Add several functions to work with refGene exon sequences #13
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@@ Coverage Diff @@
## master #13 +/- ##
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+ Coverage 34.89% 36.43% +1.53%
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Files 12 12
Lines 1192 1227 +35
Branches 21 25 +4
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+ Hits 416 447 +31
Misses 755 755
- Partials 21 25 +4
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src/varity/util.clj
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| (->> (reverse s) | ||
| (map (partial get comp-base-map)) | ||
| (apply str))) | ||
| (util-seq/revcomp s)) |
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Why did you leave varity.util/revcomp-bases? I feel you should replace all revcomp-bases in varity codebase with cljam.util.sequence/revcomp.
src/varity/ref_gene.clj
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| :end e, | ||
| :reverse? reverse?}))))) | ||
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| (defn cds-exon-seq |
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I think cds-seq is correct name. cds-exon- is wordy because CDS does not include introns.
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@totakke Done, thanks for your review! 😸 |
src/varity/ref_gene.clj
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| (cond-> (cseq/read-sequence seq-rdr exon) | ||
| reverse? util-seq/revcomp)) | ||
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| (defn ^String read-gene-sequence |
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The gene word contains more widely meanings. Thus I think you should use transcript here.
Additionally, could you add docstrings to clarify the function, such as the sequence contains 5'-UTR, CDS, and 3'-UTR.
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@federkasten I have replaced 'gene' with 'transcript' or 'ref-gene-record'. Also I've added a commit to fix :strand values (please refer to chrovis/cljam#143 (comment)) Thank you. |
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Thank you! The additional commits also seem good, so I've just merged. |
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@totakke @federkasten Thank you for your helpful comments! 😹 |
Summary
This PR adds several utility functions to
varity.ref-genemodule.Tests
lein check🆗lein test :all🆗Notes
varity.util/revcomp-baseswith more efficient implementation in cljam 0.6.0