BP_FASTAM9_TO_TABLE(1p) User Contributed Perl Documentation BP_FASTAM9_TO_TABLE(1p)NAME
fastm9_to_table - turn FASTA -m 9 output into NCBI -m 9 tabular output
SYNOPSIS
fastm9_to_table [-e evaluefilter] [-b bitscorefilter] [--header] [-o outfile] inputfile1 inputfile2 ...
DESCRIPTION
Command line options:
-e/--evalue evalue -- filter by evalue
-b/--bitscore bitscore -- filter by bitscore
--header-- boolean flag to print column header
-o/--out -- optional outputfile to write data,
otherwise will write to STDOUT
-h/--help -- show this documentation
Not technically a SearchIO script as this doesn't use any Bioperl components but is a useful and fast. The output is tabular output with
the standard NCBI -m9 columns.
queryname
hit name
percent identity
alignment length
number mismatches
number gaps
query start (if on rev-strand start > end)
query end
hit start (if on rev-strand start > end)
hit end
evalue
bit score
Additionally 3 more columns are provided
fasta score
sw-score
percent similar
query length
hit length
query gaps
hit gaps
AUTHOR - Jason Stajich
Jason Stajich jason_at_bioperl-dot-org
perl v5.14.2 2012-03-02 BP_FASTAM9_TO_TABLE(1p)
Check Out this Related Man Page
Bio::Search::HSP::HmmpfamHSP(3pm) User Contributed Perl Documentation Bio::Search::HSP::HmmpfamHSP(3pm)NAME
Bio::Search::HSP::HmmpfamHSP - A parser and HSP object for hmmpfam hsps
SYNOPSIS
# generally we use Bio::SearchIO to build these objects
use Bio::SearchIO;
my $in = Bio::SearchIO->new(-format => 'hmmer_pull',
-file => 'result.hmmer');
while (my $result = $in->next_result) {
while (my $hit = $result->next_hit) {
print $hit->name, "
";
print $hit->score, "
";
print $hit->significance, "
";
while (my $hsp = $hit->next_hsp) {
# process HSPI objects
}
}
}
DESCRIPTION
This object implements a parser for hmmpfam hsp output, a program in the HMMER package.
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:
https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Sendu Bala
Email bix@sendu.me.uk
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
new
Title : new
Usage : my $obj = Bio::Search::HSP::HmmpfamHSP->new();
Function: Builds a new Bio::Search::HSP::HmmpfamHSP object.
Returns : Bio::Search::HSP::HmmpfamHSP
Args : -chunk => [Bio::Root::IO, $start, $end] (required if no -parent)
-parent => Bio::PullParserI object (required if no -chunk)
-hsp_data => array ref with [rank query_start query_end hit_start
hit_end score evalue]
where the array ref provided to -chunk contains an IO object
for a filehandle to something representing the raw data of the
hsp, and $start and $end define the tell() position within the
filehandle that the hsp data starts and ends (optional; defaults
to start and end of the entire thing described by the filehandle)
query
Title : query
Usage : my $query = $hsp->query
Function: Returns a SeqFeature representing the query in the HSP
Returns : L<Bio::SeqFeature::Similarity>
Args : none
hit
Title : hit
Usage : my $hit = $hsp->hit
Function: Returns a SeqFeature representing the hit in the HSP
Returns : L<Bio::SeqFeature::Similarity>
Args : [optional] new value to set
gaps
Title : gaps
Usage : my $gaps = $hsp->gaps( ['query'|'hit'|'total'] );
Function : Get the number of gaps in the query, hit, or total alignment.
Returns : Integer, number of gaps or 0 if none
Args : 'query' = num conserved / length of query seq (without gaps)
'hit' = num conserved / length of hit seq (without gaps)
'total' = num conserved / length of alignment (with gaps)
default = 'total'
pvalue
Title : pvalue
Usage : my $pvalue = $hsp->pvalue();
Function: Returns the P-value for this HSP
Returns : undef (Hmmpfam reports do not have p-values)
Args : none
perl v5.14.2 2012-03-02 Bio::Search::HSP::HmmpfamHSP(3pm)