From 6a4043cd15c4d8f6c251e4a9c50b006f95cda2db Mon Sep 17 00:00:00 2001 From: martinahansen Date: Thu, 26 Jun 2008 06:57:25 +0000 Subject: [PATCH] more renaming git-svn-id: http://biopieces.googlecode.com/svn/trunk@27 74ccb610-7750-0410-82ae-013aeee3265d --- bp_bin/00README | 5 ++ bp_bin/{list_biotools => list_biopieces} | 0 bp_conf/bashrc | 8 +-- code_perl/Maasha/Biopieces.pm | 84 ++++++++++++------------ code_perl/Maasha/Common.pm | 6 +- code_perl/Maasha/Config.pm | 32 ++++----- code_perl/Maasha/Match.pm | 2 +- code_perl/Maasha/Plot.pm | 12 ++-- code_perl/Maasha/Seq.pm | 2 +- code_perl/Maasha/TwoBit.pm | 2 +- 10 files changed, 76 insertions(+), 77 deletions(-) create mode 100644 bp_bin/00README rename bp_bin/{list_biotools => list_biopieces} (100%) diff --git a/bp_bin/00README b/bp_bin/00README new file mode 100644 index 0000000..49d4a84 --- /dev/null +++ b/bp_bin/00README @@ -0,0 +1,5 @@ +This directory should only contain biopiece executables. + + + +Martin A. Hansen, June 2008 diff --git a/bp_bin/list_biotools b/bp_bin/list_biopieces similarity index 100% rename from bp_bin/list_biotools rename to bp_bin/list_biopieces diff --git a/bp_conf/bashrc b/bp_conf/bashrc index 0a57f06..10814f1 100644 --- a/bp_conf/bashrc +++ b/bp_conf/bashrc @@ -24,16 +24,10 @@ export BP_PYTHON="$BP_DIR/code_python" # Direcotry with Pyton code. export BP_RUBY="$BP_DIR/code_ruby" # Direcotry with Ruby code. -### For the Perl modules they may be contributed by different developers, so we define a variable for each. - -export BP_PERL_LIBS="$BP_PERL/Maasha" # Perl modules from the developer Maasha. -# export BP_PERL_LIBS="$BP_PERL_LIBS:$BP_PERL/" # Perl modules from a new developer. - - ### Here we add the biopiece variable to the existing PATH and PERL5LIB variables. export PATH="$PATH:$BP_BIN" -export PERL5LIB="$PERL5LIB:$BP_PERL_LIBS" +export PERL5LIB="$PERL5LIB:$BP_PERL" ### Alias allowing power scripting with biopieces. diff --git a/code_perl/Maasha/Biopieces.pm b/code_perl/Maasha/Biopieces.pm index b42a994..3841595 100644 --- a/code_perl/Maasha/Biopieces.pm +++ b/code_perl/Maasha/Biopieces.pm @@ -83,10 +83,10 @@ $SIG{ 'TERM' } = \&sig_handler; # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> GLOBALS <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< -my ( $script, $TMP_DIR ); +my ( $script, $BP_TMP ); $script = &Maasha::Common::get_scriptname(); -$TMP_DIR = &Maasha::Common::get_tmpdir(); +$BP_TMP = &Maasha::Common::get_tmpdir(); # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> LOG <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< @@ -154,9 +154,9 @@ sub run_script my ( $options, $in, $out ); - &script_list_biotools( $ENV{ 'INST_DIR'} . "/biotools/usage/" ) if $script eq "list_biotools"; + &script_list_biopieces( $ENV{ 'INST_DIR'} . "/biopieces/usage/" ) if $script eq "list_biopieces"; - &script_print_usage( $ENV{ 'INST_DIR'} . "/biotools/usage/$script" ) if -t STDIN and not @ARGV; + &script_print_usage( $ENV{ 'INST_DIR'} . "/biopieces/usage/$script" ) if -t STDIN and not @ARGV; $options = &get_options( $script ); @@ -1054,11 +1054,11 @@ sub script_print_usage } -sub script_list_biotools +sub script_list_biopieces { # Martin A. Hansen, January 2008. - # Prints the description