bp_sreformatp - Online in the Cloud

PROGRAM:

NAME

bpsreformat - convert sequence formats

DESCRIPTION

This script uses the SeqIO system that allows conversion of sequence formats either
sequence data or multiple sequence alignment data. The name comes from the fact that Sean
Eddy's program sreformat (part of the HMMER pkg) already does this. Sean's program tries
to guess the input formats while in our code we currently require your to specify what the
input and output formats are and if the data is from a multiple sequence alignment or from
straight sequence files.

Usage:

bpsreformat -if INFORMAT -of OUTFORMAT -i FILENAME -o output.FORMAT

-h/--help Print this help

-if/--informat Specify the input format

-of/--outformat Specify the output format

-i/--input Specify the input file name
(to pass in data on STDIN use minus sign as filename)
-o/--output Specify the output file name
(to pass data out on STDOUT use minus sign as filename)

--msa Specify this is multiple sequence alignment data

--special Will pass on special parameters to the AlignIO/SeqIO
object -- most of these are for Bio::AlignIO objects
Comma separated list of the following
nointerleaved -- for phylip,non-interleaved format
idlinebreak -- for phylip, makes it molphy format
percentages -- for clustalw, show % id per line

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