NAME
FAST::Bio::Search::HSP::HmmpfamHSP - A parser and HSP object for hmmpfam hsps
SYNOPSIS
# generally we use FAST::Bio::SearchIO to build these objects
my
$in
= FAST::Bio::SearchIO->new(
-format
=>
'hmmer_pull'
,
-file
=>
'result.hmmer'
);
while
(
my
$result
=
$in
->next_result) {
while
(
my
$hit
=
$result
->next_hit) {
$hit
->name,
"\n"
;
$hit
->score,
"\n"
;
$hit
->significance,
"\n"
;
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:
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
= FAST::Bio::Search::HSP::HmmpfamHSP->new();
Function: Builds a new FAST::Bio::Search::HSP::HmmpfamHSP object.
Returns : FAST::Bio::Search::HSP::HmmpfamHSP
Args :
-chunk
=> [FAST::Bio::Root::IO,
$start
,
$end
] (required
if
no
-parent)
-parent
=> FAST::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<FAST::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<FAST::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