NAME¶
Boulder::Blast - Parse and read BLAST files
SYNOPSIS¶
use Boulder::Blast;
# parse from a single file
$blast = Boulder::Blast->parse('run3.blast');
# parse and read a set of blast output files
$stream = Boulder::Blast->new('run3.blast','run4.blast');
while ($blast = $stream->get) {
# do something with $blast object
}
# parse and read a whole directory of blast runs
$stream = Boulder::Blast->new(<*.blast>);
while ($blast = $stream->get) {
# do something with $blast object
}
# parse and read from STDIN
$stream = Boulder::Blast->new;
while ($blast = $stream->get) {
# do something with $blast object
}
# parse and read as a filehandle
$stream = Boulder::Blast->newFh(<*.blast>);
while ($blast = <$stream>) {
# do something with $blast object
}
# once you have a $blast object, you can get info about it:
$query = $blast->Blast_query;
@hits = $blast->Blast_hits;
foreach $hit (@hits) {
$hit_sequence = $hit->Name; # get the ID
$significance = $hit->Signif; # get the significance
@hsps = $hit->Hsps; # list of HSPs
foreach $hsp (@hsps) {
$query = $hsp->Query; # query sequence
$subject = $hsp->Subject; # subject sequence
$signif = $hsp->Signif; # significance of HSP
}
}
DESCRIPTION¶
The
Boulder::Blast class parses the output of the
Washington
University (WU) or National Cenber for Biotechnology Information (NCBI)
series of BLAST programs and turns them into
Stone records. You may
then use the standard Stone access methods to retrieve information about the
BLAST run, or add the information to a Boulder stream.
The parser works equally well on the contents of a static file, or on
information read dynamically from a filehandle or pipe.
METHODS¶
parse() Method¶
$stone = Boulder::Blast->parse($file_path);
$stone = Boulder::Blast->parse($filehandle);
The
parse() method accepts a path to a file or a
filehandle, parses its contents, and returns a Boulder Stone object. The file
path may be absolute or relative to the current directgly. The filehandle may
be specified as an IO::File object, a FileHandle object, or a reference to a
glob ("\*FILEHANDLE" notation). If you call
parse() without any arguments, it will try to parse the
contents of standard input.
new() Method¶
$stream = Boulder::Blast->new;
$stream = Boulder::Blast->new($file [,@more_files]);
$stream = Boulder::Blast->new(\*FILEHANDLE);
If you wish, you may create the parser first with
Boulder::Blast
new(), and then invoke the parser object's
parse() method as many times as you wish to, producing a
Stone object each time.
The following tags are defined in the parsed Blast Stone object:
These top-level tags provide information about the version of the BLAST program
itself.
- Blast_program
- The name of the algorithm used to run the analysis.
Possible values include:
blastn
blastp
blastx
tblastn
tblastx
fasta3
fastx3
fasty3
tfasta3
tfastx3
tfasty3
- Blast_version
- This gives the version of the program in whatever form
appears on the banner page, e.g. "2.0a19-WashU".
- Blast_program_date
- This gives the date at which the program was compiled, if
and only if it appears on the banner page.
These top-level tags give information about the particular run, such as the
parameters that were used for the algorithm.
- Blast_run_date
- This gives the date and time at which the similarity
analysis was run, in the format "Fri Jul 6 09:32:36 1998"
- Blast_parms
- This points to a subrecord containing information about the
algorithm's runtime parameters. The following subtags are used. Others may
be added in the future:
Hspmax the value of the -hspmax argument
Expectation the value of E
Matrix the matrix in use, e.g. BLOSUM62
Ctxfactor the value of the -ctxfactor argument
Gapall The value of the -gapall argument
Thse top-level tags give information about the query sequence and the database
that was searched on.
- Blast_query
- The identifier for the search sequence, as defined by the
FASTA format. This will be the first set of non-whitespace characters
following the ">" character. In other words, the search
sequence "name".
- Blast_query_length
- The length of the query sequence, in base pairs.
- Blast_db
- The Unix filesystem path to the subject database.
- Blast_db_title
- The title of the subject database.
The search results: the Blast_hits tag.¶
Each BLAST hit is represented by the tag
Blast_hits. There may be zero,
one, or many such tags. They will be presented in reverse sorted order of
significance, i.e. most significant hit first.
Each
Blast_hits tag is a Stone subrecord containing the following
subtags:
- Name
- The name/identifier of the sequence that was hit.
- Length
- The total length of the sequence that was hit
- Signif
- The significance of the hit. If there are multiple HSPs in
the hit, this will be the most significant (smallest) value.
- Identity
- The percent identity of the hit. If there are multiple
HSPs, this will be the one with the highest percent identity.
- Expect
- The expectation value for the hit. If there are multiple
HSPs, this will be the lowest expectation value in the set.
- Hsps
- One or more sub-sub-tags, pointing to a nested record
containing information about each high-scoring segment pair (HSP). See the
next section for details.
The Hsp records: the Hsps tag¶
Each
Blast_hit tag will have at least one, and possibly several
Hsps tags, each one corresponding to a high-scoring segment pair (HSP).
These records contain detailed information about the hit, including the
alignments. Tags are as follows:
- Signif
- The significance (P value) of this HSP.
- Bits
- The number of bits of significance.
- Expect
- Expectation value for this HSP.
- Identity
- Percent identity.
- Positives
- Percent positive matches.
- Score
- The Smith-Waterman alignment score.
- Orientation
- The word "plus" or "minus". This tag is
only present for nucleotide searches, when the reverse complement match
may be present.
- Strand
- Depending on algorithm used, indicates complementarity of
match and possibly the reading frame. This is copied out of the blast
report. Possibilities include:
"Plus / Minus" "Plus / Plus" -- blastn algorithm
"+1 / -2" "+2 / -2" -- blastx, tblastx
- Query_start
- Position at which the HSP starts in the query sequence
(1-based indexing).
- Query_end
- Position at which the HSP stops in the query sequence.
- Subject_start
- Position at which the HSP starts in the subject (target)
sequence.
- Subject_end
- Position at which the HSP stops in the subject (target)
sequence.
- Query, Subject, Alignment
- These three tags contain strings which, together, create
the gapped alignment of the query sequence with the subject sequence.
For example, to print the alignment of the first HSP of the first match, you
might say:
$hsp = $blast->Blast_hits->Hsps;
print join("\n",$hsp->Query,$hsp->Alignment,$hsp->Subject),"\n";
See the bottom of this manual page for an example BLAST run.
CAVEATS¶
This module has been extensively tested with WUBLAST, but very little with NCBI
BLAST. It probably will not work with PSI Blast or other variants.
The author plans to adapt this module to parse other formats, as well as
non-BLAST formats such as the output of Fastn.
SEE ALSO¶
Boulder, Boulder::GenBank
AUTHOR¶
Lincoln Stein <lstein@cshl.org>.
Copyright (c) 1998-1999 Cold Spring Harbor Laboratory
This library is free software; you can redistribute it and/or modify it under
the same terms as Perl itself. See DISCLAIMER.txt for disclaimers of warranty.
EXAMPLE BLASTN RUN¶
This output was generated by the
quickblast.pl program, which is located
in the
eg/ subdirectory of the
Boulder distribution directory.
It is a typical
blastn (nucleotide->nucleotide) run; however long
lines (usually DNA sequences) have been truncated. Also note that per the
Boulder protocol, the percent sign (%) is escaped in the usual way. It will be
unescaped when reading the stream back in.
Blast_run_date=Fri Nov 6 14:40:41 1998
Blast_db_date=2:40 PM EST Nov 6, 1998
Blast_parms={
Hspmax=10
Expectation=10
Matrix=+5,-4
Ctxfactor=2.00
}
Blast_program_date=05-Feb-1998
Blast_db= /usr/tmp/quickblast18202aaaa
Blast_version=2.0a19-WashU
Blast_query=BCD207R
Blast_db_title= test.fasta
Blast_query_length=332
Blast_program=blastn
Blast_hits={
Signif=3.5e-74
Expect=3.5e-74,
Name=BCD207R
Identity=100%25
Length=332
Hsps={
Subject=GTGCTTTCAAACATTGATGGATTCCTCCCCTTGACATATATATATACTTTGGGTTCCCGCAA...
Signif=3.5e-74
Length=332
Bits=249.1
Query_start=1
Subject_end=332
Query=GTGCTTTCAAACATTGATGGATTCCTCCCCTTGACATATATATATACTTTGGGTTCCCGCAA...
Positives=100%25
Expect=3.5e-74,
Identity=100%25
Query_end=332
Orientation=plus
Score=1660
Strand=Plus / Plus
Subject_start=1
Alignment=||||||||||||||||||||||||||||||||||||||||||||||||||||||||||...
}
}
=
Example BLASTP run¶
Here is the output from a typical
blastp (protein->protein) run. Long
lines have again been truncated.
Blast_run_date=Fri Nov 6 14:37:23 1998
Blast_db_date=2:36 PM EST Nov 6, 1998
Blast_parms={
Hspmax=10
Expectation=10
Matrix=BLOSUM62
Ctxfactor=1.00
}
Blast_program_date=05-Feb-1998
Blast_db= /usr/tmp/quickblast18141aaaa
Blast_version=2.0a19-WashU
Blast_query=YAL004W
Blast_db_title= elegans.fasta
Blast_query_length=216
Blast_program=blastp
Blast_hits={
Signif=0.95
Expect=3.0,
Name=C28H8.2
Identity=30%25
Length=51
Hsps={
Subject=HMTVEFHVTSQSW---FGFEDHFHMIIR-AVNDENVGWGVRYLSMAF
Signif=0.95
Length=46
Bits=15.8
Query_start=100
Subject_end=49
Query=HLTQD-HGGDLFWGKVLGFTLKFNLNLRLTVNIDQLEWEVLHVSLHF
Positives=52%25
Expect=3.0,
Identity=30%25
Query_end=145
Orientation=plus
Score=45
Subject_start=7
Alignment=H+T + H W GF F++ +R VN + + W V ++S+ F
}
}
Blast_hits={
Signif=0.99
Expect=4.7,
Name=ZK896.2
Identity=24%25
Length=340
Hsps={
Subject=FSGKFTTFVLNKDQATLRMSSAEKTAEWNTAFDSRRGFF----TSGNYGL...
Signif=0.99
Length=101
Bits=22.9
Query_start=110
Subject_end=243
Query=FWGKVLGFTL-KFNLNLRLTVNIDQLEWEVLHVSLHFWVVEVSTDQTLSVE...
Positives=41%25
Expect=4.7,
Identity=24%25
Query_end=210
Orientation=plus
Score=65
Subject_start=146
Alignment=F GK F L K LR++ EW S + T +...
}
}
=