04-15-2011
Parsing a fasta sequence with start and end coordinates
Hi.. I have a seperate chromosome sequences and i wanted to parse some regions of chromosome based on start site and end site.. how can i achieve this?
For Example Chr 1 is in following format
Quote:
>chr1
GAATTCCAAAGCCAAAGATTGCATCAGTTCTGCTGCTATTTCCTCCTATCATTCTTTCTGATGTTGAAAATGATATTAAG
I need regions from 2 - 10 should give me AATTCCAAA
and in a similar way 15- 25 should give me AAGATTGCAT
and from 27 - 30 should give me AGTT
How can i do it either in perl or bioperl or awk or any other way?
Last edited by empyrean; 04-15-2011 at 02:55 AM..
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LEARN ABOUT DEBIAN
bp_gccalc
BP_GCCALC(1p) User Contributed Perl Documentation BP_GCCALC(1p)
NAME
gccalc - GC content of nucleotide sequences
SYNOPSIS
gccalc [-f/--format FORMAT] [-h/--help] filename
or
gccalc [-f/--format FORMAT] < filename
or
gccalc [-f/--format FORMAT] -i filename
DESCRIPTION
This scripts prints out the GC content for every nucleotide sequence from the input file.
OPTIONS
The default sequence format is fasta.
The sequence input can be provided using any of the three methods:
unnamed argument
gccalc filename
named argument
gccalc -i filename
standard input
gccalc < filename
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 the
web:
https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Jason Stajich
Email jason@bioperl.org
HISTORY
Based on script code (see bottom) submitted by cckim@stanford.edu
Submitted as part of bioperl script project 2001/08/06
perl v5.14.2 2012-03-02 BP_GCCALC(1p)