Fixes issue with fastq.gz files having _I1_ etc. #109
Conversation
Fixes issue with fastq.gz files having _I1_, _R1_, etc. in parts of the file-name other than the expected location.
| i2_only = [x for x in files if '_I2_' in x] | ||
| # use capturing to handle both raw files as well as trimmed and | ||
| # filtered files. We don't need to process the captured string. | ||
| i1_files = compile(r"^.*_L\d{3}_I1_\d{3}\.(trimmed\.|filtered" |
There was a problem hiding this comment.
Why the capture group, it doesn't seem like it's used?
There was a problem hiding this comment.
A side of effect of using the capture group is that I can use one regex to handle '.trimmed.fastq.gz', '.filtered.fastq.gz', and '.fastq.gz' files. Brackets ('[',']') and ORs ('|') didn't work for me.
There was a problem hiding this comment.
It is not good practice to rely on side effects... Suggest adding ?:, see
>>> import re
>>> re.compile(r'(?:foo|bar)?baz').match('baz')
<re.Match object; span=(0, 3), match='baz'>
>>> re.compile(r'(?:foo|bar)?baz').match('foobaz')
<re.Match object; span=(0, 6), match='foobaz'>
>>> re.compile(r'(?:foo|bar)?baz').match('barbaz')
<re.Match object; span=(0, 6), match='barbaz'>
>>> re.compile(r'(?:foo|bar)?baz').match('fbaz')
>>>| r1_only = [] | ||
| r2_only = [] | ||
|
|
||
| for some_path in files: |
There was a problem hiding this comment.
Please add a regression test to verify that the bug exists and these changes fix it
There was a problem hiding this comment.
Sure, I'll add a test with the old filenames to show how they fail.
There was a problem hiding this comment.
Thanks. It's important that bugs are coupled with regression tests to ensure they are fixed and don't arise again
Co-authored-by: Daniel McDonald <[email protected]>
Co-authored-by: Daniel McDonald <[email protected]>
Pull Request Test Coverage Report for Build 6698670902
💛 - Coveralls |
Fixes issue with fastq.gz files having I1, R1, etc. in parts of the file-name other than the expected location.
This fix is currently working in qiita-rc.