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Shell Programming and Scripting
Bash functions sequence ?
Post 303022360 by annacreek on Thursday 30th of August 2018 02:42:07 PM
08-30-2018
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LEARN ABOUT DEBIAN
bp_sreformat
BP_SREFORMAT(1p) User Contributed Perl Documentation BP_SREFORMAT(1p) 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 v5.14.2 2012-03-02 BP_SREFORMAT(1p)