man Boulder::Blast (3): 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.

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 = $blast->Blast_hits->Hsps;
  print join("\n",$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.

AUTHOR

Lincoln Stein <[email protected]>.

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     +...
   }
 }
 =