search

s-andrews / BamQC

Mapped QC analysis program
GNU General Public License v3.0
42 stars 8 forks source link

Allow filter when listing genomes on the command line #3

Closed s-andrews closed 8 years ago

s-andrews commented 9 years ago

When you run bamqc -b you currently get a list of everything available on the server, which is a very big list.

It would be better if b could be parameterised - so that if you supply some text afterwards it would only show lines which matched.

bamqc -b

would still get you everything, but

bamqc -b mus

would only show you cases where the species or assembly contained 'mus' somewhere in them.

pdp10 commented 8 years ago

Added.

$ ./bamqc -b mus List of genomes (species [ assemblies ]) retrieved from the Babraham Servers: Mus musculus [ GRCm38 | NCBIM33 | NCBIM34 | NCBIM35 | NCBIM36 | NCBIM37 ]

$ ./bamqc -b m?s List of genomes (species [ assemblies ]) retrieved from the Babraham Servers: B anthracis Ames [ EB1 ] B anthracis Ames ancestor [ EB1 ] B licheniformis Goettingen [ EB1 ] B licheniformis Novozymes [ EB1 ] Monodelphis domestica [ MonDom5 | MonDom_4.0 ] Mus musculus [ GRCm38 | NCBIM33 | NCBIM34 | NCBIM35 | NCBIM36 | NCBIM37 ]