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Promote error correction scripts from sandbox #1743

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Promote error correction scripts from sandbox #1743

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c6c4e9a
Moved correct-reads from sandbox to scripts
Jul 10, 2017
6c333f2
Moved error-correct-pass2 from sandbox to scripts
Jul 10, 2017
582b1d2
Removed sandbox=True from tests
Jul 11, 2017
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2 changes: 1 addition & 1 deletion examples/stamps/do.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -46,7 +46,7 @@ normalize-by-median.py -k 20 -C 10 -x 1e8 ../../data/stamps-reads.fa.gz \
abundance-dist.py stamps-dn.ct stamps-reads.fa.gz.keep stamps-dn.hist
do-partition.py -k 32 -x 1e8 -s 1e4 -T 8 stamps-part \
../../data/stamps-reads.fa.gz
../../sandbox/error-correct-pass2.py --trusted-cov 10 stamps-dn.ct \
error-correct-pass2.py --trusted-cov 10 stamps-dn.ct \
../../data/stamps-reads.fa.gz
load-into-counting.py -x 1e8 -k 20 stamps-corr.ct stamps-reads.fa.gz.corr
abundance-dist.py stamps-corr.ct stamps-reads.fa.gz.corr stamps-corr.hist
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0 sandbox/correct-reads.py → scripts/correct-reads.py
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0 sandbox/error-correct-pass2.py → scripts/error-correct-pass2.py
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15 changes: 7 additions & 8 deletions tests/test_sandbox_scripts.py
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Original file line number Diff line number Diff line change
Expand Up @@ -360,7 +360,7 @@ def test_error_correct_pass2():
outfile = utils.get_temp_filename('test-abund-read-3.fa.corr')
args = ['--trusted-cov', '5', '-o', outfile]
args.extend([hashfile, infile])
(status, out, err) = utils.runscript(script, args, sandbox=True)
(status, out, err) = utils.runscript(script, args)
assert 'trusted: 5' in out, out
assert os.path.exists(outfile)
assert os.stat(outfile).st_size > 2000
Expand All @@ -383,7 +383,7 @@ def test_error_correct_pass2_fq():
outfile = 'paired.fq.1.corr' # Warning: output file in cwd
args = ['--trusted-cov', '2']
args.extend([hashfile, infile])
(status, out, err) = utils.runscript(script, args, sandbox=True)
(status, out, err) = utils.runscript(script, args)
assert os.path.exists(outfile)
assert os.stat(outfile).st_size > 700
os.remove(outfile)
Expand All @@ -397,7 +397,7 @@ def test_correct_reads():
outfile = utils.get_temp_filename('simple-genome-reads.fa.corr')
args = ['-o', outfile]
args.extend([infile])
(status, out, err) = utils.runscript(script, args, sandbox=True)
(status, out, err) = utils.runscript(script, args)
assert 'fp rate' in err, err
assert os.path.exists(outfile)
assert os.stat(outfile).st_size > 132000
Expand All @@ -411,7 +411,7 @@ def test_correct_reads_other():
outfile = 'test-abund-read-paired.fa.corr' # Warning output in cwd
args = []
args.extend([infile])
(status, out, err) = utils.runscript(script, args, sandbox=True)
(status, out, err) = utils.runscript(script, args)
assert 'fp rate' in err, err
assert os.path.exists(outfile)
assert os.stat(outfile).st_size > 800
Expand All @@ -426,8 +426,7 @@ def test_correct_reads_duplicate():
outfile = 'test-abund-read-paired.fa.corr' # Warning output in cwd
args = []
args.extend([infile, infile])
(status, out, err) = utils.runscript(script, args, sandbox=True,
fail_ok=True)
(status, out, err) = utils.runscript(script, args, fail_ok=True)
assert 'same filename multiple times' in str(err)
assert status == 1

Expand All @@ -441,14 +440,14 @@ def test_correct_reads_fq():
outfile = utils.get_temp_filename('test-reads.fq.corr')
args = ['-o', outfile, '--savegraph', savegraph, '--variable-coverage']
args.extend([infile])
(status, out, err) = utils.runscript(script, args, sandbox=True)
(status, out, err) = utils.runscript(script, args)
assert 'fp rate' in err, err
assert os.path.exists(outfile)
assert os.stat(outfile).st_size > 1500
os.remove(outfile)
args = ['-o', outfile, '--loadgraph', savegraph]
args.extend([infile])
(status, out, err) = utils.runscript(script, args, sandbox=True)
(status, out, err) = utils.runscript(script, args)
assert 'fp rate' in err, err
assert os.path.exists(outfile)
assert os.stat(outfile).st_size > 1500