Provided by: libboulder-perl_1.30-4_all bug

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