From 8a75ef30ec2546aac6c7b668849e9750dab2f315 Mon Sep 17 00:00:00 2001 From: martinahansen Date: Fri, 5 Jun 2009 08:54:29 +0000 Subject: [PATCH] almost done git-svn-id: http://biopieces.googlecode.com/svn/trunk@482 74ccb610-7750-0410-82ae-013aeee3265d --- bp_bin/get_genome_align | 188 +++++++++++++++++++++++++++++++++++- bp_bin/get_genome_phastcons | 131 ++++++++++++++++++++++++- bp_bin/get_genome_seq | 16 +-- code_perl/Maasha/BioRun.pm | 176 --------------------------------- code_perl/Maasha/Config.pm | 72 -------------- 5 files changed, 321 insertions(+), 262 deletions(-) diff --git a/bp_bin/get_genome_align b/bp_bin/get_genome_align index fdf5bd2..a346b9c 100755 --- a/bp_bin/get_genome_align +++ b/bp_bin/get_genome_align @@ -1,6 +1,188 @@ -#!/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 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + +# Extract alignments from a multiple genome alignment. + +# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + -use warnings; use strict; +use Maasha::Biopieces; +use Maasha::Common; +use Maasha::UCSC; +use Maasha::Filesys; + + +# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + +my ( $run_time_beg, $run_time_end, $options, $in, $out, $record, $tmp_dir, $maf_track, $align, $align_num, $beg, $end, $len, $entry ); + +$options = Maasha::Biopieces::parse_options( + [ + { long => 'genome', short => 'g', type => 'genome', mandatory => 'yes', default => undef, allowed => undef, disallowed => undef }, + { long => 'chr', short => 'c', type => 'string', mandatory => 'no', default => undef, allowed => undef, disallowed => undef }, + { long => 'beg', short => 'b', type => 'uint', mandatory => 'no', default => undef, allowed => undef, disallowed => 0 }, + { long => 'end', short => 'e', type => 'uint', mandatory => 'no', default => undef, allowed => undef, disallowed => 0 }, + { long => 'len', short => 'l', type => 'uint', mandatory => 'no', default => undef, allowed => undef, disallowed => 0 }, + { long => 'strand', short => 's', type => 'string', mandatory => 'no', default => '+', allowed => '+,-', disallowed => undef }, + ] +); + +$in = Maasha::Biopieces::read_stream( $options->{ "stream_in" } ); +$out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } ); + +$tmp_dir = Maasha::Biopieces::get_tmpdir(); + +$align_num = 1; + +$maf_track = maf_track( $options->{ "genome" } ); + +if ( $options->{ "chr" } and $options->{ "beg" } and ( $options->{ "end" } or $options->{ "len" } ) ) +{ + $beg = $options->{ "beg" } - 1; + + if ( $options->{ "end" } ) { + $end = $options->{ "end" }; + } elsif ( $options->{ "len" } ) { + $end = $beg + $options->{ "len" }; + } + + $align = Maasha::UCSC::maf_extract( $tmp_dir, $options->{ "genome" }, $maf_track, $options->{ "chr" }, $beg, $end, $options->{ "strand" } ); + + foreach $entry ( @{ $align } ) + { + $entry->{ "CHR" } = $record->{ "CHR" }; + $entry->{ "CHR_BEG" } = $record->{ "CHR_BEG" }; + $entry->{ "CHR_END" } = $record->{ "CHR_END" }; + $entry->{ "STRAND" } = $record->{ "STRAND" } || '+'; + $entry->{ "Q_ID" } = $record->{ "Q_ID" }; + $entry->{ "SCORE" } = $record->{ "SCORE" }; + + Maasha::Biopieces::put_record( $entry, $out ); + } +} + +while ( $record = Maasha::Biopieces::get_record( $in ) ) +{ + if ( $record->{ "REC_TYPE" } eq "BED" ) + { + $align = Maasha::UCSC::maf_extract( $tmp_dir, $options->{ "genome" }, $maf_track, $record->{ "CHR" }, $record->{ "CHR_BEG" }, $record->{ "CHR_END" }, $record->{ "STRAND" } ); + } + elsif ( $record->{ "REC_TYPE" } eq "VMATCH" ) + { + $align = Maasha::UCSC::maf_extract( $tmp_dir, $options->{ "genome" }, $maf_track, $record->{ "S_ID" }, $record->{ "S_BEG" }, $record->{ "S_END" } + 1, $record->{ "STRAND" } ); + } + elsif ( $record->{ "REC_TYPE" } eq "PSL" ) + { + $align = Maasha::UCSC::maf_extract( $tmp_dir, $options->{ "genome" }, $maf_track, $record->{ "S_ID" }, $record->{ "S_BEG" }, $record->{ "S_END" }, $record->{ "STRAND" } ); + } + elsif ( $record->{ "REC_TYPE" } eq "BLAST" ) + { + $align = Maasha::UCSC::maf_extract( $tmp_dir, $options->{ "genome" }, $maf_track, $record->{ "S_ID" }, $record->{ "S_BEG" }, $record->{ "S_END" }, $record->{ "STRAND" } ); + } + + foreach $entry ( @{ $align } ) + { + $entry->{ "CHR" } = $record->{ "CHR" }; + $entry->{ "CHR_BEG" } = $record->{ "CHR_BEG" }; + $entry->{ "CHR_END" } = $record->{ "CHR_END" }; + $entry->{ "STRAND" } = $record->{ "STRAND" }; + $entry->{ "Q_ID" } = $record->{ "Q_ID" }; + $entry->{ "SCORE" } = $record->{ "SCORE" }; + + Maasha::Biopieces::put_record( $entry, $out ); + } + + $align_num++; +} + +Maasha::Filesys::dir_remove( $tmp_dir ); + + +# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> SUBROUTINES <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + +sub maf_track +{ + # Martin A. Hansen, April 2008. + + # Given a genome returns the corresponding mafTrack database table name. + + my ( $genome, # genome to lookup. + ) = @_; + + # Returns a string. + + my ( %hash ); + + # The below has should be in a config file - fix later. + + %hash = ( + danRer4 => 'multiz7way', + dm2 => 'multiz15way', + dm3 => 'multiz15way', + fr2 => 'multiz7way', + galGal3 => 'multiz7way', + gasAcu1 => 'multiz7way', + hg18 => 'multiz17way', + mm8 => 'multiz17way', + mm9 => 'multiz17way', + oryLat1 => 'multiz7way', + panTro2 => 'multiz17way', + tetNig1 => 'multiz7way', + ); + + Maasha::Common::error( qw(multiz track not found) ) if not exists $hash{ $genome }; + + return $hash{ $genome }; +} + + +# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + +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/bp_bin/get_genome_phastcons b/bp_bin/get_genome_phastcons index fdf5bd2..9fc75ee 100755 --- a/bp_bin/get_genome_phastcons +++ b/bp_bin/get_genome_phastcons @@ -1,6 +1,131 @@ -#!/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 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + +# Extract phastcons scores from a specified genome. + +# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + -use warnings; use strict; +use Maasha::Biopieces; +use Maasha::Filesys; +use Maasha::UCSC; + + +# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + +my ( $run_time_beg, $run_time_end, $options, $in, $out, $phastcons_file, $phastcons_index, $index, $fh_phastcons, $scores, $record ); + +$options = Maasha::Biopieces::parse_options( + [ + { long => 'genome', short => 'g', type => 'genome', mandatory => 'yes', default => undef, allowed => undef, disallowed => undef }, + { long => 'chr', short => 'c', type => 'string', mandatory => 'no', default => undef, allowed => undef, disallowed => undef }, + { long => 'beg', short => 'b', type => 'uint', mandatory => 'no', default => undef, allowed => undef, disallowed => 0 }, + { long => 'end', short => 'e', type => 'uint', mandatory => 'no', default => undef, allowed => undef, disallowed => 0 }, + { long => 'len', short => 'l', type => 'uint', mandatory => 'no', default => undef, allowed => undef, disallowed => 0 }, + { long => 'flank', short => 'f', type => 'uint', mandatory => 'no', default => 0, allowed => undef, disallowed => undef }, + ] +); + +$in = Maasha::Biopieces::read_stream( $options->{ "stream_in" } ); +$out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } ); + +$phastcons_file = "$ENV{ 'BP_DATA' }/genomes/$options->{ 'genome' }/phastcons/$options->{ 'genome' }.pp"; +$phastcons_index = "$ENV{ 'BP_DATA' }/genomes/$options->{ 'genome' }/phastcons/$options->{ 'genome' }.pp.index"; + +$index = Maasha::UCSC::fixedstep_index_retrieve( $phastcons_index ); +$fh_phastcons = Maasha::Filesys::file_read_open( $phastcons_file ); + +if ( defined $options->{ "chr" } and defined $options->{ "beg" } and ( defined $options->{ "end" } or defined $options->{ "len" } ) ) +{ + $options->{ "beg" } -= 1; # request is 1-based + $options->{ "end" } -= 1; # request is 1-based + + if ( $options->{ "len" } ) { + $options->{ "end" } = $options->{ "beg" } + $options->{ "len" } - 1; + } + + $scores = Maasha::UCSC::fixedstep_index_lookup( $index, $fh_phastcons, $options->{ "chr" }, $options->{ "beg" }, $options->{ "end" }, $options->{ "flank" } ); + + $record->{ "CHR" } = $options->{ "chr" }; + $record->{ "CHR_BEG" } = $options->{ "beg" } - $options->{ "flank" }; + $record->{ "CHR_END" } = $options->{ "end" } + $options->{ "flank" }; + + $record->{ "PHASTCONS" } = join ",", @{ $scores }; + $record->{ "PHAST_COUNT" } = scalar @{ $scores }; # DEBUG + + Maasha::Biopieces::put_record( $record, $out ); +} + +while ( $record = Maasha::Biopieces::get_record( $in ) ) +{ + if ( $record->{ "REC_TYPE" } eq "BED" ) + { + $scores = Maasha::UCSC::fixedstep_index_lookup( $index, $fh_phastcons, $record->{ "CHR" }, $record->{ "CHR_BEG" }, $record->{ "CHR_END" }, $options->{ "flank" } ); + } + elsif ( $record->{ "REC_TYPE" } eq "PSL" ) + { + $scores = Maasha::UCSC::fixedstep_index_lookup( $index, $fh_phastcons, $record->{ "S_ID" }, $record->{ "S_BEG" }, $record->{ "S_END" }, $options->{ "flank" } ); + } + elsif ( $record->{ "REC_TYPE" } eq "BLAST" ) + { + $scores = Maasha::UCSC::fixedstep_index_lookup( $index, $fh_phastcons, $record->{ "S_ID" }, $record->{ "S_BEG" }, $record->{ "S_END" }, $options->{ "flank" } ); + } + + $record->{ "PHASTCONS" } = join ",", @{ $scores } if @{ $scores }; +# $record->{ "PHAST_COUNT" } = @{ $scores } if @{ $scores }; # DEBUG + + Maasha::Biopieces::put_record( $record, $out ); +} + +close $fh_phastcons if $fh_phastcons; + + +# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< + + +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/bp_bin/get_genome_seq b/bp_bin/get_genome_seq index cde18f9..68c52bd 100755 --- a/bp_bin/get_genome_seq +++ b/bp_bin/get_genome_seq @@ -40,14 +40,14 @@ my ( $run_time_beg, $run_time_end, $options, $in, $out, $record, $genome_file, $ $options = Maasha::Biopieces::parse_options( [ - { long => 'genome', short => 'g', type => 'genome', mandatory => 'no', default => undef, allowed => undef, disallowed => undef }, - { long => 'chr', short => 'c', type => 'string', mandatory => 'no', default => undef, allowed => undef, disallowed => undef }, - { long => 'beg', short => 'b', type => 'uint', mandatory => 'no', default => undef, allowed => undef, disallowed => 0 }, - { long => 'end', short => 'e', type => 'uint', mandatory => 'no', default => undef, allowed => undef, disallowed => 0 }, - { long => 'len', short => 'l', type => 'uint', mandatory => 'no', default => undef, allowed => undef, disallowed => 0 }, - { long => 'flank', short => 'f', type => 'uint', mandatory => 'no', default => 0, allowed => undef, disallowed => undef }, - { long => 'mask', short => 'm', type => 'flag', mandatory => 'no', default => undef, allowed => undef, disallowed => undef }, - { long => 'splice', short => 's', type => 'flag', mandatory => 'no', default => undef, allowed => undef, disallowed => undef }, + { long => 'genome', short => 'g', type => 'genome', mandatory => 'yes', default => undef, allowed => undef, disallowed => undef }, + { long => 'chr', short => 'c', type => 'string', mandatory => 'no', default => undef, allowed => undef, disallowed => undef }, + { long => 'beg', short => 'b', type => 'uint', mandatory => 'no', default => undef, allowed => undef, disallowed => 0 }, + { long => 'end', short => 'e', type => 'uint', mandatory => 'no', default => undef, allowed => undef, disallowed => 0 }, + { long => 'len', short => 'l', type => 'uint', mandatory => 'no', default => undef, allowed => undef, disallowed => 0 }, + { long => 'flank', short => 'f', type => 'uint', mandatory => 'no', default => 0, allowed => undef, disallowed => undef }, + { long => 'mask', short => 'm', type => 'flag', mandatory => 'no', default => undef, allowed => undef, disallowed => undef }, + { long => 'splice', short => 's', type => 'flag', mandatory => 'no', default => undef, allowed => undef, disallowed => undef }, ] ); diff --git a/code_perl/Maasha/BioRun.pm b/code_perl/Maasha/BioRun.pm index 5cd943a..664da78 100644 --- a/code_perl/Maasha/BioRun.pm +++ b/code_perl/Maasha/BioRun.pm @@ -111,8 +111,6 @@ sub run_script if ( $script eq "print_usage" ) { script_print_usage( $in, $out, $options ) } elsif ( $script eq "complexity_seq" ) { script_complexity_seq( $in, $out, $options ) } - elsif ( $script eq "get_genome_align" ) { script_get_genome_align( $in, $out, $options ) } - elsif ( $script eq "get_genome_phastcons" ) { script_get_genome_phastcons( $in, $out, $options ) } close $in if defined $in; close $out; @@ -142,28 +140,6 @@ sub get_options data_in|i=s ); } - elsif ( $script eq "get_genome_align" ) - { - @options = qw( - genome|g=s - chr|c=s - beg|b=s - end|e=s - len|l=s - strand|s=s - ); - } - elsif ( $script eq "get_genome_phastcons" ) - { - @options = qw( - genome|g=s - chr|c=s - beg|b=s - end|e=s - len|l=s - flank|f=s - ); - } push @options, qw( stream_in|I=s @@ -260,7 +236,6 @@ sub get_options } } - Maasha::Common::error( qq(no --genome specified) ) if $script =~ /get_genome_align|get_genome_phastcons/ and not $options{ "genome" }; return wantarray ? %options : \%options; } @@ -331,157 +306,6 @@ sub script_complexity_seq } -sub script_get_genome_align -{ - # Martin A. Hansen, April 2008. - - # Gets a subalignment from a multiple genome alignment. - - my ( $in, # handle to in stream - $out, # handle to out stream - $options, # options hash - ) = @_; - - # Returns nothing. - - my ( $record, $maf_track, $align, $align_num, $beg, $end, $len, $entry ); - - $options->{ "strand" } ||= "+"; - - $align_num = 1; - - $maf_track = Maasha::Config::maf_track( $options->{ "genome" } ); - - if ( $options->{ "chr" } and $options->{ "beg" } and ( $options->{ "end" } or $options->{ "len" } ) ) - { - $beg = $options->{ "beg" } - 1; - - if ( $options->{ "end" } ) { - $end = $options->{ "end" }; - } elsif ( $options->{ "len" } ) { - $end = $beg + $options->{ "len" }; - } - - $align = Maasha::UCSC::maf_extract( $BP_TMP, $options->{ "genome" }, $maf_track, $options->{ "chr" }, $beg, $end, $options->{ "strand" } ); - - foreach $entry ( @{ $align } ) - { - $entry->{ "CHR" } = $record->{ "CHR" }; - $entry->{ "CHR_BEG" } = $record->{ "CHR_BEG" }; - $entry->{ "CHR_END" } = $record->{ "CHR_END" }; - $entry->{ "STRAND" } = $record->{ "STRAND" } || '+'; - $entry->{ "Q_ID" } = $record->{ "Q_ID" }; - $entry->{ "SCORE" } = $record->{ "SCORE" }; - - Maasha::Biopieces::put_record( $entry, $out ); - } - } - - while ( $record = Maasha::Biopieces::get_record( $in ) ) - { - if ( $record->{ "REC_TYPE" } eq "BED" ) - { - $align = Maasha::UCSC::maf_extract( $BP_TMP, $options->{ "genome" }, $maf_track, $record->{ "CHR" }, $record->{ "CHR_BEG" }, $record->{ "CHR_END" }, $record->{ "STRAND" } ); - } - elsif ( $record->{ "REC_TYPE" } eq "VMATCH" ) - { - $align = Maasha::UCSC::maf_extract( $BP_TMP, $options->{ "genome" }, $maf_track, $record->{ "S_ID" }, $record->{ "S_BEG" }, $record->{ "S_END" } + 1, $record->{ "STRAND" } ); - } - elsif ( $record->{ "REC_TYPE" } eq "PSL" ) - { - $align = Maasha::UCSC::maf_extract( $BP_TMP, $options->{ "genome" }, $maf_track, $record->{ "S_ID" }, $record->{ "S_BEG" }, $record->{ "S_END" }, $record->{ "STRAND" } ); - } - elsif ( $record->{ "REC_TYPE" } eq "BLAST" ) - { - $align = Maasha::UCSC::maf_extract( $BP_TMP, $options->{ "genome" }, $maf_track, $record->{ "S_ID" }, $record->{ "S_BEG" }, $record->{ "S_END" }, $record->{ "STRAND" } ); - } - - foreach $entry ( @{ $align } ) - { - $entry->{ "CHR" } = $record->{ "CHR" }; - $entry->{ "CHR_BEG" } = $record->{ "CHR_BEG" }; - $entry->{ "CHR_END" } = $record->{ "CHR_END" }; - $entry->{ "STRAND" } = $record->{ "STRAND" }; - $entry->{ "Q_ID" } = $record->{ "Q_ID" }; - $entry->{ "SCORE" } = $record->{ "SCORE" }; - - Maasha::Biopieces::put_record( $entry, $out ); - } - - $align_num++; - } -} - - -sub script_get_genome_phastcons -{ - # Martin A. Hansen, February 2008. - - # Get phastcons scores from genome intervals. - - my ( $in, # handle to in stream - $out, # handle to out stream - $options, # options hash - ) = @_; - - # Returns nothing. - - my ( $phastcons_file, $phastcons_index, $index, $fh_phastcons, $scores, $record ); - - $options->{ "flank" } ||= 0; - - $phastcons_file = Maasha::Config::genome_phastcons( $options->{ "genome" } ); - $phastcons_index = Maasha::Config::genome_phastcons_index( $options->{ "genome" } ); - - $index = Maasha::UCSC::fixedstep_index_retrieve( $phastcons_index ); - $fh_phastcons = Maasha::Common::read_open( $phastcons_file ); - - if ( defined $options->{ "chr" } and defined $options->{ "beg" } and ( defined $options->{ "end" } or defined $options->{ "len" } ) ) - { - $options->{ "beg" } -= 1; # request is 1-based - $options->{ "end" } -= 1; # request is 1-based - - if ( $options->{ "len" } ) { - $options->{ "end" } = $options->{ "beg" } + $options->{ "len" } - 1; - } - - $scores = Maasha::UCSC::fixedstep_index_lookup( $index, $fh_phastcons, $options->{ "chr" }, $options->{ "beg" }, $options->{ "end" }, $options->{ "flank" } ); - - $record->{ "CHR" } = $options->{ "chr" }; - $record->{ "CHR_BEG" } = $options->{ "beg" } - $options->{ "flank" }; - $record->{ "CHR_END" } = $options->{ "end" } + $options->{ "flank" }; - - $record->{ "PHASTCONS" } = join ",", @{ $scores }; - $record->{ "PHAST_COUNT" } = scalar @{ $scores }; # DEBUG - - Maasha::Biopieces::put_record( $record, $out ); - } - - while ( $record = Maasha::Biopieces::get_record( $in ) ) - { - if ( $record->{ "REC_TYPE" } eq "BED" ) - { - $scores = Maasha::UCSC::fixedstep_index_lookup( $index, $fh_phastcons, $record->{ "CHR" }, $record->{ "CHR_BEG" }, $record->{ "CHR_END" }, $options->{ "flank" } ); - } - elsif ( $record->{ "REC_TYPE" } eq "PSL" ) - { - $scores = Maasha::UCSC::fixedstep_index_lookup( $index, $fh_phastcons, $record->{ "S_ID" }, $record->{ "S_BEG" }, $record->{ "S_END" }, $options->{ "flank" } ); - } - elsif ( $record->{ "REC_TYPE" } eq "BLAST" ) - { - $scores = Maasha::UCSC::fixedstep_index_lookup( $index, $fh_phastcons, $record->{ "S_ID" }, $record->{ "S_BEG" }, $record->{ "S_END" }, $options->{ "flank" } ); - } - - $record->{ "PHASTCONS" } = join ",", @{ $scores } if @{ $scores }; -# $record->{ "PHAST_COUNT" } = @{ $scores } if @{ $scores }; # DEBUG - - Maasha::Biopieces::put_record( $record, $out ); - } - - close $fh_phastcons if $fh_phastcons; -} - - # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< 1; diff --git a/code_perl/Maasha/Config.pm b/code_perl/Maasha/Config.pm index 03bf0ec..6795431 100644 --- a/code_perl/Maasha/Config.pm +++ b/code_perl/Maasha/Config.pm @@ -183,42 +183,6 @@ sub genome_vmatch } -sub genome_phastcons -{ - # Martin A. Hansen, January 2008. - - # Returns the full path to the location of a concatenated - # PhastCons file for a given genome. - - my ( $genome, # requested genome - ) = @_; - - # Returns a string. - - my $file = "$BP_DATA/genomes/$genome/phastcons/$genome.pp"; - - return $file; -} - - -sub genome_phastcons_index -{ - # Martin A. Hansen, January 2008. - - # Returns the full path to the location of a PhastCons index - # for a given genome. - - my ( $genome, # requested genome - ) = @_; - - # Returns a string. - - my $file = "$BP_DATA/genomes/$genome/phastcons/$genome.pp.index"; - - return $file; -} - - sub genomes { # Martin A. Hansen, February 2008. @@ -290,42 +254,6 @@ sub chromosomes } -sub maf_track -{ - # Martin A. Hansen, April 2008. - - # Given a genome returns the corresponding mafTrack database table name. - - my ( $genome, # genome to lookup. - ) = @_; - - # Returns a string. - - my ( %hash ); - - # The below has should be in a config file - fix later. - - %hash = ( - danRer4 => 'multiz7way', - dm2 => 'multiz15way', - dm3 => 'multiz15way', - fr2 => 'multiz7way', - galGal3 => 'multiz7way', - gasAcu1 => 'multiz7way', - hg18 => 'multiz17way', - mm8 => 'multiz17way', - mm9 => 'multiz17way', - oryLat1 => 'multiz7way', - panTro2 => 'multiz17way', - tetNig1 => 'multiz7way', - ); - - Maasha::Common::error( qw(multiz track not found) ) if not exists $hash{ $genome }; - - return $hash{ $genome }; -} - - # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< 1; -- 2.39.5