From 9cbcae24024de52b686e79972dd91b164f9ecd78 Mon Sep 17 00:00:00 2001 From: Chinmay Rao Date: Mon, 17 Dec 2007 14:16:37 +0000 Subject: [PATCH] Committing EMBOSS v5.0 tools marscan maskfeat maskseq matcher megamerger merger and associated test files. --- tools/emboss_5/emboss_marscan.xml | 44 +++++++++++ tools/emboss_5/emboss_maskfeat.xml | 71 ++++++++++++++++++ tools/emboss_5/emboss_maskseq.xml | 71 ++++++++++++++++++ tools/emboss_5/emboss_matcher.xml | 56 ++++++++++++++ tools/emboss_5/emboss_megamerger.xml | 62 +++++++++++++++ tools/emboss_5/emboss_merger.xml | 75 +++++++++++++++++++ .../emboss_multiple_outputfile_wrapper.pl | 19 +++++ 7 files changed, 398 insertions(+) create mode 100644 tools/emboss_5/emboss_marscan.xml create mode 100644 tools/emboss_5/emboss_maskfeat.xml create mode 100644 tools/emboss_5/emboss_maskseq.xml create mode 100644 tools/emboss_5/emboss_matcher.xml create mode 100644 tools/emboss_5/emboss_megamerger.xml create mode 100644 tools/emboss_5/emboss_merger.xml create mode 100644 tools/emboss_5/emboss_multiple_outputfile_wrapper.pl diff --git a/tools/emboss_5/emboss_marscan.xml b/tools/emboss_5/emboss_marscan.xml new file mode 100644 index 00000000000..d4d10c45cd6 --- /dev/null +++ b/tools/emboss_5/emboss_marscan.xml @@ -0,0 +1,44 @@ + + Finds MAR/SAR sites in nucleic sequences + marscan -sequence $input1 -outfile $out_file1 -rformat2 $out_format1 -auto + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + You can view the original documentation here_. + + .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/marscan.html + + \ No newline at end of file diff --git a/tools/emboss_5/emboss_maskfeat.xml b/tools/emboss_5/emboss_maskfeat.xml new file mode 100644 index 00000000000..4a42ae6ae30 --- /dev/null +++ b/tools/emboss_5/emboss_maskfeat.xml @@ -0,0 +1,71 @@ + + Mask off features of a sequence + maskfeat -sequence $input1 -outseq $out_file1 -type "$type" -tolower $tolower -maskchar "$maskchar" -osformat2 $out_format1 -auto + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + You can view the original documentation here_. + + .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/maskfeat.html + + \ No newline at end of file diff --git a/tools/emboss_5/emboss_maskseq.xml b/tools/emboss_5/emboss_maskseq.xml new file mode 100644 index 00000000000..28c052997c9 --- /dev/null +++ b/tools/emboss_5/emboss_maskseq.xml @@ -0,0 +1,71 @@ + + Mask off regions of a sequence + maskseq -sequence $input1 -outseq $out_file1 -regions "$regions" -tolower $tolower -maskchar "$maskchar" -osformat2 $out_format1 -auto + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + You can view the original documentation here_. + + .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/maskseq.html + + \ No newline at end of file diff --git a/tools/emboss_5/emboss_matcher.xml b/tools/emboss_5/emboss_matcher.xml new file mode 100644 index 00000000000..42f4457ab49 --- /dev/null +++ b/tools/emboss_5/emboss_matcher.xml @@ -0,0 +1,56 @@ + + Finds the best local alignments between two sequences + matcher -asequence $input1 -bsequence $input2 -outfile $out_file1 -alternatives $alternatives -gapopen $gapopen -gapextend $gapextend -aformat3 $out_format1 -auto + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + You can view the original documentation here_. + + .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/matcher.html + + \ No newline at end of file diff --git a/tools/emboss_5/emboss_megamerger.xml b/tools/emboss_5/emboss_megamerger.xml new file mode 100644 index 00000000000..c038b89d01d --- /dev/null +++ b/tools/emboss_5/emboss_megamerger.xml @@ -0,0 +1,62 @@ + + Merge two large overlapping nucleic acid sequences + megamerger -asequence $input1 -bsequence $input2 -outseq $out_file1 -outfile $out_file2 -wordsize $wordsize -prefer $prefer -osformat3 $out_format1 -auto + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + You can view the original documentation here_. + + .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/megamerger.html + + \ No newline at end of file diff --git a/tools/emboss_5/emboss_merger.xml b/tools/emboss_5/emboss_merger.xml new file mode 100644 index 00000000000..4fff5e796d6 --- /dev/null +++ b/tools/emboss_5/emboss_merger.xml @@ -0,0 +1,75 @@ + + Merge two overlapping nucleic acid sequences + merger -asequence $input1 -bsequence $input2 -outseq $out_file1 -outfile $out_file2 -gapopen $gapopen -gapextend $gapextend -osformat4 $out_format1 -aformat3 $out_format2 -auto + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + You can view the original documentation here_. + + .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/merger.html + + \ No newline at end of file diff --git a/tools/emboss_5/emboss_multiple_outputfile_wrapper.pl b/tools/emboss_5/emboss_multiple_outputfile_wrapper.pl new file mode 100644 index 00000000000..e87c5423070 --- /dev/null +++ b/tools/emboss_5/emboss_multiple_outputfile_wrapper.pl @@ -0,0 +1,19 @@ +#! /usr/bin/perl -w +use strict; + +my $cmd_string = join (" ",@ARGV); +my $results = `$cmd_string`; +my @files = split("\n",$results); +foreach my $thisLine (@files) +{ + if ($thisLine =~ /Created /) + { + $thisLine =~ /[\w|\.]+$/; + $thisLine =$&; + print "outfile: $thisLine\n"; + } + else + { + print $thisLine,"\n"; + } +}