Human readable files/folders as Genus_species_strain
See original GitHub issueIn my (older unreleased scruffier) version of this tool I create a hierarchy like this:
Kingdom/
Genus/
species/
strain/
blah.gbk
blah.fna
blah.gff
I currently set blah
to Genus_species_strain
but that loses the GCA_xxxx
accession. I was thinking of having a a ‘mirror’ folder of symlinks with human readable names.
It was tricky to extract the strain
as it appears in up to 3 different columns sometimes, but it mostly works.
The reason for this is to make it easy to work with sequences and get human readable labels etc.
Issue Analytics
- State:
- Created 7 years ago
- Comments:6 (4 by maintainers)
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So, apart from making up my mind how to best do the cleanup, I’ve got a working implementation of this. Expect this in the next version of
ncbi-genome-download
.FIrst I try and match the strain from column 8
$x[7] =~ m/^(\S+)\s+(\S+)(\s+.*)?$/
Then if that fails I try column 9:
$x[8] =~ m/^strain=(.*)$/)
If that fails I use the assembly ID:
$strain ||= $x[0];
And then i sanitize the string:
$s =~ s/[\[\]]/ /g; $s =~ s/^\s+//g; $s =~ s/\s+$//g; $s =~ s/\s+/_/g; $s =~ s/['"]/_/g; $s =~ s{[/;:]}{-}g; $s =~ s/_+/_/g;