From 9564d95a41f0595e003827615132f34cc12c1f60 Mon Sep 17 00:00:00 2001 From: Robert Hubley Date: Tue, 20 Nov 2018 14:36:09 -0800 Subject: [PATCH] Cleanup before a distribution --- ArrayList.pm | 5 +-- ArrayListIterator.pm | 5 +-- CrossmatchSearchEngine.pm | 10 ++--- DFAMRecord.pm | 5 +-- DateRepeats | 5 +-- DeCypherSearchEngine.pm | 5 +-- FastaDB.pm | 5 +-- HMMERSearchEngine.pm | 17 +++---- Libraries/RepeatAnnotationData.pm | 0 LibraryUtils.pm | 5 +-- Matrix.pm | 5 +-- NCBIBlastSearchEngine.pm | 22 ++++----- NCBIBlastXSearchEngine.pm | 5 +-- PRSearchResult.pm | 5 +-- ProcessRepeats | 14 +++--- PubRef.pm | 5 +-- RepbaseRecord.pm | 5 +-- RepeatMasker | 74 ++++++++++++++----------------- RepeatRecord.pm | 5 +-- SearchEngineI.pm | 5 +-- SearchResult.pm | 60 +++++++++++-------------- SearchResultCollection.pm | 5 +-- SeqDBI.pm | 5 +-- SimpleBatcher.pm | 5 +-- TRF.pm | 5 +-- TRFResult.pm | 5 +-- TRFSearchResult.pm | 5 +-- Taxonomy.pm | 5 +-- WUBlastSearchEngine.pm | 5 +-- WUBlastXSearchEngine.pm | 5 +-- configure | 10 ++--- util/buildRMLibFromEMBL.pl | 5 +-- util/buildSummary.pl | 5 +-- util/calcDivergenceFromAlign.pl | 5 +-- util/createRepeatLandscape.pl | 7 +-- util/dupliconToSVG.pl | 5 +-- util/getRepeatMaskerBatch.pl | 5 +-- util/queryRepeatDatabase.pl | 5 +-- util/queryTaxonomyDatabase.pl | 5 +-- util/rmOut2Fasta.pl | 5 +-- util/rmOutToGFF3.pl | 5 +-- util/rmToUCSCTables.pl | 5 +-- util/wublastToCrossmatch.pl | 5 +-- 43 files changed, 123 insertions(+), 261 deletions(-) mode change 100644 => 100755 Libraries/RepeatAnnotationData.pm diff --git a/ArrayList.pm b/ArrayList.pm index 241c36d..24de2c3 100755 --- a/ArrayList.pm +++ b/ArrayList.pm @@ -29,10 +29,7 @@ ############################################################################### # ChangeLog # -# $Log: ArrayList.pm,v $ -# Revision 1.59 2017/02/01 21:01:53 rhubley -# Cleanup before a distribution -# +# $Log$ # ############################################################################### # To Do: diff --git a/ArrayListIterator.pm b/ArrayListIterator.pm index cd3d1a3..4d5dea0 100755 --- a/ArrayListIterator.pm +++ b/ArrayListIterator.pm @@ -26,10 +26,7 @@ ############################################################################### # ChangeLog # -# $Log: ArrayListIterator.pm,v $ -# Revision 1.42 2017/02/01 21:01:53 rhubley -# Cleanup before a distribution -# +# $Log$ # ############################################################################### # To Do: diff --git a/CrossmatchSearchEngine.pm b/CrossmatchSearchEngine.pm index 873af73..171939b 100755 --- a/CrossmatchSearchEngine.pm +++ b/CrossmatchSearchEngine.pm @@ -25,10 +25,7 @@ ############################################################################### # ChangeLog # -# $Log: CrossmatchSearchEngine.pm,v $ -# Revision 1.111 2017/02/01 21:01:53 rhubley -# Cleanup before a distribution -# +# $Log$ # ############################################################################### # To Do: @@ -278,7 +275,7 @@ sub setPathToEngine { ##-------------------------------------------------------------------------## sub getParameters { - my $this = shift; + my $this = shift; # Test if engine is available my $engine = $this->getPathToEngine(); @@ -330,6 +327,7 @@ sub getParameters { $parameters .= " -masklevel $value" if ( $value > 0 ); } if ( ( $value = $this->getMatrix() ) ) { + # test if matrix exists if ( -f $value ) { $parameters .