Feature to filter out refgene index source #61
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…'s content - responsibility to filter out predicted model accession number is now caller's one for consistency
- refGene.txt and ncbiRefSeq.txt are [GenePred format](https://genome.ucsc.edu/FAQ/FAQformat.html#format9) and not NCBI's file
Codecov Report
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## master #61 +/- ##
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Coverage 45.63% 45.64%
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Files 16 16
Lines 1970 1974 +4
Branches 60 60
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+ Hits 899 901 +2
- Misses 1011 1013 +2
Partials 60 60
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| @@ -58,24 +58,30 @@ | |||
| (update m :cds-end-stat keyword) | |||
| (update m :exon-frames parse-exon-pos))) | |||
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| (defn- load-ncbi-file | |||
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Since we released the function, I think it would be better to keep it and mark it as deprecated for backward compatibility.
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@federkasten
Thank you for the review. It sounds good but if this function was used from outside of this namespace, that should be rewritten because it is defined as private. What do you think?
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Oops. Sorry, I missed this is a private function.
| (when s | ||
| (re-find #"^(NM|NR)_.+$" s))) | ||
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| (defn- load-genepred-file |
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Very helpful in finding an appropriate name! 🙏
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| (update m :cds-end-stat keyword) | |||
| (update m :exon-frames parse-exon-pos))) | |||
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| (defn- load-ncbi-file | |||
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Oops. Sorry, I missed this is a private function.
Problem
chr6_cox_hap2but we sometimes don't need contig's records at all.Implementation
filter-fnstoload-ref-genesandload-ref-seqsto filter out unnecessary rows in these files.load-ncbi-filetoload-genepred-filebecause these files format are named as GenePred (just refactoring).