diff --git a/examples/stamps/do.sh b/examples/stamps/do.sh index d66166204f..9eb649b32a 100755 --- a/examples/stamps/do.sh +++ b/examples/stamps/do.sh @@ -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 diff --git a/sandbox/correct-reads.py b/scripts/correct-reads.py similarity index 100% rename from sandbox/correct-reads.py rename to scripts/correct-reads.py diff --git a/sandbox/error-correct-pass2.py b/scripts/error-correct-pass2.py similarity index 100% rename from sandbox/error-correct-pass2.py rename to scripts/error-correct-pass2.py diff --git a/tests/test_sandbox_scripts.py b/tests/test_sandbox_scripts.py index 90754087a7..8a3fbd7932 100644 --- a/tests/test_sandbox_scripts.py +++ b/tests/test_sandbox_scripts.py @@ -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 @@ -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) @@ -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 @@ -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 @@ -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 @@ -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