1BP_SREFORMAT(1)       User Contributed Perl Documentation      BP_SREFORMAT(1)
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NAME

6       bpsreformat - convert sequence formats
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DESCRIPTION

9       This script uses the SeqIO system that allows conversion of sequence
10       formats either sequence data or multiple sequence alignment data.  The
11       name comes from the fact that Sean Eddy's program sreformat (part of
12       the HMMER pkg) already does this.  Sean's program tries to guess the
13       input formats while in our code we currently require your to specify
14       what the input and output formats are and if the data is from a multi‐
15       ple sequence alignment or from straight sequence files.
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17       Usage:
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19       bpsreformat -if INFORMAT -of OUTFORMAT -i FILENAME -o output.FORMAT
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21         -h/--help        Print this help
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23         -if/--informat   Specify the input format
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25         -of/--outformat  Specify the output format
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27         -i/--input       Specify the input file name
28                          (to pass in data on STDIN use minus sign as filename)
29         -o/--output      Specify the output file name
30                          (to pass data out on STDOUT use minus sign as filename)
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32         --msa            Specify this is multiple sequence alignment data
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34         --special        Will pass on special parameters to the AlignIO/SeqIO
35                          object -- most of these are for Bio::AlignIO objects
36                          Comma separated list of the following
37                          nointerleaved   -- for phylip,non-interleaved format
38                          idlinebreak     -- for phylip, makes it molphy format
39                          percentages     -- for clustalw, show % id per line
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43perl v5.8.8                       2007-05-07                   BP_SREFORMAT(1)