|BP_SEQCUT(1p)||User Contributed Perl Documentation||BP_SEQCUT(1p)|
bp_seqcut.pl - cut FASTA sequences with a given range
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
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.
Matt Oates - Matt.Oates@bristol.ac.uk
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2010-11-22 - Matt Oates First features added.
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.