Mercurial > repos > peterjc > blast_rbh

changeset 36:517bf3bad66b draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh commit ed6325d44993c65dd9fbab02902ede0a9c0eeb80-dirty
author peterjc
date Tue, 23 Oct 2018 06:25:21 -0400
parents 5c78f5e6cdf2
children 69589275a0b2
files tools/blast_rbh/blast_rbh.py
diffstat 1 files changed, 3 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- a/tools/blast_rbh/blast_rbh.py	Tue Jun 05 11:40:56 2018 -0400
+++ b/tools/blast_rbh/blast_rbh.py	Tue Oct 23 06:25:21 2018 -0400
@@ -29,6 +29,7 @@
 
 
 def run(cmd):
+    """Run the given command line string."""
     return_code = os.system(cmd)
     if return_code:
         sys.exit("Error %i from: %s" % (return_code, cmd))
@@ -246,6 +247,7 @@
 
 
 def check_duplicate_ids(filename):
+    """Check for duplicate identifiers in a FASTA file."""
     # Copied from tools/ncbi_blast_plus/check_no_duplicates.py
     # TODO - just use Biopython's FASTA parser?
     if not os.path.isfile(filename):
@@ -267,6 +269,7 @@
 
 
 def make_nr(input_fasta, output_fasta, sep=";"):
+    """Make the sequences in a FASTA file non-redundant."""
     # TODO - seq-hash based to avoid loading everything into RAM?
     by_seq = dict()
     try: