Boulder::Blast(3pm) User Contributed Perl Documentation Boulder::Blast(3pm)
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.
TAGS
The following tags are defined in the parsed Blast Stone object:
Information about the program
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.
Information about the run
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
Information about the query sequence and subject database
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 = $blast->Blast_hits->Hsps;
print join("
",$hsp->Query,$hsp->Alignment,$hsp->Subject),"
";
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=||||||||||||||||||||||||||||||||||||||||||||||||||||||||||...
}
}
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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 +...
}
}
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perl v5.10.1 2002-02-04 Boulder::Blast(3pm)