Fasta subset by sequence

[TaliVeith]

Script to read fastq and, given a pattern will output sequences to stout that contain this pattern. Applied case: look for TRS leader sequence in reads and pull out those reads that contain the sequence.

Changed on the way to deal with fastq instead of fasta.

[bamueh]

You could probably run black on this.

[terrycojones]

OMG, I only just saw this, sorry!

filter-fasta.py has --sequenceRegex and --sequenceNegativeRegex that can be used to do this, and it also handles FASTA as well as FASTQ. I guess I added those options in the meantime.

I'm not sure what to do. It's fine to merge this (running black would be good) even though we don't strictly need it.

[terrycojones]

See comment in main conversation thread.