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Fast Stockholm to other formats Multiple Sequence Alignment reformater.

Project Description

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

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
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File Name & Checksum SHA256 Checksum Help Version File Type Upload Date
stockholm_reformat-0.3.1.tar.gz (53.5 kB) Copy SHA256 Checksum SHA256 Source Nov 17, 2016

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