stockholm_reformat

Fast Stockholm to other formats Multiple Sequence Alignment reformater.

Includes an API and a command line script. The pure Python version is already several times faster than the Perl script contained in the MPI Bioinformatics Toolkit.

The following outuput supported formats are:

• a3m
• fasta
• aln

Usage

From Python:

stockholm_reformat.parse_a3m('inputfile.sto', 'outputfile.a3m')
stockholm_reformat.parse_fasta('inputfile.sto', 'outputfile.fasta')
stockholm_reformat.parse_aln('inputfile.sto', 'outputfile.aln')

If you have a working C compiler, you may have the compiled versions installed:

stockholm_reformat.cparse_a3m('inputfile.sto', 'outputfile.a3m')
stockholm_reformat.cparse_fasta('inputfile.sto', 'outputfile.fasta')
stockholm_reformat.cparse_aln('inputfile.sto', 'outputfile.aln')

They are around twice as fast.

Both input and output can be provided as file names or file handles.

From the command line:

$ stockholm_to_a3m input.sto output.a3m
$ stockholm_to_fasta input.sto output.fasta
$ stockholm_to_aln input.sto output.aln