Add UMI support #72
Add UMI support #72
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| """ | ||
| nt = re.compile("\*n([atcg])") | ||
| nts = "".join(re.findall(nt, cs_string)) | ||
|
|
||
| if umi_before > 0: | ||
| nts = nts[umi_before:] |
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Does this really work? If there are substitutions/deletions/insertions in the alignment both the reference and query nucleotide will be in the cs string right?
For example:
cg:Z:6M2D21M cs:Z::1*at:2*ac:1-ac:21
Or am I missing something?
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It works if you add the correct number of N's into the template sequence. So we need to know that the index region is e.g., exactly 10 nt index + 9 nt UMI long. That way we can read the sequence directly from the CS string. Unrelated example:
cs:Z::33*nt*nc*nc*ng*ng*na*ng*na:9
Insertions and deletions will of course affect this perfect picture, but I don't think too terribly.
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Fair enough. I think we could use the fact that we're looking specifically for cases where there is an n to the left inside the *na* section. But we can leave that for later
| @@ -38,6 +38,7 @@ | |||
| entry_points={ | |||
| "console_scripts": [ | |||
| "anglerfish=anglerfish.anglerfish:anglerfish", | |||
| "anglerfish-explore=anglerfish.explore.cli:main", | |||
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Nice! Although I don't know what the effect of this is. Does it make the explore command executable or add it to the path?
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With conda, and I guess with most package managers, both! So now this will work:
% anglerfish-explore --help
Usage: anglerfish-explore [OPTIONS]
Options:
-f, --fastq TEXT Fastq file to align [required]
...
I'm thinking maybe for a 1.0 release we can unify these commands. I'm open to having them as subcommands, eg. anglerfish run and anglerfish explore
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Great work! This breaks the explore command a tiny bit for UMI:s. I've located the issue and I should be able to create a fix for it. Separate PR I guess. Your call if it should be included in this release or not. If I can fix it quickly I think it would make sense to include it.
I was thinking of doing a release on Friday, if you can't get a fix out in time it's not a huge deal. Also I think this code, the adaptor handling parts, could do with simplifying or refactoring. For instance the separate I7 and I5 handling could be DRY'd up. But that's for another time. |
anglerfish-explorecommand as entrypoint