from the usage for each of the biotools. + # Prints the description from the usage for each of the biopieces. my ( $path, # full path to usage directory ) = @_; @@ -2755,7 +2755,7 @@ sub script_get_genome_align $end = $beg + $options->{ "len" }; } - $align = &Maasha::UCSC::maf_extract( $TMP_DIR, $options->{ "genome" }, $maf_track, $options->{ "chr" }, $beg, $end, $options->{ "strand" } ); + $align = &Maasha::UCSC::maf_extract( $BP_TMP, $options->{ "genome" }, $maf_track, $options->{ "chr" }, $beg, $end, $options->{ "strand" } ); foreach $entry ( @{ $align } ) { @@ -2775,15 +2775,15 @@ sub script_get_genome_align { 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" } ); + $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 "PSL" ) { - $align = &Maasha::UCSC::maf_extract( $TMP_DIR, $options->{ "genome" }, $maf_track, $record->{ "S_ID" }, $record->{ "S_BEG" }, $record->{ "S_END" }, $record->{ "STRAND" } ); + $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( $TMP_DIR, $options->{ "genome" }, $maf_track, $record->{ "S_ID" }, $record->{ "S_BEG" }, $record->{ "S_END" }, $record->{ "STRAND" } ); + $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 } ) @@ -3159,9 +3159,9 @@ sub script_patscan_seq push @args, "-m $options->{ 'max_hits' }" if $options->{ 'max_hits' }; push @args, "-n $options->{ 'max_misses' }" if $options->{ 'max_hits' }; - $seq_file = "$TMP_DIR/patscan.seq"; - $pat_file = "$TMP_DIR/patscan.pat"; - $out_file = "$TMP_DIR/patscan.out"; + $seq_file = "$BP_TMP/patscan.seq"; + $pat_file = "$BP_TMP/patscan.pat"; + $out_file = "$BP_TMP/patscan.out"; $fh_out = &Maasha::Common::write_open( $seq_file ); @@ -3302,8 +3302,8 @@ sub script_blast_seq $options->{ "database" } = &Maasha::Config::genome_blast( $options->{ 'genome' } ) if $options->{ 'genome' }; - $tmp_in = "$TMP_DIR/blast_query.seq"; - $tmp_out = "$TMP_DIR/blast.result"; + $tmp_in = "$BP_TMP/blast_query.seq"; + $tmp_out = "$BP_TMP/blast.result"; $fh_out = &Maasha::Common::write_open( $tmp_in ); @@ -3420,7 +3420,7 @@ sub script_blat_seq $blat_args .= " -stepSize=$options->{ 'step_size' }"; $blat_args .= " -ooc=" . &Maasha::Config::genome_blat_ooc( $options->{ "genome" }, 11 ) if $options->{ 'ooc' }; - $query_file = "$TMP_DIR/blat.seq"; + $query_file = "$BP_TMP/blat.seq"; $fh_out = &Maasha::Common::write_open( $query_file ); @@ -3440,7 +3440,7 @@ sub script_blat_seq $blat_args .= " -t=dnax" if $type eq "protein"; $blat_args .= " -q=$type"; - $result_file = "$TMP_DIR/blat.psl"; + $result_file = "$BP_TMP/blat.psl"; &Maasha::Common::run( "blat", "$genome_file $query_file $blat_args $result_file > /dev/null 2>&1" ); @@ -3483,13 +3483,13 @@ sub script_match_seq if ( @entries == 1 ) { - $results = &Maasha::Match::match_mummer( [ $entries[ 0 ] ], [ $entries[ 0 ] ], $options, $TMP_DIR ); + $results = &Maasha::Match::match_mummer( [ $entries[ 0 ] ], [ $entries[ 0 ] ], $options, $BP_TMP ); map { &put_record( $_, $out ) } @{ $results }; } elsif ( @entries == 2 ) { - $results = &Maasha::Match::match_mummer( [ $entries[ 0 ] ], [ $entries[ 1 ] ], $options, $TMP_DIR ); + $results = &Maasha::Match::match_mummer( [ $entries[ 0 ] ], [ $entries[ 1 ] ], $options, $BP_TMP ); map { &put_record( $_, $out ) } @{ $results }; } @@ -3574,7 +3574,7 @@ sub script_vmatch_seq &put_record( $record, $out ); } - $result_file = &Maasha::Match::match_vmatch( $TMP_DIR, \@records, \@index_files, $options ); + $result_file = &Maasha::Match::match_vmatch( $BP_TMP, \@records, \@index_files, $options ); undef @records; @@ -3931,7 +3931,7 @@ sub script_write_2bit $mask = 1 if not $options->{ "no_mask" }; - $tmp_file = "$TMP_DIR/write_2bit.fna"; + $tmp_file = "$BP_TMP/write_2bit.fna"; $fh_tmp = &Maasha::Common::write_open( $tmp_file ); $fh_out = &write_stream( $options->{ "data_out" } ); @@ -4067,7 +4067,7 @@ sub script_plot_phastcons_profiles $AoA = &Maasha::Matrix::matrix_flip( $AoA ); - $plot = &Maasha::Plot::lineplot_simple( $AoA, $options, $TMP_DIR ); + $plot = &Maasha::Plot::lineplot_simple( $AoA, $options, $BP_TMP ); $fh = &write_stream( $options->{ "data_out" } ); @@ -4734,7 +4734,7 @@ sub script_random_records $options->{ "num" } ||= 10; - $tmp_file = "$TMP_DIR/random_records.tmp"; + $tmp_file = "$BP_TMP/random_records.tmp"; $fh_out = &Maasha::Common::write_open( $tmp_file ); @@ -4850,7 +4850,7 @@ sub script_count_vals my ( $num, $record, %count_hash, @records, $tmp_file, $fh_out, $fh_in, $cache ); - $tmp_file = "$TMP_DIR/count_cache.tmp"; + $tmp_file = "$BP_TMP/count_cache.tmp"; $fh_out = &Maasha::Common::write_open( $tmp_file ); @@ -5121,7 +5121,7 @@ sub script_plot_matches $options->{ "xlabel" } ||= $data[ 0 ]->{ "Q_ID" }; $options->{ "ylabel" } ||= $data[ 0 ]->{ "S_ID" }; - $result = &Maasha::Plot::dotplot_matches( \@data, $options, $TMP_DIR ); + $result = &Maasha::Plot::dotplot_matches( \@data, $options, $BP_TMP ); $fh = &write_stream( $options->{ "data_out" } ); @@ -5394,7 +5394,7 @@ sub script_upload_to_ucsc $options->{ "color" } ||= join( ",", int( rand( 255 ) ), int( rand( 255 ) ), int( rand( 255 ) ) ); $options->{ "chunk_size" } ||= 10_000_000_000; # Due to 32-bit UCSC compilation really large tables cannot be loaded in one go. - $file = "$TMP_DIR/ucsc_upload.tmp"; + $file = "$BP_TMP/ucsc_upload.tmp"; $append = 0; @@ -5414,7 +5414,7 @@ sub script_upload_to_ucsc $record->{ "CHR_BEG" } = $record->{ "S_BEG" } if not defined $record->{ "CHR_BEG" }; $record->{ "CHR_END" } = $record->{ "S_END" } if not defined $record->{ "CHR_END" }; - $fh_hash{ $record->{ "CHR" } } = &Maasha::Common::write_open( "$TMP_DIR/$record->{ 'CHR' }" ) if not exists $fh_hash{ $record->{ "CHR" } }; + $fh_hash{ $record->{ "CHR" } } = &Maasha::Common::write_open( "$BP_TMP/$record->{ 'CHR' }" ) if not exists $fh_hash{ $record->{ "CHR" } }; $fh_out = $fh_hash{ $record->{ "CHR" } }; @@ -5427,9 +5427,9 @@ sub script_upload_to_ucsc foreach $chr ( sort keys %fh_hash ) { - &Maasha::Common::run( "bedSort", "$TMP_DIR/$chr $TMP_DIR/$chr" ); + &Maasha::Common::run( "bedSort", "$BP_TMP/$chr $BP_TMP/$chr" ); - $fh_in = &Maasha::Common::read_open( "$TMP_DIR/$chr" ); + $fh_in = &Maasha::Common::read_open( "$BP_TMP/$chr" ); undef $block; @@ -5478,7 +5478,7 @@ sub script_upload_to_ucsc &Maasha::UCSC::fixedstep_put_entry( $chr, $beg_block, $block, $fh_out ); - unlink "$TMP_DIR/$chr"; + unlink "$BP_TMP/$chr"; } close $fh_out; @@ -5486,14 +5486,14 @@ sub script_upload_to_ucsc $wig_file = "$options->{ 'table' }.wig"; $wib_file = "$options->{ 'table' }.wib"; - $wib_dir = "$ENV{ 'DATA_DIR' }/genomes/$options->{ 'database' }/wib"; + $wib_dir = "$ENV{ 'BP_DATA' }/genomes/$options->{ 'database' }/wib"; &Maasha::Common::dir_create_if_not_exists( $wib_dir ); # &Maasha::Common::run( "wigEncode", "$file $wig_file $wib_file > /dev/null 2>&1" ); - `cd $TMP_DIR && wigEncode $file $wig_file $wib_file > /dev/null 2>&1`; - &Maasha::Common::run( "mv", "$TMP_DIR/$wib_file $wib_dir" ); + `cd $BP_TMP && wigEncode $file $wig_file $wib_file > /dev/null 2>&1`; + &Maasha::Common::run( "mv", "$BP_TMP/$wib_file $wib_dir" ); unlink $file; @@ -5581,7 +5581,7 @@ sub script_upload_to_ucsc close $fh_out; if ( $format eq "BED" ) { - &Maasha::UCSC::bed_upload_to_ucsc( $TMP_DIR, $file, $options, $append ); + &Maasha::UCSC::bed_upload_to_ucsc( $BP_TMP, $file, $options, $append ); } elsif ( $format eq "PSL" ) { &Maasha::UCSC::psl_upload_to_ucsc( $file, $options, $append ); } @@ -5607,7 +5607,7 @@ sub script_upload_to_ucsc { $type = "bed $columns"; - &Maasha::UCSC::bed_upload_to_ucsc( $TMP_DIR, $file, $options, $append ); + &Maasha::UCSC::bed_upload_to_ucsc( $BP_TMP, $file, $options, $append ); } elsif ( $format eq "BED_SS" ) { @@ -5615,7 +5615,7 @@ sub script_upload_to_ucsc $type = "sec_struct"; - &Maasha::UCSC::bed_upload_to_ucsc( $TMP_DIR, $file, $options, $append ); + &Maasha::UCSC::bed_upload_to_ucsc( $BP_TMP, $file, $options, $append ); } elsif ( $format eq "PSL" ) { @@ -5627,7 +5627,7 @@ sub script_upload_to_ucsc { $type = "wig 0"; - &Maasha::UCSC::wiggle_upload_to_ucsc( $TMP_DIR, $wib_dir, $file, $options ); + &Maasha::UCSC::wiggle_upload_to_ucsc( $BP_TMP, $wib_dir, $file, $options ); } unlink $file; @@ -5805,7 +5805,7 @@ sub sig_handler sleep 1; - if ( -d $TMP_DIR ) + if ( -d $BP_TMP ) { if ( $sig =~ /MAASHA_ERROR/ ) { print STDERR "\nProgram '$script' had an error" . " - Please wait for temporary data to be removed\n"; @@ -5818,9 +5818,9 @@ sub sig_handler } # This is a really bad solution, potentially, anyone can include this module and set - # the TMP_DIR to point at any dir and thus take out the machine !!! + # the BP_TMP to point at any dir and thus take out the machine !!! - &Maasha::Common::dir_remove( $TMP_DIR ); + &Maasha::Common::dir_remove( $BP_TMP ); } exit( 0 ); @@ -5830,9 +5830,9 @@ sub sig_handler END { # This is a really bad solution, potentially, anyone can include this module and set - # the TMP_DIR to point at any dir and thus take out the machine !!! + # the BP_TMP to point at any dir and thus take out the machine !!! - &Maasha::Common::dir_remove( $TMP_DIR ); + &Maasha::Common::dir_remove( $BP_TMP ); } diff --git a/code_perl/Maasha/Common.pm b/code_perl/Maasha/Common.pm index b430484..a6d63e1 100644 --- a/code_perl/Maasha/Common.pm +++ b/code_perl/Maasha/Common.pm @@ -484,20 +484,20 @@ sub get_tmpdir # Martin A. Hansen, April 2008. # Create a temporary directory based on - # $ENV{ 'TMP_DIR' } and sessionid. + # $ENV{ 'BP_TMP' } and sessionid. # Returns a path. my ( $user, $sid, $path ); - &Maasha::Common::error( qq(no TMP_DIR set in %ENV) ) if not -d $ENV{ 'TMP_DIR' }; + &Maasha::Common::error( qq(no BP_TMP set in %ENV) ) if not -d $ENV{ 'BP_TMP' }; $user = $ENV{ 'USER' }; $user =~ s/\.