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.\" ========================================================================
.\"
.IX Title "BP_SEQCUT 1p"
.TH BP_SEQCUT 1p "2021-08-15" "perl v5.32.1" "User Contributed Perl Documentation"
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.SH "NAME"
bp_seqcut.pl \- cut FASTA sequences with a given range
.SH "USAGE"
.IX Header "USAGE"
.Vb 2
\& 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
.Ve
.SH "Description"
.IX Header "Description"
A script to cut \s-1FASTA\s0 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.
.SH "AUTHOR"
.IX Header "AUTHOR"
\&\fBMatt Oates\fR \- \fIMatt.Oates@bristol.ac.uk\fR
.SH "FEEDBACK"
.IX Header "FEEDBACK"
.SS "Mailing Lists"
.IX Subsection "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.
.PP
.Vb 2
\&  bioperl\-l@bioperl.org                  \- General discussion
\&  http://bioperl.org/wiki/Mailing_lists  \- About the mailing lists
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.SS "Reporting Bugs"
.IX Subsection "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:
.PP
.Vb 1
\&  https://github.com/bioperl/bioperl\-live/issues
.Ve
.SH "EDIT HISTORY"
.IX Header "EDIT HISTORY"
2010\-11\-22 \- Matt Oates
First features added.
.SH "DEPENDENCY"
.IX Header "DEPENDENCY"
\&\fBGetopt::Long\fR Used to parse command line options.
\&\fBPod::Usage\fR Used for usage and help output.
\&\fBBio::SeqIO\fR Used to cut up sequences and parse \s-1FASTA.\s0