04-15-2011
No its not giving correct results.. I have the fasta file of 300,000 bp long.. but i need the sequences for some specific sites.. The above code in awk only giving the sequence of one line no matter how much length you give.. Also if the start site is after the first line, we are not getting any information about it..
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aTGTGCTGGgTGGGTGCCTGTTgCCccATGCTCCAGTtCAGGATTtCAGGCAttCTCATG
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AGAGGGAATTGG
AGGGGCCTGGAG
GGTTCTCTTC
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HI,
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4353..5633
6795..9354
1034..14456
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>0001
agttcgaggtcagaatt
>0002
agttcgag
>0003
ggtaacctga
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>0001
agttcgaggtcagaatt
>0003
ggtaacctga
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Below are my custom period start and end dates based on a calender, these dates are placed in a file, for each period i need to split into three weeks for each period row, example is given below.
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LEARN ABOUT DEBIAN
bp_oligo_count
BP_OLIGO_COUNT(1p) User Contributed Perl Documentation BP_OLIGO_COUNT(1p)
NAME
oligo_count - oligo count and frequency
SYNOPSIS
Usage: oligo_count [-h/--help] [-l/--length OLIGOLENGTH]
[-f/--format SEQFORMAT] [-i/--in/-s/--sequence SEQFILE]
[-o/--out OUTFILE]
DESCRIPTION
This scripts counts occurrence and frequency for all oligonucleotides of given length.
It can be used to determine what primers are useful for frequent priming of nucleic acid for random labeling.
Note that this script could be run by utilizing the compseq program which is part of EMBOSS.
OPTIONS
The default sequence format is fasta. If no outfile is given, the results will be printed to standard out. All other options can entered
interactively.
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 - Charles C. Kim
Email cckim@stanford.edu
HISTORY
Written July 2, 2001
Submitted to bioperl scripts project 2001/08/06
>> 100 x speed optimization by Heikki Lehvaslaiho
perl v5.14.2 2012-03-02 BP_OLIGO_COUNT(1p)