#!/usr/bin/env perl
+# Copyright (C) 2007-2009 Martin A. Hansen.
+
+# This program is free software; you can redistribute it and/or
+# modify it under the terms of the GNU General Public License
+# as published by the Free Software Foundation; either version 2
+# of the License, or (at your option) any later version.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, write to the Free Software
+# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+
+# http://www.gnu.org/copyleft/gpl.html
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DESCRIPTION <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# BLAST sequences in the stream against a specified database or genome.
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
use warnings;
use strict;
+use Maasha::Biopieces;
+use Maasha::Common;
+use Maasha::Seq;
+use Maasha::Fasta;
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+my ( $options, $in, $out, $tmp_dir, $tmp_in, $tmp_out, $q_type, $s_type, $record, $entry,
+ $fh_in, $fh_out, $progs_ok, $program );
+
+$progs_ok = 'blastn,blastp,tblastn,blastx,tblastx';
+
+$options = Maasha::Biopieces::parse_options(
+ [
+ { long => 'database', short => 'd', type => 'file', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
+ { long => 'genome', short => 'g', type => 'genome', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
+ { long => 'program', short => 'p', type => 'string', mandatory => 'no', default => undef, allowed => $progs_ok, disallowed => undef },
+ { long => 'e_val', short => 'e', type => 'float', mandatory => 'no', default => 10, allowed => undef, disallowed => undef },
+ { long => 'filter', short => 'f', type => 'string', mandatory => 'no', default => 'no', allowed => 'yes,no', disallowed => undef },
+ { long => 'cpus', short => 'c', type => 'uint', mandatory => 'no', default => 1, allowed => undef, disallowed => 0 },
+ { long => 'no_gaps', short => 'G', type => 'flag', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
+ { long => 'megablast', short => 'm', type => 'flag', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
+ { long => 'extend_threshold', short => 'E', type => 'uint', mandatory => 'no', default => 0, allowed => undef, disallowed => undef },
+ { long => 'word_size', short => 'W', type => 'uint', mandatory => 'no', default => 0, allowed => undef, disallowed => undef },
+ { long => 'single_hit', short => 's', type => 'flag', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
+ ]
+);
+
+Maasha::Common::error( qq(both --database and --genome specified) ) if $options->{ "genome" } and $options->{ "database" };
+Maasha::Common::error( qq(no --database or --genome specified) ) if not $options->{ "genome" } and not $options->{ "database" };
+
+$in = Maasha::Biopieces::read_stream( $options->{ "stream_in" } );
+$out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } );
+
+$options->{ "database" } = "$ENV{ 'BP_DATA' }/genomes/$options->{ 'genome' }/blast/$options->{ 'genome' }.fna" if $options->{ 'genome' };
+
+$tmp_dir = Maasha::Biopieces::get_tmpdir();
+$tmp_in = "$tmp_dir/blast_query.seq";
+$tmp_out = "$tmp_dir/blast.result";
+
+$fh_out = Maasha::Filesys::file_write_open( $tmp_in );
+
+while ( $record = Maasha::Biopieces::get_record( $in ) )
+{
+ if ( $entry = Maasha::Fasta::biopiece2fasta( $record ) )
+ {
+ $q_type = Maasha::Seq::seq_guess_type( $record->{ 'SEQ' } ) if not $q_type;
+
+ Maasha::Fasta::put_entry( $entry, $fh_out );
+ }
+
+ Maasha::Biopieces::put_record( $record, $out );
+}
+
+close $fh_out;
+
+$s_type = guess_database_type( $options->{ 'database' } );
+
+$program = $options->{ 'program' } || guess_program( $q_type, $s_type );
+
+if ( $options->{ 'filter' } eq 'yes' ) {
+ $options->{ 'filter' } = 'T';
+} else {
+ $options->{ 'filter' } = 'F';
+}
+
+if ( $options->{ 'no_gaps' } ) {
+ $options->{ 'gapped' } = 'F';
+} else {
+ $options->{ 'gapped' } = 'T';
+}
+
+if ( $options->{ 'megablast' } ) {
+ $options->{ 'megablast' } = 'T';
+} else {
+ $options->{ 'megablast' } = 'F';
+}
+
+if ( $options->{ 'single_hit' } ) {
+ $options->{ 'single_hit' } = 1
+} else {
+ $options->{ 'single_hit' } = 0
+}
+
+if ( $options->{ 'verbose' } )
+{
+ Maasha::Common::run(
+ "blastall",
+ join( " ",
+ "-p $program",
+ "-e $options->{ 'e_val' }",
+ "-a $options->{ 'cpus' }",
+ "-g $options->{ 'gapped' }",
+ "-n $options->{ 'megablast' }",
+ "-m 8",
+ "-i $tmp_in",
+ "-d $options->{ 'database' }",
+ "-F $options->{ 'filter' }",
+ "-P $options->{ 'single_hit' }",
+ "-W $options->{ 'word_size' }",
+ "-f $options->{ 'extend_threshold' }",
+ "-o $tmp_out",
+ )
+ );
+}
+else
+{
+ Maasha::Common::run(
+ "blastall",
+ join( " ",
+ "-p $program",
+ "-e $options->{ 'e_val' }",
+ "-a $options->{ 'cpus' }",
+ "-m 8",
+ "-i $tmp_in",
+ "-d $options->{ 'database' }",
+ "-F $options->{ 'filter' }",
+ "-P $options->{ 'single_hit' }",
+ "-W $options->{ 'word_size' }",
+ "-f $options->{ 'extend_threshold' }",
+ "-o $tmp_out",
+ "> /dev/null 2>&1"
+ )
+ );
+}
+
+unlink $tmp_in;
+
+$fh_in = Maasha::Filesys::file_read_open( $tmp_out );
+
+while ( $entry = get_tab_entry( $fh_in ) )
+{
+ $record = blast_tab2biopiece( $entry );
+
+ Maasha::Biopieces::put_record( $record, $out );
+}
+
+close $fh_out;
+
+unlink $tmp_out;
+
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> SUBROUTINES <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+sub guess_database_type
+{
+ # Martin A. Hansen, May 2009
+
+ # Guess the type of BLAST database from the database
+ # filename assuming that it is a protein database if
+ # a .phr file exists.
