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.