From 7a366bcec42f93df3da2b33996a96216158faa67 Mon Sep 17 00:00:00 2001 From: Chinmay Rao Date: Mon, 17 Dec 2007 14:38:16 +0000 Subject: [PATCH] Committing EMBOSS v5.0 tools tcode textsearch tmap twofeat vectorstrip wordmatch with associated functional test files --- tools/emboss_5/emboss_tcode.xml | 43 +++++++++ tools/emboss_5/emboss_textsearch.xml | 57 ++++++++++++ tools/emboss_5/emboss_tmap.xml | 38 ++++++++ tools/emboss_5/emboss_twofeat.xml | 129 ++++++++++++++++++++++++++ tools/emboss_5/emboss_vectorstrip.xml | 81 ++++++++++++++++ tools/emboss_5/emboss_wordmatch.xml | 73 +++++++++++++++ 6 files changed, 421 insertions(+) create mode 100644 tools/emboss_5/emboss_tcode.xml create mode 100644 tools/emboss_5/emboss_textsearch.xml create mode 100644 tools/emboss_5/emboss_tmap.xml create mode 100644 tools/emboss_5/emboss_twofeat.xml create mode 100644 tools/emboss_5/emboss_vectorstrip.xml create mode 100644 tools/emboss_5/emboss_wordmatch.xml diff --git a/tools/emboss_5/emboss_tcode.xml b/tools/emboss_5/emboss_tcode.xml new file mode 100644 index 00000000000..b65f71a57d3 --- /dev/null +++ b/tools/emboss_5/emboss_tcode.xml @@ -0,0 +1,43 @@ + + Fickett TESTCODE statistic to identify protein-coding DNA + tcode -sequence $input1 -outfile $out_file1 -window "$window" -step "$step" -rformat $out_format1 -auto + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + You can view the original documentation here_. + + .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/tcode.html + + \ No newline at end of file diff --git a/tools/emboss_5/emboss_textsearch.xml b/tools/emboss_5/emboss_textsearch.xml new file mode 100644 index 00000000000..acc08286b79 --- /dev/null +++ b/tools/emboss_5/emboss_textsearch.xml @@ -0,0 +1,57 @@ + + Search sequence documentation. Slow, use SRS and Entrez! + textsearch -sequence $input1 -outfile $out_file1 -pattern "$pattern" -casesensitive -heading $heading -usa $usa -accession $accession -name $search_name -description $description -html + $html_out1 -auto + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + You can view the original documentation here_. + + .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/textsearch.html + + \ No newline at end of file diff --git a/tools/emboss_5/emboss_tmap.xml b/tools/emboss_5/emboss_tmap.xml new file mode 100644 index 00000000000..9238b3491bf --- /dev/null +++ b/tools/emboss_5/emboss_tmap.xml @@ -0,0 +1,38 @@ + + Displays membrane spanning regions + emboss_single_outputfile_wrapper.pl tmap -sequences $input1 -outfile $out_file1 -goutfile $out_file2 -graph png -rformat $out_format1 -auto + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + You can view the original documentation here_. + + .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/tmap.html + + \ No newline at end of file diff --git a/tools/emboss_5/emboss_twofeat.xml b/tools/emboss_5/emboss_twofeat.xml new file mode 100644 index 00000000000..1337d586708 --- /dev/null +++ b/tools/emboss_5/emboss_twofeat.xml @@ -0,0 +1,129 @@ + + Finds neighbouring pairs of features in sequences + twofeat -sequence $input1 -outfile $out_file1 -atype "$atype" -btype "$btype" -minrange "$minrange" -maxrange "$maxrange" -asource "$asource" -asense $asense -aminscore "$aminscore" + -amaxscore "$amaxscore" -atag "$atag" -avalue "$avalue" -bsource "$bsource" -bsense "$bsense" -bminscore "$bminscore" -bmaxscore "$bmaxscore" -btag "$btag" -bvalue "$bvalue" -overlap $overlap + -rangetype $rangetype -sense $sense -order $order -twoout $twoout -typeout "$typeout" -rformat2 $out_format1 -auto + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + You can view the original documentation here_. + + .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/twofeat.html + + \ No newline at end of file diff --git a/tools/emboss_5/emboss_vectorstrip.xml b/tools/emboss_5/emboss_vectorstrip.xml new file mode 100644 index 00000000000..13752bc0956 --- /dev/null +++ b/tools/emboss_5/emboss_vectorstrip.xml @@ -0,0 +1,81 @@ + + Strips out DNA between a pair of vector sequences + vectorstrip -sequence $input1 -vectorsfile $input2 -outseq $ofile1 -outfile $ofile2 -vectorfile yes -mismatch "$mismatch" -besthits $besthits -linkera "$linkera" -linkerb + "$linkerb" -osformat4 $out_format1 -auto + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + You can view the original documentation here_. + + .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/vectorstrip.html + + diff --git a/tools/emboss_5/emboss_wordmatch.xml b/tools/emboss_5/emboss_wordmatch.xml new file mode 100644 index 00000000000..315dca92fa7 --- /dev/null +++ b/tools/emboss_5/emboss_wordmatch.xml @@ -0,0 +1,73 @@ + + Finds all exact matches of a given size between 2 sequences + wordmatch -asequence $input1 -bsequence $input2 -outfile $out_file1 -aoutfeat $out_file2 -boutfeat $out_file3 -wordsize "$wordsize" -aformat3 $out_format1 -offormat4 $out_format2 + -offormat5 $out_format3 -auto + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +.. class:: warningmark + +The input datasets need to be sequences. + +----- + + You can view the original documentation here_. + + .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/wordmatch.html + +