| Previous changeset 3:78dd29aa7fc1 (2017-02-20) Next changeset 5:a91be6005274 (2017-03-28) |
|
Commit message:
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/t_coffee commit 988b1fc1cb8739e45648465adbf099f3fdaf87f8 |
|
modified:
filter_by_fasta_ids.py |
| b |
| diff -r 78dd29aa7fc1 -r fa59d6fea7f5 filter_by_fasta_ids.py --- a/filter_by_fasta_ids.py Mon Feb 20 06:25:50 2017 -0500 +++ b/filter_by_fasta_ids.py Fri Mar 03 07:29:32 2017 -0500 |
| [ |
| @@ -9,20 +9,20 @@ def FASTAReader_gen(fasta_filename): - fasta_file = open(fasta_filename) - line = fasta_file.readline() - while True: - if not line: - return - assert line.startswith('>'), "FASTA headers must start with >" - header = line.rstrip() - sequence_parts = [] + with open(fasta_filename) as fasta_file: line = fasta_file.readline() - while line and line[0] != '>': - sequence_parts.append(line.rstrip()) + while True: + if not line: + return + assert line.startswith('>'), "FASTA headers must start with >" + header = line.rstrip() + sequence_parts = [] line = fasta_file.readline() - sequence = "".join(sequence_parts) - yield Sequence(header, sequence) + while line and line[0] != '>': + sequence_parts.append(line.rstrip()) + line = fasta_file.readline() + sequence = "".join(sequence_parts) + yield Sequence(header, sequence) def target_match(target, search_entry): @@ -47,7 +47,6 @@ work_summary['wanted'] = len(targets) - # output = open(sys.argv[3], "w") for entry in FASTAReader_gen(sys.argv[2]): target_matched_results = target_match(targets, entry.header) if target_matched_results: |