BP_SREFORMAT(1) User Contributed Perl Documentation BP_SREFORMAT(1)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
perl v5.14.1 2011-07-22 BP_SREFORMAT(1)
