Mercurial > repos > peterjc > sample_seqs
changeset 16:4c79e75c4576 draft
v0.2.4 Depends on Biopython 1.67 via legacy Tool Shed package or bioconda.
| author | peterjc |
|---|---|
| date | Thu, 11 May 2017 07:22:26 -0400 |
| parents | 19306a5f88b2 |
| children | 279828615e8c |
| files | tools/sample_seqs/README.rst tools/sample_seqs/sample_seqs.py tools/sample_seqs/sample_seqs.xml |
| diffstat | 3 files changed, 8 insertions(+), 4 deletions(-) [+] |
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--- a/tools/sample_seqs/README.rst Wed May 10 12:46:56 2017 -0400 +++ b/tools/sample_seqs/README.rst Thu May 11 07:22:26 2017 -0400 @@ -71,7 +71,8 @@ - Planemo for Tool Shed upload (``.shed.yml``, internal change only). v0.2.3 - Do the Biopython imports at the script start (internal change only). - Clarify paired read example in help text. - - Depends on Biopython 1.67 via legacy Tool Shed package or bioconda. +v0.2.4 - Depends on Biopython 1.67 via legacy Tool Shed package or bioconda. + - Style changes to Python code (internal change only). ======= ======================================================================
--- a/tools/sample_seqs/sample_seqs.py Wed May 10 12:46:56 2017 -0400 +++ b/tools/sample_seqs/sample_seqs.py Thu May 11 07:22:26 2017 -0400 @@ -63,7 +63,7 @@ options, args = parser.parse_args() if options.version: - print("v0.2.3") + print("v0.2.4") sys.exit(0) try: @@ -146,6 +146,7 @@ sys.stderr.write("Sampling every %ith sequence\n" % N) def sampler(iterator): + """Sample every Nth sequence.""" global N count = 0 for record in iterator: @@ -157,11 +158,12 @@ percent = float(options.percent) / 100.0 except ValueError: sys.exit("Bad -p percent argument %r" % options.percent) - if percent <= 0.0 or 1.0 <= percent: + if not(0.0 <= percent <= 1.0): sys.exit("Bad -p percent argument %r" % options.percent) sys.stderr.write("Sampling %0.3f%% of sequences\n" % (100.0 * percent)) def sampler(iterator): + """Sample given percentage of sequences.""" global percent count = 0 taken = 0 @@ -215,6 +217,7 @@ assert taken == N, "Picked %i, wanted %i" % (taken, N) else: def sampler(iterator): + """Sample given number of sequences.""" # Mimic the percentage sampler, with double check on final count global N, total # Do we need a floating point fudge factor epsilon?
--- a/tools/sample_seqs/sample_seqs.xml Wed May 10 12:46:56 2017 -0400 +++ b/tools/sample_seqs/sample_seqs.xml Thu May 11 07:22:26 2017 -0400 @@ -1,4 +1,4 @@ -<tool id="sample_seqs" name="Sub-sample sequences files" version="0.2.3"> +<tool id="sample_seqs" name="Sub-sample sequences files" version="0.2.4"> <description>e.g. to reduce coverage</description> <requirements> <requirement type="package" version="1.67">biopython</requirement>