03-03-2013
How to delete text between two characters in line?
Hi,
I have a large text file with the following format:
>gi|347545744|gb|JN204951.1| Dismorphia spio voucher 5
ATCAAATTCCTTCCTCTCCTTAAA
>gi|17544664774|gb|WN204922.32| Rodapara nigens gene region
CCGGGCAAATTCCTTCCTCTCCTTAAA
>gi|555466400|gb|SG255122.8| Bombyx mandariana genbank 3
CCGGGCAAATTCCTTCCTCTCCTTAAA
in each line, I would like the text between the ">" and the first space deleted. The text should be outputted like:
>Dismorphia spio voucher 5
ATCAAATTCCTTCCTCTCCTTAAA
>Rodapara nigens gene region
CCGGGCAAATTCCTTCCTCTCCTTAAA
>Bombyx mandariana genbank 3
CCGGGCAAATTCCTTCCTCTCCTTAAA
The lines that need to be edited all begin with ">". Is there a quick way to do this?
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LEARN ABOUT DEBIAN
bio::tools::geneid
Bio::Tools::Geneid(3pm) User Contributed Perl Documentation Bio::Tools::Geneid(3pm)
NAME
Bio::Tools::Geneid - Results of one geneid run
SYNOPSIS
use Bio::Tools::Geneid;
my $gid = Bio::Tools::Geneid(-file => "geneid.out");
while (my $gene = $gid->next_prediction)
{
my @transcripts = $gene->transcripts;
foreach my $t (@transcripts)
{
my @exons = $t->exons;
foreach my $e (@exons)
{
printf("Exon %d..%d
", $e->start, $e->end);
}
}
}
DESCRIPTION
This is the parser for the output of geneid by Enrique Blanco and Roderic Guigo (IMIM-UPF). See http://www1.imim.es/software/geneid. It
relies on native geneid output format internally and will work with geneid versions 1.0 and 1.1. Currently this module supports only the
default mode of operation which is to predict exons and assemble an optimal gene prediction.
It takes either a file handle or a file name and returns a Bio::SeqFeature::Gene::GeneStructure object.
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 one
of the Bioperl mailing lists. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Support
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address
it. Please include a thorough description of the problem with code and data examples if at all possible.
Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the
web:
https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Keith James
Email: kdj@sanger.ac.uk
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
new
Title : new
Usage : $obj->new(-file = "<geneid.out");
$obj->new(-fh => *GI);
Function: Constructor for geneid wrapper. Takes either a file
: or filehandle
Returns : L<Bio::Tools::Geneid>
next_prediction
Title : next_prediction
Usage : while($gene = $geneid->next_prediction)
{
# do something
}
Function: Returns the gene structure prediction of the geneid result
file. Call this method repeatedly until FALSE is returned.
Returns : A Bio::SeqFeature::Gene::GeneStructure object
Args : None
_add_exon
Title : _add_exon
Usage : $obj->_add_exon($gene, $transcript, ... exon data ...)
Function: Adds a new exon to both gene and transcript from the data
: supplied as args
Example :
Returns : Nothing
_set_strand
Title : _set_strand
Usage : $obj->_set_strand($gene)
Function: Sets the overall gene strand to the same strand as all
: the exons if they are all on the same strand, or to strand 0
: if the exons are on different strands.
Example :
Returns : Nothing
_target_id
Title : _target_id
Usage : $obj->_target_id
Function: get/set for genomic sequence id
Example :
Returns : A target ID
perl v5.14.2 2012-03-02 Bio::Tools::Geneid(3pm)