saved fasta files incorrectly - Bug fixed #740
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Codecov Report
@@ Coverage Diff @@
## master #740 +/- ##
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- Coverage 88.63% 88.41% -0.22%
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Files 30 30
Lines 4777 4783 +6
Branches 46 46
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- Hits 4234 4229 -5
- Misses 540 551 +11
Partials 3 3
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pranathivemuri
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there is a test that fails randomly and here is the error - https://travis-ci.com/dib-lab/sourmash/jobs/236306024#L842 1. I ran it locally it passes 2. I went through other branches, it seemed like it failed in those branches randomly as well 3. the travis test passed in this commit a2ef27a and after adding two more lines in test, and no change in program at all, this commit 818e088 it failed. So, I am assuming there is some random thing going on or it doesn't like the generator! |
sourmash/command_compute.py
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| @@ -84,7 +84,7 @@ def compute(args): | |||
| parser.add_argument('-p', '--processes', default=2, type=int, | |||
| help='For 10x input only (i.e input-is-10x flag is True, ' | |||
| 'Number of processes to use for reading 10x bam file') | |||
| parser.add_argument('--save-fastas', type=str, | |||
| parser.add_argument('--save-fastas', action='store_true', | |||
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Awesome work! Would it be possible to provide a directory or prefix to save all the created fastas to?
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changed to take a path instead
pranathivemuri
changed the title
pranathivemuri
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I opened #755 to discuss coverage for |
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test_cmd_signature is failing - https://travis-ci.com/dib-lab/sourmash/jobs/248344113#L536 |
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Merged, as the failing test is not an issue of this PR. Thanks @pranathivemuri ! |
When saving the fasta files for each unique barcode, I was repeatedly writing the name and the sequence, for the same barcode. I.E the fasta file should have had only one > followed by barcode name. But by using >{}{} barcode inside the loop, for every sequence I was repeating the >barcode. I corrected that in this PR.
I have also updated the comments
And made save_fastas cli argument a boolean
@olgabot @ctb Sorry about the error! not ready for review yet!
make testDid it pass the tests?make coverageIs the new code covered?without a major version increment. Changing file formats also requires a
major version number increment.
changes were made?