Fix the append behavior in normalize-by-median.py (#745) #843
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jenkins, please test this |
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ready for review |
| @@ -514,6 +514,21 @@ def test_normalize_by_median(): | |||
| assert len(seqs) == 1, seqs | |||
| assert seqs[0].startswith('GGTTGACGGGGCTCAGGGGG'), seqs | |||
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| # Testing for the apppend option | |||
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please make a separate test function instead -- more granular tests are generally better. So,
- copy the test function twice
- rename both copies
- remove the outfile/append tests from the original
- have one copy do the append test
- have the other copy do the not-append test
thanks!
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@ctb please review |
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LGTM on a skim - might ask @mr-c to review/merge since I can't get to it 'til much later today or maybe tomorrow. |
| @@ -192,6 +192,9 @@ def get_parser(): | |||
| dest='single_output_filename', | |||
| default='', help='only output a single' | |||
| ' file with the specified filename') | |||
| parser.add_argument('--append', default=False, action='store_true', | |||
| help='append reads to the outputfile. ' | |||
| 'Only with -o specified') | |||
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I would word the help text this way: "appends reads instead of replacing the output file (only if -o/--out is specified)'
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Nice work; thanks! |
ctb
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Feb 25, 2015
Fix the append behavior in normalize-by-median.py (#745)
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Fix #745: in normalize-by-median.py, change to the default behavior to overwrite the sequences output file. Also add a new argument --append to append new reads to the output file.
I also added a test for the --append option in test_scripts.py