|
FASTASequence - Perl extension Biooinformatics |
FASTASequence - Perl extension Biooinformatics
use FASTASequence; my $fasta = qq~>sp|P01815|HV2B_HUMAN Ig heavy chain V-II region COR - Homo sapiens (Human). QVTLRESGPALVKPTQTLTLTCTFSGFSLSSTGMCVGWIRQPPGKGLEWLARIDWDDDKY YNTSLETRLTISKDTSRNQVVLTMDPVDTATYYCARITVIPAPAGYMDVWGRGTPVTVSS ~; my $seq = FASTASequence->new($fasta);
This should be the abstract for FASTASequence. The abstract is used when making PPD (Perl Package Description) files. If you don't want an ABSTRACT you should also edit Makefile.PL to remove the ABSTRACT_FROM option.
This perl module is a simple utility to simplify the job of bioinformatics. It parses several information about a given FASTA-Sequence such as:
my $accession = $seq->getAccessionNr();
returns the AccessionNr of the FASTA-Sequence
my $description = $seq->getDescription();
returns the description standing in the first line of the FASTA-format (without the accession number)
my $sequence = $seq->getSequence();
returns the sequence
my $crc64_checksum = $seq->getCrc64();
returns the crc64 checksum of the sequence. This checksum corresponds with the crc64 checksum of SWISS-PROT
$seq->addDBRef(DB, REFERENCE_AC);
DB is the name of the referenced database
REFERENCE_AC is the accession number in the referenced database
$seq->seq2file(FILENAME, OPTIONS);
FILENAME is the path of the file where the sequence has to be stored.
OPTIONS is a hash, which contains the options:
my $indexes = $seq->allIndexesOf(EXPR);
returns a reference on an array, which contains all indexes of EXPR in the sequence
my $length = $seq->getSequenceLength();
returns the length of the sequence
my $hashref = $seq->getDBRefs();
| returns a hashreference. The hash contains all references | |
| hashref = {'SWISS-PROT' => 'P01815'}, |
my $fasta_sequence = $seq->getFASTA();
returns the sequence in FASTA-format
use FASTASequence;
my $fasta = qq~>sp|P01815|HV2B_HUMAN Ig heavy chain V-II region COR - Homo sapiens (Human).
QVTLRESGPALVKPTQTLTLTCTFSGFSLSSTGMCVGWIRQPPGKGLEWLARIDWDDDKY
YNTSLETRLTISKDTSRNQVVLTMDPVDTATYYCARITVIPAPAGYMDVWGRGTPVTVSS
~;
my $seq = FASTASequence->new($fasta);
print 'The sequence of '.$seq->getAccessionNr().' is '.$seq->getSequence(),"\n";
print 'This sequence contains '.scalar($seq->allIndexesOf('C').' times Cystein at the following positions:';
print $_+1.', ' for(@{$seq->allIndexesOf('C')});
This module can parse the following formats:
The structure of the hash for the example is:
$VAR1 = {
'seq_length' => 120,
'accession_nr' => 'P01815',
'text' => 'QVTLRESGPALVKPTQTLTLTCTFSGFSLSSTGMCVGWIRQPPGKGLEWLARIDWDDDKYYNTSLETRLTISKDTSRNQVVLTMDPVDTATYYCARITVIPAPAGYMDVWGRGTPVTVSS',
'crc64' => '158A8B29AE7EEB98',
'dbrefs' => {},
'description' => 'Ig heavy chain V-II region COR - Homo sapiens (Human).'
}
if you miss something please contact me.
There is no bug known. If you experienced any problems, please contact me.
http://perl-modules.renee-baecker.de
the crc64-routine is based on the SWISS::CRC64 module.
Renee Baecker, <module@renee-baecker.de>
Copyright 2004 by Renee Baecker
This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself.
|
FASTASequence - Perl extension Biooinformatics |