# HG changeset patch # User m-zytnicki # Date 1379508682 14400 # Node ID e454402ba9d98be7c6f48d0d61af3ccc57fb4d2d # Parent 5f796c5c579fcbcf6980e167c65dbd85b7f0de71 Deleted selected files diff -r 5f796c5c579f -r e454402ba9d9 CompareOverlappingAdapt.xml --- a/CompareOverlappingAdapt.xml Wed Sep 18 08:32:38 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,153 +0,0 @@ - - Provide the queries that overlap with a reference. - - PYTHONPATH - - - ../Java/Python/CompareOverlappingAdapt.py -i $formatType.inputFileName1 - #if $formatType.FormatInputFileName1 == 'bed': - -f bed - #elif $formatType.FormatInputFileName1 == 'gff': - -f gff - #elif $formatType.FormatInputFileName1 == 'gff2': - -f gff2 - #elif $formatType.FormatInputFileName1 == 'gff3': - -f gff3 - #elif $formatType.FormatInputFileName1 == 'sam': - -f sam - #elif $formatType.FormatInputFileName1 == 'gtf': - -f gtf - #end if - -j $formatType2.inputFileName2 - #if $formatType2.FormatInputFileName2 == 'bed': - -g bed - #elif $formatType2.FormatInputFileName2 == 'gff': - -g gff - #elif $formatType2.FormatInputFileName2 == 'gff2': - -g gff2 - #elif $formatType2.FormatInputFileName2 == 'gff3': - -g gff3 - #elif $formatType2.FormatInputFileName2 == 'sam': - -g sam - #elif $formatType2.FormatInputFileName2 == 'gtf': - -g gtf - #end if - -o $outputFileGff - #if $OptionDistance.Dist == 'Yes': - -d $OptionDistance.distance - #end if - #if $OptionCollinearOrAntiSens.OptionCA == 'Collinear': - -c - #elif $OptionCollinearOrAntiSens.OptionCA == 'AntiSens': - -a - #end if - $InvertMatch - $NotOverlapping - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -This script may be the most important one. It basically compares two sets of transcripts and keeps those from the first set which overlap with the second one. The first set is considered as the query set (basically, your data) and the second one is the reference set (RefSeq data, for example). - -It is vital to understand that it will output the elements of the first file which overlap with the elements of the second one. - -Various modifiers are also available: - --Invert selection (report those which do not overlap). - --Restrict to collinear / anti-sense overlapping data. - --Keep the query data even if they do not strictly overlap with the reference data, but are located not further away than *n* nucleotide from some reference data. - -Some option reverses the selection. Put in other words, it performs the comparison as usual, and outputs all those query data which do not overlap. - -