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        "author": "Paul-Michael Agapow",
        "author_email": "agapow@bbsrc.ac.uk",
        "bugtrack_url": null,
        "classifiers": [
            "Development Status :: 4 - Beta",
            "Environment :: Console",
            "Intended Audience :: Science/Research",
            "License :: OSI Approved :: BSD License",
            "Programming Language :: Python",
            "Topic :: Scientific/Engineering :: Bio-Informatics",
            "Topic :: Software Development :: Libraries :: Python Modules",
            "Topic :: Text Processing"
        ],
        "description": "Introduction\n============\n\nBiopython scripts for converting molecular sequences.\n\nBioinformatics is bedevilled by a large number of file formats. Biopython\nprovides classes and IO functions that allow interconversion. This module\nprovides scripts that use Biopython internally to simply convert multiple\nfiles on the commandline.\n\n\nInstallation\n============\n\nbioscripts.convert [#homepage]_ can be installed in a number of ways.\nBiopython [#biopython]_ is a prerequisite.\n\nVia easy_install or equivalent\n------------------------------\n\nFrom the commandline call::\n\n\t% easy_install bioscripts.convert\n\t\nSuperuser privileges may be required. \n\n\nVia setup.py\n------------\n\nDownload a source tarball, unpack it and call setup.py to\ninstall::\n\n\t% tar zxvf bioscripts.convert.tgz\n\t% cd bioscripts.convert\n\t% python setup.py install\n\t\nSuperuser privileges may be required. \n\n\n\nUsage\n=====\n\n\n::\n\n\tconvbioseq.py [options] FORMAT INFILES ...\n\t\nor::\n\n\tconvalign.py [options] FORMAT INFILES ...\n\nwith the options:\n\n  --version             show program's version number and exit\n  -h, --help            show this help message and exit\n  -i FORMAT, --input-format=FORMAT\n                        The format of the input biosequence files. If not\n                        supplied, this will be inferred from the extension of \n                        the files.\n  -e EXTENSION, --output-extension=EXTENSION\n                        The extension of the output biosequence files. If not\n                        supplied, this will be inferred from the output format.\n  -t TYPE, --seqtype=TYPE\n                        The type of sequence (dna or protein) being converted.\n                        Often this can be inferred from the input file, but \n                        sometimes must be explicitly set.\n\nFORMAT must be one of clustal, fasta, genbank, nexus, phd, phylip, qual,\nstockholm, tab. The input formats inferred from extensions are clustal\n('.aln'), genbank ('.genbank'), nexus ('.nxs'), nexus ('.nexus'), phylip\n('.phylip'), stockholm ('.sth'), phd ('.phd'), qual ('.qual'), phylip\n('.phy'), clustal ('.clustal'), genbank ('.gb'), tab ('.tab'), fasta\n('.fasta'), stockholm ('.stockholm'). The default extensions for output\nformats are '.aln' (clustal), '.nexus' (nexus), '.phy' (phylip), '.phd' (phd),\n'.qual' (qual), '.gb' (genbank), '.sth' (stockholm), '.fasta' (fasta).\n\nFor example::\n\n\t% convbioseq.py clustal one.fasta two.nxs three.stockholm\n\nwill produce three clustal formatted files 'one.aln', 'two.aln' and\n'three.aln' from files it assumes are Fasta, Nexus and Stockholm formatted\nrespectively.\n\n\t% convbioseq.py -i phylip clustal one.fasta two.nxs\n\nwill produce two Phylip formatted files 'one.phy' and 'two.phy' and from files\nit assumes are Fasta formatted.\n\n\t% convbioseq.py -e foo clustal one.fasta two.nxs\n\t\nwill produce two Clustal formatted files 'one.foo' and 'two.foo' from files\nit assumes are Fasta and Nexus formatted respectively.\t\n\n\n\nLimitations\n===========\n\nThis module is not intended for importing, but the setuptools packaging and\ninfrastructure make for simple distribution of scripts, allowing the checking\nof prerequisites, consistent installation and updating.\n\nThe ``bioscripts`` namespace was chosen as a convenient place to \"keep\" these\nscripts and is open to other developers.\n\nDue to limitations on identifiers in certain formats, sequence names\nmay differ between input and output files. Also, not all formats understood by\nBiopython have been enabled, due to being untested or incomplete.\n\nDepending on your platform, the scripts may be installed as ``.py`` scripts,\nor some form of executable, or both.\n\nSome formats (e.g. FASTA) do not specify sequence type, while others (e.g. \nNEXUS), absolutely require it. Thus, the sequence type option may need to be \nexplicitly specified. Older versions of Biopython contain a bug that will prevent \nconversion to nexus format for associated reasons.\n\n\nReferences\n==========\n\n.. [#homepage] `bioscripts.convert homepage <http://www.agapow/net/software/bioscripts.convert>`__\n\n.. [#biopython] `Biopython homepage <http://www.biopython.org>`__\n\n.. [#setuptools] `Installing setuptools <http://peak.telecommunity.com/DevCenter/setuptools#installing-setuptools>`__\n\n\n\n\nChangelog\n=========\n\n0.2 - 2009/4/14\n---------------\n\n* Initial release\n\n\n0.3.1 - 2009/4/16\n-----------------\n\n* First public release\n\n* Added alignment converter\n\n* Corrections to documentation",
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        "keywords": "bioinformatics conversion",
        "license": "BSD",
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