= " -matrix $value"; @@ -385,6 +383,7 @@ sub search { my %nameValuePairs = @_; if ( %nameValuePairs ) { + # TODO: Consider deprecating this way of setting up the object while ( my ( $name, $value ) = each( %nameValuePairs ) ) { my $method = "set" . _ucFirst( $name ); @@ -401,6 +400,7 @@ sub search { # Get matrix name for post-processing results my @matrixName = (); if ( ( my $value = $this->getMatrix() ) ) { + # test if matrix exists if ( -f $value ) { my @path = split( /[\\\/]/, $value ); diff --git a/DFAMRecord.pm b/DFAMRecord.pm index 1dba714..f63b474 100755 --- a/DFAMRecord.pm +++ b/DFAMRecord.pm @@ -20,10 +20,7 @@ ############################################################################### # ChangeLog # -# $Log: DFAMRecord.pm,v $ -# Revision 1.19 2017/02/01 21:01:53 rhubley -# Cleanup before a distribution -# +# $Log$ # ############################################################################### # diff --git a/DateRepeats b/DateRepeats index 7dc3aff..a07a8a1 100755 --- a/DateRepeats +++ b/DateRepeats @@ -21,10 +21,7 @@ # # ChangeLog # -# $Log: DateRepeats,v $ -# Revision 1.93 2017/02/01 21:01:53 rhubley -# Cleanup before a distribution -# +# $Log$ # ############################################################################### # diff --git a/DeCypherSearchEngine.pm b/DeCypherSearchEngine.pm index e1cd573..7f5d319 100755 --- a/DeCypherSearchEngine.pm +++ b/DeCypherSearchEngine.pm @@ -26,10 +26,7 @@ ############################################################################### # ChangeLog # -# $Log: DeCypherSearchEngine.pm,v $ -# Revision 1.49 2017/02/01 21:01:54 rhubley -# Cleanup before a distribution -# +# $Log$ # ############################################################################### # To Do: diff --git a/FastaDB.pm b/FastaDB.pm index cbe9700..ac7ca70 100755 --- a/FastaDB.pm +++ b/FastaDB.pm @@ -57,10 +57,7 @@ ################################################################################ # ChangeLog: # -# $Log: FastaDB.pm,v $ -# Revision 1.107 2017/02/01 21:01:54 rhubley -# Cleanup before a distribution -# +# $Log$ # ################################################################################ # diff --git a/HMMERSearchEngine.pm b/HMMERSearchEngine.pm index 562f879..755bef2 100755 --- a/HMMERSearchEngine.pm +++ b/HMMERSearchEngine.pm @@ -25,10 +25,7 @@ ############################################################################### # ChangeLog # -# $Log: HMMERSearchEngine.pm,v $ -# Revision 1.40 2017/02/01 21:01:54 rhubley -# Cleanup before a distribution -# +# $Log$ # ############################################################################### # To Do: @@ -509,14 +506,14 @@ sub search { print "HMMER returned a the following result code >$resultCode<\n" if ( $this->getDEBUG() ); - ## + ## ## DEBUGING for Kaitlin ## - #if ( $resultCode ) - #{ - # my $lowerCode = ( $? & 255 ); - # print "ERROR returned from nhmmer invocation: 16bit code = $?, high 8bits = $resultCode, lower 8bits = $lowerCode, error file = $errFile, output file = $outFile\n"; - #} +#if ( $resultCode ) +#{ +# my $lowerCode = ( $? & 255 ); +# print "ERROR returned from nhmmer invocation: 16bit code = $?, high 8bits = $resultCode, lower 8bits = $lowerCode, error file = $errFile, output file = $outFile\n"; +#} print $CLASS . "::search: " diff --git a/Libraries/RepeatAnnotationData.pm b/Libraries/RepeatAnnotationData.pm old mode 100644 new mode 100755 diff --git a/LibraryUtils.pm b/LibraryUtils.pm index 160b1aa..ac3d1bb 100755 --- a/LibraryUtils.pm +++ b/LibraryUtils.pm @@ -20,10 +20,7 @@ # # ChangeLog # -# $Log: LibraryUtils.pm,v $ -# Revision 1.6 2017/02/01 21:01:54 rhubley -# Cleanup before a distribution -# +# $Log$ # ############################################################################### # diff --git a/Matrix.pm b/Matrix.pm index bbe495c..50488c2 100755 --- a/Matrix.pm +++ b/Matrix.pm @@ -26,10 +26,7 @@ ############################################################################### # ChangeLog # -# $Log: Matrix.pm,v $ -# Revision 1.21 2017/02/01 21:01:54 rhubley -# Cleanup before a distribution -# +# $Log$ # ############################################################################### # To Do: diff --git a/NCBIBlastSearchEngine.pm b/NCBIBlastSearchEngine.pm index ff05629..76ca743 100755 --- a/NCBIBlastSearchEngine.pm +++ b/NCBIBlastSearchEngine.pm @@ -25,14 +25,7 @@ ############################################################################### # ChangeLog # -# $Log: NCBIBlastSearchEngine.pm,v $ -# Revision 1.48 2017/04/17 19:01:11 rhubley -# - Allow number of cores to be set with RMBlast -# - Deprecate -int and -low options -# -# Revision 1.47 2017/02/01 21:01:54 rhubley -# Cleanup before a distribution -# +# $Log$ # ############################################################################### # To Do: @@ -476,8 +469,8 @@ sub getParameters { # on? if ( defined( $value = $this->getCores() ) ) { $parameters .