From f640e8319ec14c27b355eaa69cda5ac4ab9e35f2 Mon Sep 17 00:00:00 2001 From: martinahansen Date: Sun, 24 May 2009 20:45:58 +0000 Subject: [PATCH] migrated assemble_tag_contigs git-svn-id: http://biopieces.googlecode.com/svn/trunk@403 74ccb610-7750-0410-82ae-013aeee3265d --- bp_bin/assemble_tag_contigs | 122 ++++++++++++++++++++++++++++++++- code_c/Maasha/src/inc/common.h | 5 +- code_perl/Maasha/BioRun.pm | 71 ------------------- code_perl/Maasha/UCSC/BED.pm | 8 +-- 4 files changed, 126 insertions(+), 80 deletions(-) diff --git a/bp_bin/assemble_tag_contigs b/bp_bin/assemble_tag_contigs index fdf5bd2..8bdeda5 100755 --- a/bp_bin/assemble_tag_contigs +++ b/bp_bin/assemble_tag_contigs @@ -1,6 +1,122 @@ -#!/usr/bin/env perl +#!/usr/bin/env perl -w + +# 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 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + +# Assemble tag contigs from overlapping BED type records in the stream. + +# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + -use warnings; use strict; +use Maasha::Biopieces; +use Maasha::Filesys; +use Maasha::UCSC::BED; + + +# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + +my ( $run_time_beg, $run_time_end, $options, $in, $out, $tmp_dir, $bed_file, $tag_file, $fh_in, $fh_out, + $cols, $record, $bed_entry, $file_hash, $chr, $strand ); + +$options = Maasha::Biopieces::parse_options( + [ + { long => 'check', short => 'C', type => 'flag', mandatory => 'no', default => undef, allowed => undef, disallowed => undef }, + ] +); + +$in = Maasha::Biopieces::read_stream( $options->{ "stream_in" } ); +$out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } ); + +$tmp_dir = Maasha::Biopieces::get_tmpdir(); + +$bed_file = "$tmp_dir/assemble_tag_contigs.bed"; +$fh_out = Maasha::Filesys::file_write_open( $bed_file ); +$cols = 6; # we only need the first 6 BED columns + +while ( $record = Maasha::Biopieces::get_record( $in ) ) +{ + if ( $bed_entry = Maasha::UCSC::BED::biopiece2bed( $record, $cols ) ) + { + $strand = $record->{ 'STRAND' } || '+'; + + Maasha::UCSC::BED::bed_entry_put( $bed_entry, $fh_out, $cols, $options->{ 'check' } ); + } +} + +close $fh_out; + +$file_hash = Maasha::UCSC::BED::bed_file_split_on_chr( $bed_file, $tmp_dir, $cols ); + +unlink $bed_file; + +foreach $chr ( sort keys %{ $file_hash } ) +{ + $bed_file = $file_hash->{ $chr }; + $tag_file = "$bed_file.tc"; + + Maasha::Common::run( "bed2tag_contigs", "< $bed_file > $tag_file" ); + + $fh_in = Maasha::Filesys::file_read_open( $tag_file ); + + while ( $bed_entry = Maasha::UCSC::BED::bed_entry_get( $fh_in, $cols, $options->{ 'check' } ) ) + { + if ( $record = Maasha::UCSC::BED::bed2biopiece( $bed_entry ) ) { + Maasha::Biopieces::put_record( $record, $out ); + } + } + + close $fh_in; + + unlink $bed_file; + unlink $tag_file; +} + +Maasha::Filesys::dir_remove( $tmp_dir ); + + +# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + +BEGIN +{ + $run_time_beg = Maasha::Biopieces::run_time(); + + Maasha::Biopieces::log_biopiece(); +} + +END +{ + Maasha::Biopieces::close_stream( $in ); + Maasha::Biopieces::close_stream( $out ); + + $run_time_end = Maasha::Biopieces::run_time(); + + Maasha::Biopieces::run_time_print( $run_time_beg, $run_time_end, $options ); +} + + +# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + +__END__ -use Maasha::BioRun; diff --git a/code_c/Maasha/src/inc/common.h b/code_c/Maasha/src/inc/common.h index 4d33bf7..b9e10a6 100644 --- a/code_c/Maasha/src/inc/common.h +++ b/code_c/Maasha/src/inc/common.h @@ -12,6 +12,7 @@ #include #include +typedef unsigned int uint; typedef unsigned char uchar; typedef unsigned short ushort; typedef long long llong; @@ -51,8 +52,8 @@ typedef char boolean; /* Function that prints "pong" to stderr. */ void maasha_ping(); -/* Return a binary number as a string of 1's and 0's. */ -char *bits2string( uint bin ); +// /* Return a binary number as a string of 1's and 0's. */ +// char *bits2string( uint bin ); /* >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<*/ diff --git a/code_perl/Maasha/BioRun.pm b/code_perl/Maasha/BioRun.pm index 32be349..d9973a8 100644 --- a/code_perl/Maasha/BioRun.pm +++ b/code_perl/Maasha/BioRun.pm @@ -130,7 +130,6 @@ sub run_script elsif ( $script eq "read_solid" ) { script_read_solid( $in, $out, $options ) } elsif ( $script eq "read_mysql" ) { script_read_mysql( $in, $out, $options ) } elsif ( $script eq "read_ucsc_config" ) { script_read_ucsc_config( $in, $out, $options ) } - elsif ( $script eq "assemble_tag_contigs" ) { script_assemble_tag_contigs( $in, $out, $options ) } elsif ( $script eq "length_seq" ) { script_length_seq( $in, $out, $options ) } elsif ( $script eq "uppercase_seq" ) { script_uppercase_seq( $in, $out, $options ) } elsif ( $script eq "complexity_seq" ) { script_complexity_seq( $in, $out, $options ) } @@ -329,12 +328,6 @@ sub get_options num|n=s ); } - elsif ( $script eq "assemble_tag_contigs" ) - { - @options = qw( - check|C - ); - } elsif ( $script eq "calc_fixedstep" ) { @options = qw( @@ -1696,70 +1689,6 @@ sub script_read_ucsc_config } -sub script_assemble_tag_contigs -{ - # Martin A. Hansen, November 2008. - - # Assemble tags from the stream into - # tag contigs. - - # The current implementation is quite - # slow because of heavy use of temporary - # files. - - my ( $in, # handle to in stream - $out, # handle to out stream - $options, # options hash - ) = @_; - - # Returns nothing. - - my ( $bed_file, $tag_file, $fh_in, $fh_out, $cols, $record, $bed_entry, $file_hash, $chr, $strand ); - - $bed_file = "$BP_TMP/assemble_tag_contigs.bed"; - $fh_out = Maasha::Filesys::file_write_open( $bed_file ); - $cols = 6; # we only need the first 6 BED columns - - while ( $record = Maasha::Biopieces::get_record( $in ) ) - { - if ( $bed_entry = Maasha::UCSC::BED::biopiece2bed( $record, $cols ) ) - { - $strand = $record->{ 'STRAND' } || '+'; - - Maasha::UCSC::BED::bed_entry_put( $bed_entry, $fh_out, $cols, $options->{ 'check' } ); - } - } - - close $fh_out; - - $file_hash = Maasha::UCSC::BED::bed_file_split_on_chr( $bed_file, $BP_TMP, $cols ); - - unlink $bed_file; - - foreach $chr ( sort keys %{ $file_hash } ) - { - $bed_file = $file_hash->{ $chr }; - $tag_file = "$bed_file.tc"; - - Maasha::Common::run( "bed2tag_contigs", "< $bed_file > $tag_file" ); - - $fh_in = Maasha::Filesys::file_read_open( $tag_file ); - - while ( $bed_entry = Maasha::UCSC::BED::bed_entry_get( $fh_in, $cols, $options->{ 'check' } ) ) - { - if ( $record = Maasha::UCSC::BED::bed2biopiece( $bed_entry ) ) { - Maasha::Biopieces::put_record( $record, $out ); - } - } - - close $fh_in; - - unlink $bed_file; - unlink $tag_file; - } -} - - sub script_length_seq { # Martin A. Hansen, August 2007. diff --git a/code_perl/Maasha/UCSC/BED.pm b/code_perl/Maasha/UCSC/BED.pm index a7a878f..3b57757 100644 --- a/code_perl/Maasha/UCSC/BED.pm +++ b/code_perl/Maasha/UCSC/BED.pm @@ -130,10 +130,10 @@ sub bed_entry_get $line = <$fh>; - $line =~ tr/\n\r//d; # some people have carriage returns in their BED files -> Grrrr - return if not defined $line; + $line =~ tr/\n\r//d; # some people have carriage returns in their BED files -> Grrrr + if ( not defined $cols ) { $cols = 1 + $line =~ tr/\t//; } @@ -554,7 +554,7 @@ sub biopiece2bed $bed_entry[ blockCount ] = $bp_record->{ "BLOCK_COUNT" }; $bed_entry[ blockSizes ] = $bp_record->{ "BLOCK_LENS" }; $bed_entry[ blockStarts ] = join ",", @begs; - $bed_entry[ thickEnd ]; + $bed_entry[ thickEnd ] = $bp_record->{ "THICK_END" } + 1; } elsif ( defined $bp_record->{ "BLOCK_COUNT" } and defined $bp_record->{ "BLOCK_LENS" } and @@ -563,7 +563,7 @@ sub biopiece2bed $bed_entry[ blockCount ] = $bp_record->{ "BLOCK_COUNT" }; $bed_entry[ blockSizes ] = $bp_record->{ "BLOCK_LENS" }; $bed_entry[ blockStarts ] = $bp_record->{ "Q_BEGS" }; - $bed_entry[ thickEnd ]; + $bed_entry[ thickEnd ] = $bp_record->{ "THICK_END" } + 1; } return wantarray ? @bed_entry : \@bed_entry; -- 2.39.5