skip trimming option #124
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skip trimming option #124
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thanks! there are some failures btw cc @antgonza |
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A fix for the file path is coming in - its passing on my system. But this is ready for review. |
antgonza
reviewed
Dec 7, 2016
| input_seqs=sequence_generator(seqs_fp), trim_len=trim_length): | ||
| out_f.write(">%s\n%s\n" % (label, seq)) | ||
| if skip_trim: | ||
| for label, seq in sequence_generator(seqs_fp): |
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This is basically duplicating the file, right? Can we do something smarter?
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What about creating a simple symlink?
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That's cool! I didn't know about that.
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Ok. I think this is ready to merge! |
antgonza
approved these changes
Dec 8, 2016
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Thanks! |
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This adds an option to ignore trimming.
So you should be able to specify a flag to completely ignore trimming.
Here a test case is added. In addition, I have tested out the CLI on some of the test datasets.
Note that this is a little tricky to test, so any suggestions on improving this will be welcome.
But I believe that this should cover the gist of it.