= " -num_threads $value "; - }else - { + } + else { $parameters .= " -num_threads 4 "; } @@ -610,12 +603,13 @@ sub search { my $outFile = $outputDirName . "/ncResults-$currentTime-$$.out"; # TODO DEBUGGING - if ( $this->getDEBUG ) - { - system("cp " . $this->getQuery() . " $outputDirName" . "/before-$currentTime-$$.fa" ); + if ( $this->getDEBUG ) { + system( "cp " + . $this->getQuery() + . " $outputDirName" + . "/before-$currentTime-$$.fa" ); } - open OUT, ">$outFile"; while ( <$POUTPUT> ) { print OUT $_; diff --git a/NCBIBlastXSearchEngine.pm b/NCBIBlastXSearchEngine.pm index 8bfb4ea..7aee88d 100755 --- a/NCBIBlastXSearchEngine.pm +++ b/NCBIBlastXSearchEngine.pm @@ -25,10 +25,7 @@ ############################################################################### # ChangeLog # -# $Log: NCBIBlastXSearchEngine.pm,v $ -# Revision 1.22 2017/02/01 21:01:54 rhubley -# Cleanup before a distribution -# +# $Log$ # ############################################################################### # To Do: diff --git a/PRSearchResult.pm b/PRSearchResult.pm index 4c6661a..3013c31 100755 --- a/PRSearchResult.pm +++ b/PRSearchResult.pm @@ -19,10 +19,7 @@ ############################################################################### # ChangeLog # -# $Log: PRSearchResult.pm,v $ -# Revision 1.29 2017/02/01 21:01:54 rhubley -# Cleanup before a distribution -# +# $Log$ # ############################################################################### # To Do: diff --git a/ProcessRepeats b/ProcessRepeats index 6a55159..f1f706c 100755 --- a/ProcessRepeats +++ b/ProcessRepeats @@ -27,10 +27,7 @@ ############################################################################### # ChangeLog # -# $Log: ProcessRepeats,v $ -# Revision 1.279 2017/02/01 21:01:54 rhubley -# Cleanup before a distribution -# +# $Log$ # ############################################################################### # @@ -2552,7 +2549,7 @@ CYCLE3: ## matrix is also fixed to the average GC background rather ## than the actual GC bin used to identify the original alignment. ## Original alignment search parameters: - ## 180 cutoff, + ## 180 cutoff, ## 7-11 minmatch, ## 18p## matrix, ## -30 gap open, @@ -6100,8 +6097,8 @@ sub generateOutput { printf $OUT " have been counted as one element\n"; printf $OUT "%54s\n", $exclnote; printf $OUT "\n"; - if ( $options{'species'} ) - { + + if ( $options{'species'} ) { printf $OUT "The query species was assumed to be %-14s\n", $options{'species'}; } @@ -7647,8 +7644,7 @@ sub joinDNATransposonFragments { # Fake a range if hit name my @curRanges = (); if ( $curName eq $curHitName ) { - if ( $chainEndHash->{ $currentAnnot->getPRID() } ) - { + if ( $chainEndHash->{ $currentAnnot->getPRID() } ) { push @curRanges, { 'start' => 1, diff --git a/PubRef.pm b/PubRef.pm index 3bab88e..d156fbb 100755 --- a/PubRef.pm +++ b/PubRef.pm @@ -20,10 +20,7 @@ ############################################################################### # ChangeLog # -# $Log: PubRef.pm,v $ -# Revision 1.46 2017/02/01 21:01:54 rhubley -# Cleanup before a distribution -# +# $Log$ # ############################################################################### # diff --git a/RepbaseRecord.pm b/RepbaseRecord.pm index 49363e3..ea52806 100755 --- a/RepbaseRecord.pm +++ b/RepbaseRecord.pm @@ -20,10 +20,7 @@ ############################################################################### # ChangeLog # -# $Log: RepbaseRecord.pm,v $ -# Revision 1.46 2017/02/01 21:01:54 rhubley -# Cleanup before a distribution -# +# $Log$ # ############################################################################### # diff --git a/RepeatMasker b/RepeatMasker index 9f13edb..cfe1275 100755 --- a/RepeatMasker +++ b/RepeatMasker @@ -34,14 +34,7 @@ ############################################################################### # ChangeLog: # -# $Log: RepeatMasker,v $ -# Revision 1.332 2017/04/17 19:01:11 rhubley -# - Allow number of cores to be set with RMBlast -# - Deprecate -int and -low options -# -# Revision 1.331 2017/02/01 21:01:55 rhubley -# Cleanup before a distribution -# +# $Log$ # ############################################################################### # @@ -451,10 +444,9 @@ else { $options{'engine'} = $engine; } -if ( defined $options{'int'} || defined $options{'low'} ) -{ - die "\nThe options -int and -low have been deprecated. Please use either\n" . - "-noint or -nolow instead.\n\n"; +if ( defined $options{'int'} || defined $options{'low'} ) { + die "\nThe options -int and -low have been deprecated. Please use either\n" + . "-noint or -nolow instead.\n\n"; } if ( !-e $RepeatMaskerConfig::TRF_PRGM ) { @@ -486,16 +478,16 @@ elsif ( $engine eq "hmmer" ) { pathToEngine => $RepeatMaskerConfig::NHMMSCAN_PRGM, DEBUG => $engineDEBUG ); - # Used to allow a single instance to use all the cores ( ie. default nhmmer + # Used to allow a single instance to use all the cores ( ie. default nhmmer # prior to 3.2 ). Now ( like nhmmer 3.2 ) we require the user to be explicit - # about how many parallel proceses to use. + # about how many parallel proceses to use. # BEFORE: #if ( exists $options{'parallel'} && $options{'parallel'} > 1 ) { - # Limit nhmmer cores to 2 per batch. - #$searchEngine->setCores( 2 ); + # Limit nhmmer cores to 2 per batch. + #$searchEngine->setCores( 2 ); #} # NOW: - # For each parallel batch invoke nhmmer with 2 cores each. I.e -pa 4 + # For each parallel batch invoke nhmmer with 2 cores each. I.e -pa 4 # would run 4 nhmmer jobs each using 2 cores $searchEngine->setCores( 2 ); @@ -2850,10 +2842,9 @@ sub runStage { # my $cmMaskLevel = 101; - if ( $DEBUG ) - { + if ( $DEBUG ) { print "Saving pre-stage maskfile to: $maskfile-$stage\n"; - system("cp $maskfile $maskfile-$stage"); + system( "cp $maskfile $maskfile-$stage" ); } my ( $minmatch, $bandwidth, $resultsCollection ) = &search( @@ -5129,25 +5120,25 @@ sub filterResults { # other consensus seqs are only there to correctly classify # matches - # this (high) limit prevents cutting out ancient elements - # misassigned as young elements - # - # WARNING: This only looks back one. So...in a case like this: - # - # Original Annotations: - # #0: 511 15.96 0.00 0.00 CebAlb_disco_line_24154 693 786 (615) C L1PA8_3end#LINE/L1 (1) 918 825 - # #1: 341 24.37 9.92 0.84 CebAlb_disco_line_24154 693 811 (590) C L1PA8A_3end#LINE/L1 (0) 878 748 - # #2: 508 19.81 0.00 0.00 CebAlb_disco_line_24154 693 798 (603) C L1PA7_3end#LINE/L1 (1) 900 795 - # - # Deleting annotation (1): Filter #9 - < 75% identical. - # Doing actual removals: - # Removing element 1 - # Final Annotations: - # #0: 511 15.96 0.00 0.00 CebAlb_disco_line_24154 693 786 (615) C L1PA8_3end#LINE/L1 (1) 918 825 - # #1: 508 19.81 0.00 0.00 CebAlb_disco_line_24154 693 798 (603) C L1PA7_3end#LINE/L1 (1) 900 795 - # - # This should be fixed. - # +# this (high) limit prevents cutting out ancient elements +# misassigned as young elements +# +# WARNING: This only looks back one. So...in a case like this: +# +# Original Annotations: +# #0: 511 15.96 0.00 0.00 CebAlb_disco_line_24154 693 786 (615) C L1PA8_3end#LINE/L1 (1) 918 825 +# #1: 341 24.37 9.92 0.84 CebAlb_disco_line_24154 693 811 (590) C L1PA8A_3end#LINE/L1 (0) 878 748 +# #2: 508 19.81 0.00 0.00 CebAlb_disco_line_24154 693 798 (603) C L1PA7_3end#LINE/L1 (1) 900 795 +# +# Deleting annotation (1): Filter #9 - < 75% identical. +# Doing actual removals: +# Removing element 1 +# Final Annotations: +# #0: 511 15.96 0.00 0.00 CebAlb_disco_line_24154 693 786 (615) C L1PA8_3end#LINE/L1 (1) 918 825 +# #1: 508 19.81 0.00 0.00 CebAlb_disco_line_24154 