+
+ # Returns string;
+ if ( -f $options->{ 'database' } . ".phr" or -f $options->{ 'database' } . ".pal" ) {
+ return "PROTEIN";
+ } else {
+ return "NUCLEOTIDE";
+ }
+}
+
+
+sub guess_program
+{
+ # Martin A. Hansen, May 2009
+
+ # Guess what BLAST program to use based on the
+ # sequence type of the query and subject sequences.
+
+ my ( $q_type, # query sequence type
+ $s_type, # subject sequence type
+ ) = @_;
+
+ # Returns string.
+
+ my ( $program );
+
+ if ( $q_type ne "PROTEIN" and $s_type ne "PROTEIN" ) {
+ $program = "blastn";
+ } elsif ( $q_type eq "PROTEIN" and $s_type eq "PROTEIN" ) {
+ $program = "blastp";
+ } elsif ( $q_type ne "PROTEIN" and $s_type eq "PROTEIN" ) {
+ $program = "blastx";
+ } elsif ( $q_type eq "PROTEIN" and $s_type ne "PROTEIN" ) {
+ $program = "tblastn";
+ }
+
+ return $program;
+}
+
+
+
+sub get_tab_entry
+{
+ # Martin A. Hansen, May 2009.
+
+ # Get the next tabular entry from a filehandle to a BLAST file.
+
+ my ( $fh, # filehandle
+ ) = @_;
+
+ # Returns a list
+
+ my ( $line, @fields );
+
+ while ( $line = <$fh> )
+ {
+ next if $line =~ /^#/;
+
+ @fields = split /\s+/, $line;
+
+ return wantarray ? @fields : \@fields;
+ }
+
+ return undef;
+}
+
+
+sub blast_tab2biopiece
+{
+ # Martin A. Hansen, May 2009.
+
+ # Get the next BLAST tabular entry and convert it to
+ # a biopiece record that is returned.
+
+ my ( $entry, # BLAST tabular entry
+ ) = @_;
+
+ # Returns a hashref.
+
+ my ( %record );
+
+ $record{ "REC_TYPE" } = "BLAST";
+ $record{ "Q_ID" } = $entry->[ 0 ];
+ $record{ "S_ID" } = $entry->[ 1 ];
+ $record{ "IDENT" } = $entry->[ 2 ];
+ $record{ "ALIGN_LEN" } = $entry->[ 3 ];
+ $record{ "MISMATCHES" } = $entry->[ 4 ];
+ $record{ "GAPS" } = $entry->[ 5 ];
+ $record{ "Q_BEG" } = $entry->[ 6 ] - 1; # BLAST is 1-based
+ $record{ "Q_END" } = $entry->[ 7 ] - 1; # BLAST is 1-based
+ $record{ "S_BEG" } = $entry->[ 8 ] - 1; # BLAST is 1-based
+ $record{ "S_END" } = $entry->[ 9 ] - 1; # BLAST is 1-based
+ $record{ "E_VAL" } = $entry->[ 10 ];
+ $record{ "BIT_SCORE" } = $entry->[ 11 ];
+
+ if ( $record{ "S_BEG" } > $record{ "S_END" } )
+ {
+ $record{ "STRAND" } = '-';
+
+ ( $record{ "S_BEG" }, $record{ "S_END" } ) = ( $record{ "S_END" }, $record{ "S_BEG" } );
+ }
+ else
+ {
+ $record{ "STRAND" } = '+';
+ }
+
+ return wantarray ? %record : \%record;
+}
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+BEGIN
+{
+ Maasha::Biopieces::status_set();
+}
+
+
+END
+{
+ Maasha::Biopieces::status_log();
+}
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
-use Maasha::Biotools;
+__END__
projects / biopieces.git / blobdiff