We often have to convert sequence files between formats and do little manipulations on them, and it's not worth writing scripts for that. seqmagick
is a kickass little utility to expose the file format conversion in BioPython in a convenient way. Instead of having a big mess of scripts, there is one that takes arguments:
seqmagick convert a.fasta b.phy # convert from fasta to phylip
seqmagick mogrify --ungap a.fasta # remove all gaps from a.fasta, in place
seqmagick info *.{fasta,sto} # describe all FASTA and Stockholm
# files in the current directory
seqmagick protparam a.fasta # output masses and predicted
# isoelectric points
Features include:
- Modifying sequences: Remove gaps, reverse complement, reverse, change case,
- Remove gaps
- Reverse & reverse complement
- Trim to a range of residues
- Change case
- Sort by length or ID (or mass or pI)
- more
- Displaying information about sequence files
- Subsetting sequence files by:
- Position
- ID
- Deduplication
- more
- Filtering sequences by quality score
- Trimming alignments to a region of interest defined by the forward and reverse primers
Want to learn more? Head to the Documentation.
seqmagick
is free software under the GPL v3.