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BP_SEQCUT(1)          User Contributed Perl Documentation         BP_SEQCUT(1)


NAME

       bp_seqcut.pl


USAGE

        bp_seqcut.pl [options -h,-s,-e,-f,-w] <FILES>...
        bp_seqcut.pl [options -h,-f,-w] s-e <FILES>...

          -h this help message
          -s which residue to start cutting on
          -e which residue to finish cutting on
          -f format of the files, defaults to FASTA but you can specify anything supported by SeqIO from BioPerl
          -w hard wrap width, this might not be supported depending on which format you are using

Description
       A script to cut FASTA sequences with a given range `fastacut -s 1 -e 10
       *.fasta` or `fastacut 1-10 *.fasta`.  This is just a convenience
       wrapper around the Bio::SeqIO module. Useful if you wish to trim out a
       section of an alignment to build a profile of a specific region of
       sequence.


AUTHOR

       Matt Oates - Matt.Oates@bristol.ac.uk


FEEDBACK

   Mailing Lists
       User feedback is an integral part of the evolution of this and other
       Bioperl modules. Send your comments and suggestions preferably to the
       Bioperl mailing list.  Your participation is much appreciated.

         bioperl-l@bioperl.org                  - General discussion
         http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

   Reporting Bugs
       Report bugs to the Bioperl bug tracking system to help us keep track of
       the bugs and their resolution. Bug reports can be submitted via email
       or the web:

         https://github.com/bioperl/bioperl-live/issues


EDIT HISTORY

       2010-11-22 - Matt Oates  First features added.

DEPENDANCY Getopt::Long Used to parse command line options. Pod::Usage Used
       for usage and help output. Bio::SeqIO Used to cut up sequences and
       parse FASTA.

perl v5.20.2                      2015-09-15                      BP_SEQCUT(1)

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