Package: bioscripts.convert
IntroductionBiopython scripts for converting molecular sequences.Bioinformatics is bedevilled by a large number of file formats. Biopython
provides classes and IO functions that allow interconversion. This module
provides scripts that use Biopython internally to simply convert multiple
files on the commandline.Installationbioscripts.convert[1]can be installed in a number of ways.
Biopython[2]is a prerequisite.Via easy_install or equivalentFrom the commandline call:% easy_install bioscripts.convertSuperuser privileges may be required.Via setup.pyDownload a source tarball, unpack it and call setup.py to
install:% tar zxvf bioscripts.convert.tgz
% cd bioscripts.convert
% python setup.py installSuperuser privileges may be required.Usageconvbioseq.py [options] FORMAT INFILES ...or:convalign.py [options] FORMAT INFILES ...with the options:--versionshow program’s version number and exit-h,--helpshow this help message and exit-iFORMAT,--input-format=FORMATThe format of the input biosequence files. If not
supplied, this will be inferred from the extension of
the files.-eEXTENSION,--output-extension=EXTENSIONThe extension of the output biosequence files. If not
supplied, this will be inferred from the output format.-tTYPE,--seqtype=TYPEThe type of sequence (dna or protein) being converted.
Often this can be inferred from the input file, but
sometimes must be explicitly set.FORMAT must be one of clustal, fasta, genbank, nexus, phd, phylip, qual,
stockholm, tab. The input formats inferred from extensions are clustal
(‘.aln’), genbank (‘.genbank’), nexus (‘.nxs’), nexus (‘.nexus’), phylip
(‘.phylip’), stockholm (‘.sth’), phd (‘.phd’), qual (‘.qual’), phylip
(‘.phy’), clustal (‘.clustal’), genbank (‘.gb’), tab (‘.tab’), fasta
(‘.fasta’), stockholm (‘.stockholm’). The default extensions for output
formats are ‘.aln’ (clustal), ‘.nexus’ (nexus), ‘.phy’ (phylip), ‘.phd’ (phd),
‘.qual’ (qual), ‘.gb’ (genbank), ‘.sth’ (stockholm), ‘.fasta’ (fasta).For example:% convbioseq.py clustal one.fasta two.nxs three.stockholmwill produce three clustal formatted files ‘one.aln’, ‘two.aln’ and
‘three.aln’ from files it assumes are Fasta, Nexus and Stockholm formatted
respectively.% convbioseq.py -i phylip clustal one.fasta two.nxswill produce two Phylip formatted files ‘one.phy’ and ‘two.phy’ and from files
it assumes are Fasta formatted.% convbioseq.py -e foo clustal one.fasta two.nxswill produce two Clustal formatted files ‘one.foo’ and ‘two.foo’ from files
it assumes are Fasta and Nexus formatted respectively.LimitationsThis module is not intended for importing, but the setuptools packaging and
infrastructure make for simple distribution of scripts, allowing the checking
of prerequisites, consistent installation and updating.Thebioscriptsnamespace was chosen as a convenient place to “keep” these
scripts and is open to other developers.Due to limitations on identifiers in certain formats, sequence names
may differ between input and output files. Also, not all formats understood by
Biopython have been enabled, due to being untested or incomplete.Depending on your platform, the scripts may be installed as.pyscripts,
or some form of executable, or both.Some formats (e.g. FASTA) do not specify sequence type, while others (e.g.
NEXUS), absolutely require it. Thus, the sequence type option may need to be
explicitly specified. Older versions of Biopython contain a bug that will prevent
conversion to nexus format for associated reasons.References[1]bioscripts.convert homepage[2]Biopython homepage[3]Installing setuptoolsChangelog0.2 - 2009/4/14Initial release0.3.1 - 2009/4/16First public releaseAdded alignment converterCorrections to documentation