column)) try: count = writer.write_file(iterator)