693 798 (603) C L1PA7_3end#LINE/L1 (1) 900 795 +# +# This should be fixed. +# if ( $diverge + $gaps < 25 ) { if ( $name =~ /_3end\#/ && $left < 20 ) { @@ -5976,6 +5967,7 @@ sub postProcessSearch { # Check for overlaps if ( $prevName eq $name && $prevBeg <= $end ) { $len = $prevBeg - $begin; + # Handle special case where something like this occurs: # ---------> # -----> @@ -6144,7 +6136,6 @@ sub addExcisionSet { $i++; } - # # Add ranges to excision list # @@ -6153,7 +6144,8 @@ sub addExcisionSet { my $start = $range->[ 1 ]; my $end = $range->[ 2 ]; - print "$subroutine: Adding range: $id:$start-$end ( " . ( $end-$start+1) . " )\n" + print "$subroutine: Adding range: $id:$start-$end ( " + . ( $end - $start + 1 ) . " )\n" if ( $DEBUG ); my $posAdjustment = 0; diff --git a/RepeatRecord.pm b/RepeatRecord.pm index 6fd9f56..b5ed3f3 100755 --- a/RepeatRecord.pm +++ b/RepeatRecord.pm @@ -20,10 +20,7 @@ ############################################################################### # ChangeLog # -# $Log: RepeatRecord.pm,v $ -# Revision 1.4 2017/02/01 21:01:55 rhubley -# Cleanup before a distribution -# +# $Log$ # ############################################################################### # diff --git a/SearchEngineI.pm b/SearchEngineI.pm index 67fed51..3a84072 100755 --- a/SearchEngineI.pm +++ b/SearchEngineI.pm @@ -28,10 +28,7 @@ ############################################################################### # ChangeLog # -# $Log: SearchEngineI.pm,v $ -# Revision 1.82 2017/02/01 21:01:55 rhubley -# Cleanup before a distribution -# +# $Log$ # ############################################################################### # diff --git a/SearchResult.pm b/SearchResult.pm index bb47346..08592c6 100755 --- a/SearchResult.pm +++ b/SearchResult.pm @@ -50,10 +50,7 @@ ############################################################################### # ChangeLog # -# $Log: SearchResult.pm,v $ -# Revision 1.120 2017/02/01 21:01:55 rhubley -# Cleanup before a distribution -# +# $Log$ # ############################################################################### # To Do: @@ -149,8 +146,8 @@ use constant AlignWithQuerySeq => 2; # the subj sequences all in the forward direction use constant AlignWithSubjSeq => 3; use constant OutFileFormat => 4; -use constant CompressedAlignCSV => 5; # Deprecated -use constant CompressedAlignFormat => 5; +use constant CompressedAlignCSV => 5; # Deprecated +use constant CompressedAlignFormat => 5; use constant PSL => 6; use constant RangeHighlightedAlignment => 7; use constant CIGARFormat => 8; @@ -1174,10 +1171,10 @@ sub toStringFormatted { elsif ( $format == SearchResult::OutFileFormat ) { return $obj->_toOUTFileFormat(); } - elsif ( $format == SearchResult::CompressedAlignFormat ) { + elsif ( $format == SearchResult::CompressedAlignFormat ) { return $obj->_toCAF( $displayParams ); } - elsif ( $format == SearchResult::CIGARFormat ) { + elsif ( $format == SearchResult::CIGARFormat ) { return $obj->_toCIGAR( $displayParams ); } else { @@ -1959,13 +1956,13 @@ sub _toCSVFormat { $obj->_toCAF( $displayParams ); } - + ##-------------------------------------------------------------------------## ## Use: my $cafString = $obj->_toCAF(); ## -## Yet another Compressed Alignment Format (yaCAF or just CAF). +## Yet another Compressed Alignment Format (yaCAF or just CAF). ## This format was developed for the use case where sequence databases -## may not be available for either the query or the subject of an +## may not be available for either the query or the subject of an ## alignment and where it's still desirable to communicate the aligment ## in a semi-succinct fashion. ## @@ -1984,7 +1981,7 @@ sub _toCSVFormat { ## Subj : AACAA ## would be encoded as: "AAG/CAA" ## -## Finally gaps are encoded by surrounding the deleted sequence or the +## Finally gaps are encoded by surrounding the deleted sequence or the ## inserted sequence (relative to the query) by either "+" or "-". For ## instance the following alignment: ## Query: AAGCTA--A @@ -2081,18 +2078,17 @@ sub _toCAF { return $cRec; } - ##-------------------------------------------------------------------------## ## Use: my $cigarString = $obj->_toCIGAR(); ## -## Basic CIGAR (SAM variant) format. Alignments are encoded using +## Basic CIGAR (SAM variant) format. Alignments are encoded using ## three operators "M" for matches, "I" or insertions, and "D" for ## deletions. The operators are *proceeded* by an integer indicating ## how many runs of the operator are to be performed. This is a lossy ## encoding and requires the two original aligned strings to reproduce ## the alignment. -## -## ie. +## +## ie. ## Query: AAGACTT---A ## Subj : AAT--CTAATA ## @@ -2106,27 +2102,25 @@ sub _toCIGAR { my $qrySeq = $obj->getQueryString(); my $sbjSeq = $obj->getSubjString(); - my $outStr = ""; + my $outStr = ""; my $prevState = ""; - my $count = 0; - my $state = ""; - for ( my $i = 0; $i < length($qrySeq); $i++ ) - { - my $qChar = substr($qrySeq,$i,1); - my $sChar = substr($sbjSeq,$i,1); - if ( $qChar ne "-" && $sChar ne "-" ) - { + my $count = 0; + my $state = ""; + for ( my $i = 0 ; $i < length( $qrySeq ) ; $i++ ) { + my $qChar = substr( $qrySeq, $i, 1 ); + my $sChar = substr( $sbjSeq, $i, 1 ); + if ( $qChar ne "-" && $sChar ne "-" ) { $state = "M"; - }elsif ( $qChar eq "-" ) - { + } + elsif ( $qChar eq "-" ) { $state = "I"; - }else - { + } + else { $state = "D"; } - if ( $state ne $prevState ) - { + if ( $state ne $prevState ) { + # emit $outStr .= "$count$state"; $count = 0; @@ -2134,8 +2128,7 @@ sub _toCIGAR { $prevState = $state; $count++; } - if ( $count ) - { + if ( $count ) { $outStr .= "$count$state"; } @@ -2172,7 +2165,6 @@ sub _toCIGAR { return $cRec; } - ##-------------------------------------------------------------------------## ## Use: my $cmString = $obj->_toCrossMatchFormat( $alignmentMode, ## $displayParams ); diff --git a/SearchResultCollection.pm b/SearchResultCollection.pm index 7b8c8a1..effb101 100755 --- a/SearchResultCollection.pm +++ b/SearchResultCollection.pm @@ -29,10 +29,7 @@ ############################################################################### # ChangeLog # -# $Log: SearchResultCollection.pm,v $ -# Revision 1.88 2017/02/01 21:01:55 rhubley -# Cleanup before a distribution -# +# $Log$ # ############################################################################### # To Do: diff --git a/SeqDBI.pm b/SeqDBI.pm index b559921..9a70670 100755 --- a/SeqDBI.pm +++ b/SeqDBI.pm @@ -20,10 +20,7 @@ ############################################################################### # ChangeLog # -# $Log: SeqDBI.pm,v $ -# Revision 1.79 2017/02/01 21:01:55 rhubley -# Cleanup before a distribution -# +# $Log$ # ################################################################################ # diff --git a/SimpleBatcher.pm b/SimpleBatcher.pm index b088296..c1adb1a 100755 --- a/SimpleBatcher.pm +++ b/SimpleBatcher.pm @@ -23,10 +23,7 @@ ############################################################################### # ChangeLog # -# $Log: SimpleBatcher.pm,v $ -# Revision 1.81 2017/02/01 21:01:55 rhubley -# Cleanup before a distribution -# +# $Log$ # ################################################################################ # diff --git a/TRF.pm b/TRF.pm index dd875f5..7f95c26 100755 --- a/TRF.pm +++ b/TRF.pm @@ -53,10 +53,7 @@ ############################################################################### # ChangeLog # -# $Log: TRF.pm,v $ -# Revision 1.56 2017/02/01 21:01:55 rhubley -# Cleanup before a distribution -# +# $Log$ # ############################################################################### # To Do: diff --git a/TRFResult.pm b/TRFResult.pm index 0b31ed1..0658583 100755 --- a/TRFResult.pm +++ b/TRFResult.pm @@ -40,10 +40,7 @@ ############################################################################### # ChangeLog # -# $Log: TRFResult.pm,v $ -# Revision 1.49 2017/02/01 21:01:55 rhubley -# Cleanup before a distribution -# +# $Log$ # ############################################################################### # To Do: diff --git a/TRFSearchResult.pm b/TRFSearchResult.pm index 8a130ad..4982667 100755 --- a/TRFSearchResult.pm +++ b/TRFSearchResult.pm @@ -21,10 +21,7 @@ ############################################################################### # ChangeLog # -# $Log: TRFSearchResult.pm,v $ -# Revision 1.21 2017/02/01 21:01:55 rhubley -# Cleanup before a distribution -# +# $Log$ # ############################################################################### # To Do: diff --git a/Taxonomy.pm b/Taxonomy.pm index 9bdf084..c5538fd 100755 --- a/Taxonomy.pm +++ b/Taxonomy.pm @@ -23,10 +23,7 @@ ############################################################################### # ChangeLog # -# $Log: Taxonomy.pm,v $ -# Revision 1.101 2017/02/01 21:01:56 rhubley -# Cleanup before a distribution -# +# $Log$ # ############################################################################### # To Do: diff --git a/WUBlastSearchEngine.pm b/WUBlastSearchEngine.pm index fd3bf83..01aaccd 100755 --- a/WUBlastSearchEngine.pm +++ b/WUBlastSearchEngine.pm @@ -25,10 +25,7 @@ ############################################################################### # ChangeLog # -# $Log: WUBlastSearchEngine.pm,v $ -# Revision 1.139 2017/02/01 21:01:56 rhubley -# Cleanup before a distribution -# +# $Log$ # ############################################################################### # To Do: diff --git a/WUBlastXSearchEngine.pm b/WUBlastXSearchEngine.pm index 0fbe4ac..81e5e8a 100755 --- a/WUBlastXSearchEngine.pm +++ b/WUBlastXSearchEngine.pm @@ -25,10 +25,7 @@ ############################################################################### # ChangeLog # -# $Log: WUBlastXSearchEngine.pm,v $ -# Revision 1.57 2017/02/01 21:01:56 rhubley -# Cleanup before a distribution -# +# $Log$ # ############################################################################### # To Do: diff --git a/configure b/configure index fb18855..53eb447 100755 --- a/configure +++ b/configure @@ -18,10 +18,7 @@ ############################################################################### # ChangeLog # -# $Log: configure,v $ -# Revision 1.99 2017/02/01 21:01:56 rhubley -# Cleanup before a distribution -# +# $Log$ # ############################################################################### # @@ -234,10 +231,9 @@ system( ); ## Uncompress taxonomy.dat -if ( -s "$rmLocation/Libraries/taxonomy.dat.gz" ) -{ +if ( -s "$rmLocation/Libraries/taxonomy.dat.gz" ) { print "\n -- Uncompressing taxonomy.dat..."; - system("gunzip $rmLocation/Libraries/taxonomy.dat.gz"); + system( "gunzip $rmLocation/Libraries/taxonomy.dat.gz" ); } ## diff --git a/util/buildRMLibFromEMBL.pl b/util/buildRMLibFromEMBL.pl index 3314433..db05a44 100755 --- a/util/buildRMLibFromEMBL.pl +++ b/util/buildRMLibFromEMBL.pl @@ -21,10 +21,7 @@ # # ChangeLog # -# $Log: buildRMLibFromEMBL.pl,v $ -# Revision 1.47 2017/02/01 21:01:56 rhubley -# Cleanup before a distribution -# +# $Log$ # ############################################################################### # diff --git a/util/buildSummary.pl b/util/buildSummary.pl index ea239d5..c667d82 100755 --- a/util/buildSummary.pl +++ b/util/buildSummary.pl @@ -24,10 +24,7 @@ # # ChangeLog # -# $Log: buildSummary.pl,v $ -# Revision 1.36 2017/02/01 21:01:56 rhubley -# Cleanup before a distribution -# +# $Log$ # ############################################################################### # diff --git a/util/calcDivergenceFromAlign.pl b/util/calcDivergenceFromAlign.pl index 28f085e..0cce9d6 100755 --- a/util/calcDivergenceFromAlign.pl +++ b/util/calcDivergenceFromAlign.pl @@ -20,10 +20,7 @@ # # ChangeLog # -# $Log: calcDivergenceFromAlign.pl,v $ -# Revision 1.27 2017/02/01 21:01:56 rhubley -# Cleanup before a distribution -# +# $Log$ # ############################################################################### # diff --git