//g; $sid = &Maasha::Common::get_sessionid(); - $path = "$ENV{ 'TMP_DIR' }/$user\_$sid"; + $path = "$ENV{ 'BP_TMP' }/$user\_$sid"; &Maasha::Common::dir_create( $path ); diff --git a/code_perl/Maasha/Config.pm b/code_perl/Maasha/Config.pm index e25f3f2..b713973 100644 --- a/code_perl/Maasha/Config.pm +++ b/code_perl/Maasha/Config.pm @@ -38,19 +38,19 @@ use vars qw( @ISA @EXPORT ); # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> GLOBALS <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< -my ( $HOME, $PATH, $DATA_DIR, $TMP_DIR, $INST_DIR ); +my ( $HOME, $PATH, $BP_DATA, $BP_TMP, $BP_DIR ); $HOME = $ENV{ "HOME" }; $PATH = $ENV{ "PATH" }; -$DATA_DIR = $ENV{ "DATA_DIR" }; -$TMP_DIR = $ENV{ "TMP_DIR" }; -$INST_DIR = $ENV{ "INST_DIR" }; +$BP_DIR = $ENV{ "BP_DIR" }; +$BP_DATA = $ENV{ "BP_DATA" }; +$BP_TMP = $ENV{ "BP_TMP" }; warn qq(WARNING: HOME not set in env\n) if not defined $HOME; warn qq(WARNING: PATH not set in env\n) if not defined $PATH; -warn qq(WARNING: DATA_DIR not set in env\n) if not defined $DATA_DIR; -warn qq(WARNING: TMP_DIR not set in env\n) if not defined $TMP_DIR; -warn qq(WARNING: INST_DIR not set in env\n) if not defined $INST_DIR; +warn qq(WARNING: BP_DIR not set in env\n) if not defined $BP_DIR; +warn qq(WARNING: BP_DATA not set in env\n) if not defined $BP_DATA; +warn qq(WARNING: BP_TMP not set in env\n) if not defined $BP_TMP; # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< @@ -90,7 +90,7 @@ sub genome_fasta # Returns string. - my $genome_file = "$DATA_DIR/genomes/$genome/$genome.fna"; + my $genome_file = "$BP_DATA/genomes/$genome/$genome.fna"; if ( not -f $genome_file ) { &Maasha::Common::error( qq(Genome file "$genome_file" for genome "$genome" not found) ); @@ -112,7 +112,7 @@ sub genome_fasta_index # Returns string. - my $index = "$DATA_DIR/genomes/$genome/$genome.fna.index"; + my $index = "$BP_DATA/genomes/$genome/$genome.fna.index"; if ( not -f $index ) { &Maasha::Common::error( qq(Index file "$index" for genome -> $genome not found) ); @@ -133,7 +133,7 @@ sub genome_blast # Returns string. - my $file = "$DATA_DIR/genomes/$genome/blast/$genome.fna"; + my $file = "$BP_DATA/genomes/$genome/blast/$genome.fna"; return $file; } @@ -152,7 +152,7 @@ sub genome_blat_ooc # Returns string. - my $ooc_file = "$DATA_DIR/genomes/$genome/blat/$tile_size.ooc"; + my $ooc_file = "$BP_DATA/genomes/$genome/blat/$tile_size.ooc"; &Maasha::Common::error( qq(ooc file "$ooc_file" not found for genome -> $genome) ) if not -f $ooc_file; @@ -175,7 +175,7 @@ sub genome_vmatch @chrs = &chromosomes( $genome ); - map { $_ = "$DATA_DIR/genomes/$genome/vmatch/$_" } @chrs; + map { $_ = "$BP_DATA/genomes/$genome/vmatch/$_" } @chrs; # needs robustness check @@ -195,7 +195,7 @@ sub genome_phastcons # Returns a string. - my $file = "$DATA_DIR/genomes/$genome/phastcons/$genome.pp"; + my $file = "$BP_DATA/genomes/$genome/phastcons/$genome.pp"; return $file; } @@ -213,7 +213,7 @@ sub genome_phastcons_index # Returns a string. - my $file = "$DATA_DIR/genomes/$genome/phastcons/$genome.pp.index"; + my $file = "$BP_DATA/genomes/$genome/phastcons/$genome.pp.index"; return $file; } @@ -230,7 +230,7 @@ sub genomes my ( %genome_hash, $fh, $line, @genomes, $org ); - $fh = &Maasha::Common::read_open( "$INST_DIR/conf/genomes.conf" ); + $fh = &Maasha::Common::read_open( "$BP_DIR/conf/genomes.conf" ); while ( $line = <$fh> ) { @@ -265,7 +265,7 @@ sub chromosomes my ( $fh_in, $line, $org, $chr, %genome_hash, @chrs ); - $fh_in = &Maasha::Common::read_open( "$INST_DIR/conf/genomes.conf" ); + $fh_in = &Maasha::Common::read_open( "$BP_DIR/bp_conf/genomes.conf" ); while ( $line = <$fh_in> ) { diff --git a/code_perl/Maasha/Match.pm b/code_perl/Maasha/Match.pm index 5f97856..8f52d8d 100644 --- a/code_perl/Maasha/Match.pm +++ b/code_perl/Maasha/Match.pm @@ -59,7 +59,7 @@ sub match_mummer my ( @args, $arg, $file_in1, $file_in2, $cmd, $file_out, $fh, $line, $result, @results ); - $tmp_dir ||= $ENV{ "TMP_DIR" }; + $tmp_dir ||= $ENV{ "BP_TMP" }; $options->{ "word_size" } ||= 20; $options->{ "direction" } ||= "both"; diff --git a/code_perl/Maasha/Plot.pm b/code_perl/Maasha/Plot.pm index 8c76a53..225433d 100644 --- a/code_perl/Maasha/Plot.pm +++ b/code_perl/Maasha/Plot.pm @@ -67,7 +67,7 @@ sub lineplot_simple my ( $tmp_file, $pid, $fh_in, $fh_out, $cmd, $i, $line, @lines, $xtic_space, @plot_cmd ); - $tmp_dir ||= $ENV{ 'TMP_DIR' }; + $tmp_dir ||= $ENV{ 'BP_TMP' }; $tmp_file = "$tmp_dir/lineplot_simple.tab"; @@ -332,7 +332,7 @@ sub dotplot_matches my ( $forward_file, $backward_file, $pid, $fh_forward, $fh_backward, $fh_in, $fh_out, $cmd, $match, $line, @lines, $q_max, $s_max ); - $tmp_dir ||= $ENV{ 'TMP_DIR' }; + $tmp_dir ||= $ENV{ 'BP_TMP' }; $forward_file = "$tmp_dir/match_f.tab"; $backward_file = "$tmp_dir/match_r.tab"; @@ -439,13 +439,13 @@ sub karyogram if ( $options->{ "genome" } eq "human" ) { - $karyo_file = "/Users/m.hansen/maasha/perl_scripts/biotools/karyo_data/human_cytobands.txt"; -# $karyo_file = "/home/m.hansen/maasha/perl_scripts/biotools/karyo_data/human_cytobands.txt"; + $karyo_file = "/Users/m.hansen/maasha/perl_scripts/biopieces/karyo_data/human_cytobands.txt"; +# $karyo_file = "/home/m.hansen/maasha/perl_scripts/biopieces/karyo_data/human_cytobands.txt"; } else { - $karyo_file = "/Users/m.hansen/maasha/perl_scripts/biotools/karyo_data/mouse_cytobands.txt"; - # $karyo_file = "/home/m.hansen/maasha/perl_scripts/biotools/karyo_data/mouse_cytobands.txt"; + $karyo_file = "/Users/m.hansen/maasha/perl_scripts/biopieces/karyo_data/mouse_cytobands.txt"; + # $karyo_file = "/home/m.hansen/maasha/perl_scripts/biopieces/karyo_data/mouse_cytobands.txt"; } $karyo = &parse_karyo_data( $karyo_file ); diff --git a/code_perl/Maasha/Seq.pm b/code_perl/Maasha/Seq.pm index 1d5d5cb..f2b8089 100644 --- a/code_perl/Maasha/Seq.pm +++ b/code_perl/Maasha/Seq.pm @@ -531,7 +531,7 @@ sub fold_struct_contrastruct my ( $tmp_file, $out_file1, $out_file2, $fh, $line, $struct, @AoA, $i, $temp, $index ); - $tmp_dir ||= $ENV{ 'TMP_DIR' }; + $tmp_dir ||= $ENV{ 'BP_TMP' }; $tmp_file = "$tmp_dir/fold.fna"; $out_file1 = "$tmp_dir/fold.out1"; diff --git a/code_perl/Maasha/TwoBit.pm b/code_perl/Maasha/TwoBit.pm index cc9d600..1d839bc 100644 --- a/code_perl/Maasha/TwoBit.pm +++ b/code_perl/Maasha/TwoBit.pm @@ -35,7 +35,7 @@ use vars qw( @ISA @EXPORT ); use Data::Dumper; -use Inline ( C => <<'END_C', DIRECTORY => $ENV{ "TMP_DIR" } ); +use Inline ( C => <<'END_C', DIRECTORY => $ENV{ "BP_TMP" } ); int find_block_beg( char *string, char c, int beg, int len ) { -- 2.39.5