Bio::FeatureIO::ptt(3)User Contributed Perl DocumentatioBio::FeatureIO::ptt(3)NAMEBio::FeatureIO::ptt - read/write features in PTT format
SYNOPSIS
# read features
my $fin = Bio::FeatureIO->new(-file=>'genes.ptt', -format=>'ptt');
my @cds;
while (my $f = $fin->next_feature) {
push @cds, $f if $f->strand > 0;
}
# write features (NOT IMPLEMENTED)
my $fout = Bio::FeatureIO->new(-fh=>\*STDOUT, -format=>'ptt');
for my $f (@cds) {
$fout->write_feature($f);
}
DESCRIPTION
The PTT file format is a table of protein features. It is used mainly
by NCBI who produce PTT files for all their published genomes found in
<ftp://ftp.ncbi.nih.gov/genomes/>. It has the following format:
Line 1
Description of sequence to which the features belong
eg. "Leptospira interrogans chromosome II, complete sequence -
0..358943"
It is usually equivalent to the DEFINITION line of a Genbank file,
with the length of the sequence appended. It is unclear why "0" is
used as a starting range, it should be "1".
Line 2
Number of feature lines in the table
eg. "367 proteins"
Line 3
Column headers, tab separated
eg. "Location Strand Length PID Gene Synonym Code COG
Product"
Location : "begin..end" span of feature
Strand : "+" or "-"
Length : number of amino acids excluding the stop codon
PID : analogous to Genbank /db_xref="GI:xxxxxxxxx"
Gene : analogous to Genbank /gene="xxxx"
Synonym : analogous to Genbank /locus_tag="xxxx"
Synonym : analogous to Genbank /locus_tag="xxxx"
COG : CDD COG code with COG letter categories appended
Product : analogous to Genbank /product="xxxx"
Line 4 onwards
Feature lines, nine columns, tab separated, "-" used for empty
fields
eg. "2491..3423 + 310 24217063 metF LB002 - COG0685E
5,10-methylenetetrahydrofolate reductase"
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
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 of
the bugs and their resolution. Bug reports can be submitted via the
web:
http://bugzilla.open-bio.org/
AUTHOR - Torsten Seemann
Email torsten.seemann AT infotech.monash.edu.au
CONTRIBUTORS
Based on bed.pm and gff.pm by Allen Day.
APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
_initialize
Title : _initialize
Function: Reading? parses the header of the input
Writing?
next_feature
Title : next_feature
Usage : $io->next_feature()
Function: read the next feature from the PTT file
Example :
Args :
Returns : Bio::SeqFeatureI object
write_feature (NOT IMPLEMENTED)
Title : write_feature
Usage : $io->write_feature($feature)
Function: write a Bio::SeqFeatureI object in PTT format
Example :
Args : Bio::SeqFeatureI object
Returns :
description
Title : description
Usage : $obj->description($newval)
Function: set/get the PTT file description for/from line one
Example :
Returns : value of description (a scalar)
Args : on set, new value (a scalar or undef, optional)
protein_count
Title : protein_count
Usage : $obj->protein_count($newval)
Function: set/get the PTT protein count for/from line two
Example :
Args : on set, new value (a scalar or undef, optional)
Returns : value of protein_count (a scalar)
perl v5.14.1 2011-07-22 Bio::FeatureIO::ptt(3)
