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#---------------------------------------------------------------------------
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# PROGRAM : parse_blast.pl
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# PURPOSE : To demonstrate parsing features of the Bio::Tools::Blast.pm module.
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# AUTHOR : Steve Chervitz (sac@bioperl.org)
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# REVISION: $Id: parse_blast.pl,v 1.9 2002/01/11 08:05:38 sac Exp $
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# WEBSITE : http://bio.perl.org/Projects/Blast/
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# USAGE : parse_blast.pl -h
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# EXAMPLES: parse_blast.pl -eg
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# Set the require ".../blast_config.pl" to point to the proper location
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# of the blast_config.pl file. See blast_config.pl for additional steps.
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# Sample BLAST output files can be found in examples/blast/out/ of the
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# distribution. This script can process Blast report files specified
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# on the command line or supplied via a STDIN stream.
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# This demo script does not exercise all of the functionality of the Blast
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# object. See parse_blast2.pl and parse_positions.pl script for some other
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# manipulations and the documentation in the Bio::Tools::Blast.pm,
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# accessible from the above website or by running Blast.pm through pod2html.
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# * Create an example that shows how to parse with HTML-formatted
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# reports. The new Blast.pm module no longer parses such reports
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# sac, 11 Mar 1999: Merged parse_stream.pl with parse.pl to create
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# parse_blast.pl. Replaces parse_stream.pl and parse.pl.
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# sac, 4 Sep 1998: Added example of using -filt_func option.
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# sac, 16 Jun 1998: Added installation comment, require statement comments.
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# Minor alteration of seq_inds() calls.
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# sac, 15 Jul 1998: Segregated code into parse2.pl which was formerly in
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# parse.pl but commented out.
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#---------------------------------------------------------------------------
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# Using blast_config.pl in the examples/blast distribution directory:
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require "blast_config.pl";
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# Proper path to blast_config.pl after you install it in your system:
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#require "/share/www-data/html/perlOOP/bioperl/bin/blast/blast_config.pl";
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# Using vars from blast_config to prevent warning messages under -w.
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use vars qw($ID $VERSION $DESC $MONITOR %blastParam @objects
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$opt_in $opt_table $opt_compress $opt_filt_func);
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$ID = 'parse_blast.pl';
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$DESC = "Demonstrates parsing Blast reports using Bio::Tools::Blast.pm";
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# $hit->frac_aligned_hit >= 0.8; };
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&blast_general_params;
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# THESE NEED TO BE UPDATED TO INCLUDE MORE STREAM PARSING EXAMPLES
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(Run these in the examples/blast/ directory of the distribution.)
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./$ID out/blastp.2.gz -signif 1e-15 -table 1
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./$ID out/blastp.2.gz -signif 1e-15 -table 1 -exponent -desc
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./$ID out/blastp.2.gz -signif 1e-15 -table 2
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./$ID out/blastp.2.wu -check_all -filt_func '\$hit->gaps == 0' -table 2
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./$ID out/blastp.205.gz -signif 1e-1 -nostats
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./$ID out/blastp.2.gz -noaligns -signif 1e-5
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./$ID -signif 1e-5 -table 1 < out/tblastn.2 > parsed.out
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./$ID out/blastx.2.email.gz -table 1 -signif 1e-4
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./$ID out/blastn.2* -table 1 -best -nostats > parsed.out2
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./$ID out/tblastn.206.out.gz -table 2 -signif 0.1
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./$ID out/blastp.1.gz # should issue some warnings.
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gzip -cd out/blastp.2* | ./$ID -signif 1e-5 -table 2 > blast.table2
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cat ./out/blastx* | ./$ID -table 1 > blast.table1
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print_blasts.pl ./out | ./$ID -best -noshare
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The '-noshare' argument is necessary because the out/ directory
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contains a mixed bag of Blast reports (version 1, 2, blastp, tblastn,
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gapped, ungapped, etc.). Most of the time, -noshare is unnecessary
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since all reports have the same program, version, gapping, etc.
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The "print_blasts.pl dir" syntax or the parse_multi.pl script are
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recommended when working with large numbers of Blast reports (thousands).
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The Blasts reports located in "dir" can be compressed or not.
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Parsing large numbers of Blast reports can lead to serious
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memory usage problems. See documentation in parse_multi.pl and
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Blast.pm for more information (including a workaround).
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&init_blast(\&parse_usage);
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if(!@ARGV and $opt_in) { push @ARGV, $opt_in; }
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# Building object(s) from files specified on command line.
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# Each file should contain one report.
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# Note that we don't really need to capture the $blast_object
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# created by create_blast() since we can always access it via
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# the global $blastObj defined in blast_config.pl.
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# However, doing so makes things more obvious.
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$MONITOR && print STDERR "\nParsing Blast report file(s).\n";
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# Load the file into the Blast parameters.
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next unless -f and -s;
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$blastParam{-file} = $_;
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# Create the Blast object with the specified parameters.
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# Using functions provided by blast_config.pl
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# which also supplies $blastObj.
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$blast_obj = &create_blast;
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$opt_table ? &print_table($blast_obj) : &show_results($blast_obj);
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$opt_compress && $blast_obj->compress_file;
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$blast_obj->destroy(); # important when crunching lots of reports.
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my $er = "\nFILE: $blastParam{-file}\n$@\n";
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print STDERR ".", $count % 50 ? '' : "\n";
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# @ARGV is empty. Build Blast objects from STDIN stream.
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# May contain one or more reports.
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print STDERR "\nParsing Blast stream from STDIN.\n";
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# Process each Blast as you go.
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$blastParam{-exec_func} = \&print_table;
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# Alternatively, try this:
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#? $blastParam{-exec_func} = \&display_hit_info();
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# Save all the Blast objects.
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$blastParam{-save_array} = \@objects;
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eval { &parse_stream; };
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die "\n*** TROUBLE:\n$@\n";
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printf STDERR "\n*** %d Blast reports produced fatal errors:\n", scalar(@errs);
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foreach(@errs) { print STDERR $_; }
added
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examples/blast/parse_blast.pl
