remove space in genome header and special nt in hairpin for mirdeep2 … #79
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| perl -ane 's/y/N/ig;print;' $hairpin > hairpin_yn.fa | ||
| awk '{ gsub(/Y/,"N",\$0); gsub(/B/,"N",\$0); gsub(/K/,"N",\$0); gsub(/M/,"N",\$0); gsub(/R/,"N",\$0); gsub(/S/,"N",\$0); gsub(/W/,"N",\$0); print}' $hairpin > hairpin_ok.fa |
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I think you're just adding other nucleotides beyond Y here, right? Is there a reason that we can't just do:
perl -ane 's/[ybkmrsw]/N/ig;print;' $hairpin > hairpin_yn.faI'd be inclined to use this type of command instead as it's a lot more succinct / easy to read and also case-insensitive..
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Also I'm not sure I see where you are removing spaces in the headers? Am I missing that somewhere?
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thanks for having a look
I am fine with the perl command instead of mine but maybe use a different name for the output file as we do not only remove Y nt
I am removing spaces in headers for the genome file, not the hairpin file, it is at another location in the code
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I am removing spaces in headers for the genome file, not the hairpin file, it is at another location in the code
Right, that's what I was wondering - but I can't see that in this pull request, right?
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I have now added the actual command to remove spaces in genome headers
this is to take into account the files generated by the lint command
Co-authored-by: Phil Ewels <[email protected]>
In order for mirdeep2 to work on the 11.1 version of the pig genome, I had to remove spaces in the genome headers and to replace special nucleotide characters by N in the hairpin file.
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