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

NAME - cut FASTA sequences with a given range

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


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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.

2021-08-15 perl v5.32.1