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svn path=/bioperl-live/tags/release-0-05/; revision=970
bioperl · Apr 25, 1999 · d0bcf4b · d0bcf4b
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commit d0bcf4b
Showing 1 changed file with 146 additions and 0 deletions.
diff --git a/examples/blast/run.pl b/examples/blast/run.pl
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+#!/usr/bin/perl -w
+
+#---------------------------------------------------------------------------
+# PROGRAM  : run.pl
+# PURPOSE  : To demonstrate how to run and parse Blast reports using the 
+#            Bio::Tools::Blast.pm module.
+# AUTHOR   : Steve A. Chervitz (sac@genome.stanford.edu)
+# CREATED  : 3 Feb 1998
+# REVISION : $Id$
+# WEBSITE  : http://bio.perl.org/Projects/Blast/
+# USAGE    : run.pl -h
+# EXAMPLES : run.pl -eg
+#
+# INSTALLATION: 
+#    Set the require ".../blast_config.pl" to point to the proper location
+#    of the blast_config.pl file. See blast_config.pl for additional steps.
+#
+# This is basically identical to the parse.pl script 
+# with additional options added for running a Blast report.
+#
+# This demo script does not exercise all of the functionality of the Blast object.
+# See the POD for the Bio::Tools::Blast.pm, accessible from the above URL.
+#
+# MODIFIED:
+#  sac, 16 Jun 1998: Added installation comment, require statement comments.
+#                    Minor example change.
+#---------------------------------------------------------------------------
+
+# Using blast_config.pl in the examples/blast distribution directory:
+require "blast_config.pl"; 
+# Proper path to blast_config.pl after you install it in your system:
+#require "/share/www-data/html/perlOOP/bioperl/bin/blast/blast_config.pl";
+
+require Bio::Seq;
+
+# Using vars from blast_config to prevent warning messages under -w.
+use vars qw($ID $VERSION $DESC $MONITOR %runParam %blastParam 
+	    $opt_seq $opt_seqfmt $opt_html $opt_parse 
+	    $opt_dna $opt_table $opt_compress);
+
+$ID      = 'run.pl';
+$VERSION = 0.1;
+$DESC    = "Demonstrates running a single Blast report using Bio::Tools::Blast.pm";
+
+#--------------
+sub run_usage {
+#--------------
+    print STDERR "$ID, v$VERSION\n$DESC.\n";
+    print STDERR <<"QQ_USAGE_QQ";
+
+Usage: run.pl [ parameters ] seq.file
+
+run.pl obtains the query sequence to be Blasted from a 
+file specified on the command line. 
+For running multiple sequences, see blast_seqs.pl.
+
+QQ_USAGE_QQ
+
+    print STDERR "Hit <RETURN> to view parameters."; <STDIN>;
+    &blast_run_params;
+    &blast_general_params;
+}
+
+#------------
+sub examples {
+#------------
+<<"QQ_EG_QQ";
+(Run these in the examples/blast/ directory of the distribution.)
+
+  ./$ID seq/yel009c.fasta -prog blastp -db swissprot -signif 1e-15 -html > out.gap2
+  ./$ID seq/ymr284w.fasta -prog blastp -nogap -db yeast > out.nogap2
+  ./$ID seq/acc1.dna.fasta -prog blastx -db ecoli -vers 1 -signif 1e-20 -nomon > out1
+  ./$ID -html -noparse -prog blastp -db nr seq/yel009c.fasta 
+
+QQ_EG_QQ
+}
+
+##### MAIN ######
+
+&init_blast(\&run_usage );
+
+if(not -s ($opt_seq ||= $ARGV[0]))  {
+    die "\nPlease specify a file containing a sequence.\n",
+    "    Use the -seq option or list the file as the last arg.\n\n";
+}
+
+
+&set_blast_params();
+
+# Create a new sequence object (query sequence)
+$qseq = new Bio::Seq ( -file => $opt_seq,
+		       -ffmt => $opt_seqfmt,
+		       # $opt_dna is no longer used.
+		       # Automatic sequence type detection is still
+		       # an open issue.
+		       # -type => $opt_dna ? 'Dna' : 'Amino'
+		     );
+
+#print "\nSEQ ${\$qseq->id} IN FASTA FORMAT:\n";
+#print $qseq->layout('Fasta'); <STDIN>;
+
+if($qseq->id =~ /^no_id/i) {
+    $opt_seq =~ /\/([\w_.]+)$/;
+    $qseq->id($1 || $opt_seq);
+}
+
+# Load the sequence object in to the run parameters
+# and then load the run parameters into the Blast object
+# parameters (used for constructing the Blast object).
+$runParam{-seqs}  = [ $qseq ];
+$blastParam{-run} = \%runParam;
+
+
+# Create the Blast object with the specified parameters.
+# This will launch the analysis and then parse it (if desired).
+# Note this uses the global $blastObj from blast_config.pl.
+
+eval { 
+    $blastObj = &create_blast;  # provided by blast_config.pl
+    $file = $blastObj->file;
+    $MONITOR and print STDERR "Blast output saved to: $file\n\n";
+
+    if($opt_html and not $opt_parse) {
+
+# Uncomment the following 4 lines to send the HTML version to STDOUT.
+#	 $file = $opt_parse ? "$file.html" : $file;
+#	 open( HTML, $file) or die "Can't open HTML file: $file: $!\n\n";
+#	 while(<HTML>) { print; }
+#	 close HTML;
+	 exit 0;
+    }
+};
+
+$@ and die $@;
+
+$MONITOR = 0;
+# Run some functions provided by blast_config.pl:
+$opt_table ? &print_table($blastObj) : &show_results($blastObj);
+
+$opt_compress && (print STDERR "\nCompressing file.", $blastObj->compress_file);
+
+&wrap_up_blast;
+
+
+
+