a/util/createRepeatLandscape.pl b/util/createRepeatLandscape.pl index 8055203..e397a16 100755 --- a/util/createRepeatLandscape.pl +++ b/util/createRepeatLandscape.pl @@ -26,10 +26,7 @@ # # ChangeLog # -# $Log: createRepeatLandscape.pl,v $ -# Revision 1.14 2017/02/01 21:01:57 rhubley -# Cleanup before a distribution -# +# $Log$ # ############################################################################### # @@ -158,7 +155,7 @@ =head1 AUTHORS # -t=i: Number paramters # my @getopt_args = ( - '-version', # print out the version and exit + '-version', # print out the version and exit '-div=s', '-maxScale=s', '-g=s', diff --git a/util/dupliconToSVG.pl b/util/dupliconToSVG.pl index 8e3510a..e525168 100755 --- a/util/dupliconToSVG.pl +++ b/util/dupliconToSVG.pl @@ -25,10 +25,7 @@ # # ChangeLog # -# $Log: dupliconToSVG.pl,v $ -# Revision 1.29 2017/02/01 21:01:57 rhubley -# Cleanup before a distribution -# +# $Log$ # ############################################################################### # diff --git a/util/getRepeatMaskerBatch.pl b/util/getRepeatMaskerBatch.pl index 30cc5e2..ca845f3 100755 --- a/util/getRepeatMaskerBatch.pl +++ b/util/getRepeatMaskerBatch.pl @@ -19,10 +19,7 @@ ############################################################################### # ChangeLog: # -# $Log: getRepeatMaskerBatch.pl,v $ -# Revision 1.16 2017/02/01 21:01:57 rhubley -# Cleanup before a distribution -# +# $Log$ # ############################################################################### # diff --git a/util/queryRepeatDatabase.pl b/util/queryRepeatDatabase.pl index 1fd3f30..708c2b5 100755 --- a/util/queryRepeatDatabase.pl +++ b/util/queryRepeatDatabase.pl @@ -20,10 +20,7 @@ # # ChangeLog # -# $Log: queryRepeatDatabase.pl,v $ -# Revision 1.100 2017/02/01 21:01:57 rhubley -# Cleanup before a distribution -# +# $Log$ # ############################################################################### # diff --git a/util/queryTaxonomyDatabase.pl b/util/queryTaxonomyDatabase.pl index b0bab4f..a580a9a 100755 --- a/util/queryTaxonomyDatabase.pl +++ b/util/queryTaxonomyDatabase.pl @@ -20,10 +20,7 @@ # # ChangeLog # -# $Log: queryTaxonomyDatabase.pl,v $ -# Revision 1.77 2017/02/01 21:01:57 rhubley -# Cleanup before a distribution -# +# $Log$ # ############################################################################### # diff --git a/util/rmOut2Fasta.pl b/util/rmOut2Fasta.pl index d7ad5b9..5871ba6 100755 --- a/util/rmOut2Fasta.pl +++ b/util/rmOut2Fasta.pl @@ -19,10 +19,7 @@ ############################################################################### # ChangeLog: # -# $Log: rmOut2Fasta.pl,v $ -# Revision 1.6 2017/02/01 21:01:57 rhubley -# Cleanup before a distribution -# +# $Log$ # ############################################################################### # diff --git a/util/rmOutToGFF3.pl b/util/rmOutToGFF3.pl index 5015578..33655a5 100755 --- a/util/rmOutToGFF3.pl +++ b/util/rmOutToGFF3.pl @@ -20,10 +20,7 @@ # # ChangeLog # -# $Log: rmOutToGFF3.pl,v $ -# Revision 1.35 2017/02/01 21:01:58 rhubley -# Cleanup before a distribution -# +# $Log$ # ############################################################################### # diff --git a/util/rmToUCSCTables.pl b/util/rmToUCSCTables.pl index 9b0b6f9..df20ec7 100755 --- a/util/rmToUCSCTables.pl +++ b/util/rmToUCSCTables.pl @@ -23,10 +23,7 @@ # # ChangeLog # -# $Log: rmToUCSCTables.pl,v $ -# Revision 1.24 2017/02/01 21:01:58 rhubley -# Cleanup before a distribution -# +# $Log$ # ############################################################################### # diff --git a/util/wublastToCrossmatch.pl b/util/wublastToCrossmatch.pl index fe31d0f..1022109 100755 --- a/util/wublastToCrossmatch.pl +++ b/util/wublastToCrossmatch.pl @@ -26,10 +26,7 @@ # # ChangeLog # -# $Log: wublastToCrossmatch.pl,v $ -# Revision 1.9 2017/02/01 21:01:58 rhubley -# Cleanup before a distribution -# +# $Log$ # ############################################################################### #