# HG changeset patch # User yhoogstrate # Date 1431938959 14400 # Node ID ab0323782bb5211267cbb251f31ab38077468438 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/featurecounts commit cc900436bad9c6cca1f73d438c1f158d3bfc4318-dirty diff -r 000000000000 -r ab0323782bb5 README.rst --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.rst Mon May 18 04:49:19 2015 -0400 @@ -0,0 +1,59 @@ +FeatureCounts wrapper for Galaxy +================================ + +http://bioinf.wehi.edu.au/featureCounts/ +http://subread.sourceforge.net/ + +FeatureCounts as part of the SUBREAD package is "a highly efficient and +accurate read summarization program". + +Development +----------- + +* Repository-Maintainer: Youri Hoogstrate +* Repository-Developers: Youri Hoogstrate, Marius van den Beek + +* Repository-Development: https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools + +The tool wrapper has been written by Youri Hoogstrate from the Erasmus +Medical Center (Rotterdam, Netherlands) on behalf of the Translational +Research IT (TraIT) project: + +http://www.ctmm.nl/en/programmas/infrastructuren/traitprojecttranslationeleresearch + +More tools by the Translational Research IT (TraIT) project can be found in the following repository: + +http://toolshed.dtls.nl/ + +License +------- + +**featureCounts**: + +GPL (>=3) + +**featurecounts2bed**: + +GPL (>=3) + +**This wrapper**: + + Copyright (C) 2013-2014 Youri Hoogstrate + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with this program. If not, see . + +Acknowledgements +---------------- + +I would like to thank Marius van den Beek for his contributions to this project. \ No newline at end of file diff -r 000000000000 -r ab0323782bb5 featurecounts.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/featurecounts.xml Mon May 18 04:49:19 2015 -0400 @@ -0,0 +1,281 @@ + + + Measure gene expression in RNA-Seq experiments from SAM or BAM files. + + featurecounts + featurecounts2bed + + featureCounts -v + + #* + The following script is written in the "Cheetah" language: + http://www.cheetahtemplate.org/docs/users_guide_html_multipage/contents.html + *# + + ## Check 01: do the alignments have a dbkey and is the option set to using it? + #if $reference_gene_sets_source.source_select == "attribute" and len({ alignment.metadata.dbkey:True for alignment in $alignments }.keys()) != 1 + echo "Invalid number of dbkeys are found: ${ len({ alignment.metadata.dbkey:True for alignment in $alignments }.keys()) }, while only one should be used. Make sure that the alignments are done on the same reference genome and that 'tool-data/gene_sets.loc' is configured properly!" >&2 + #else + ## Check 02: are all alignments from the same type (bam || sam) + #if len({ alignment.extension:True for alignment in $alignments }.keys()) != 1 + echo "Either all files must be SAM or all files must be BAM, no mixture is allowed." >&2 + #else + featureCounts + -a + #if $reference_gene_sets_source.source_select == "indexed_filtered" + "$reference_gene_sets_source.reference_gene_sets" + #else if $reference_gene_sets_source.source_select == "indexed_all" + "$reference_gene_sets_source.reference_gene_sets" + #else if $reference_gene_sets_source.source_select == "history" + "$reference_gene_sets_source.reference_gene_sets" + #else + #* + This is a workaround to obtain the "genome.fa" file that + corresponds to the dbkey of the alignments. + Because this file is "calculated" during run-time, it can + be used in a workflow. + *# + "${ filter( lambda x: str( x[0] ) == str( { alignment.metadata.dbkey:True for alignment in $alignments }.keys()[0] ), $__app__.tool_data_tables[ 'gene_sets' ].get_fields() )[0][2] }" + #end if + + -o "$output" + -T $threads + + #if $extended_parameters.parameters == "extended" + -t $extended_parameters.gff_feature_type + -g $extended_parameters.gff_feature_attribute + $extended_parameters.summarization_level + $extended_parameters.contribute_to_multiple_features + $extended_parameters.protocol + $extended_parameters.multimapping_counts + -Q $extended_parameters.mapping_quality + $extended_parameters.fragment_counting + $extended_parameters.check_distance + -d $extended_parameters.minimum_fragment_length + -D $extended_parameters.maximum_fragment_length + $extended_parameters.only_both_ends + $extended_parameters.exclude_chimerics + $extended_parameters.namesort + #end if + + #for $alignment in $alignments + ${alignment} + #end for + + 2>&1 + + #set $columns = [str(i+7) for i, alignment in enumerate($alignments)] + #set $columns=",".join($columns) + + #if $format == "tabdel_default" or $format.value == "tabdel_default" + ; cp $output tmp.txt + ; egrep -v "^#" tmp.txt > tmp2.txt + ; cut -f 1,$columns tmp2.txt > tmp_left.txt + ; cut -f 6 tmp2.txt > tmp_right.txt + ; paste tmp_left.txt tmp_right.txt > $output + #elif $format == "tabdel_short" or $format.value == "tabdel_short" + ; cp $output tmp.txt + ; egrep -v "^#" tmp.txt | cut -f 1,$columns > $output + #end if + + ## For every alignment, replace its filename for: "hid: sample name" + #for $alignment in $alignments + #set $alignment_escaped = str($alignment).replace('/', '\/').replace('.', '\.') + #set $alignment_name_escaped = str(alignment.hid)+": "+str($alignment.name).replace('\t',' ').replace('\\','\\\\').replace("'","\\'").replace('/','\/') + + #if $format.value == "tabdel_default" or $format.value == "tabdel_short" + ; sed -e '1 s/$alignment_escaped/${alignment_name_escaped}/g' $output > tmp.txt + #elif $format.value == "bed": + ; featurecounts2bed.sh -f "$output" > tmp.txt + #else + ; sed -e '1,2 s/$alignment_escaped/${alignment_name_escaped}/g' $output > tmp.txt + #end if + + ; mv tmp.txt $output + + ; sed -e '1 s/$alignment_escaped/${alignment_name_escaped}/g' $output".summary" > tmp.txt + ; mv tmp.txt $output".summary" + #end for + ; mv $output".summary" $output_summary + #end if + #end if + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +featureCounts +############# + +Overview +-------- +FeatureCounts is a light-weight read counting program written entirely in the C programming language. It can be used to count both gDNA-seq and RNA-seq reads for genomic features in in SAM/BAM files. +It has a variety of advanced parameters but its major strength is its outstanding performance: analysis of a 10GB SE BAM file takes about 7 minutes on a single average CPU (Homo Sapiens genome) [1]. + +Input formats +------------- +Alignments should be provided in either: + +- SAM format, http://samtools.sourceforge.net/samtools.shtml#5 +- BAM format + +Gene regions should be provided in the GFF/GTF format: + +- http://genome.ucsc.edu/FAQ/FAQformat.html#format3 +- http://www.ensembl.org/info/website/upload/gff.html + +Installation +------------ + +1. Make sure you have proper GFF/GTF files (corresponding to your reference genome used for the aligment) uploaded to your history. + +2. Make sure that your gene_sets.loc is configured properly as data table. This is generally done by copying the right information into: tool_data_table_conf.xml. More info at: https://wiki.galaxyproject.org/Admin/Tools/Data%20Tables + +License +------- + +**featureCounts / subread package**: + +- GNU General Public License version 3.0 (GPLv3) + +Contact +------- + +The tool wrapper has been written by Youri Hoogstrate from the Erasmus +Medical Center (Rotterdam, Netherlands) on behalf of the Translational +Research IT (TraIT) project: + +http://www.ctmm.nl/en/programmas/infrastructuren/traitprojecttranslationeleresearch + +More tools by the Translational Research IT (TraIT) project can be found +in the following toolsheds: + +http://toolshed.dtls.nl/ + +http://toolshed.g2.bx.psu.edu/ + +http://testtoolshed.g2.bx.psu.edu/ + +References +---------- +**featureCounts: an efficient general purpose program for assigning sequence reads to genomic features.** + +*Liao Y1, Smyth GK, Shi W.* - Bioinformatics. 2014 Apr 1;30(7):923-30. + +- http://www.ncbi.nlm.nih.gov/pubmed/24227677 +- http://dx.doi.org/10.1093/bioinformatics/btt656 + + +Acknowledgements +---------------- + +I would like to thank Marius van den Beek for his contributions to this project. + + + 10.1093/bioinformatics/btt656 + + diff -r 000000000000 -r ab0323782bb5 featurecounts2bed.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/featurecounts2bed.sh Mon May 18 04:49:19 2015 -0400 @@ -0,0 +1,78 @@ +#!/bin/bash + +# featurecounts2bed - converts featureCounts output to BED format + +# Copyright 2013-2014, Youri Hoogstrate + +# This program is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. + +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License at for +# more details. + +# This tool has been written by Youri Hoogstrate from the Erasmus +# Medical Center (Rotterdam, Netherlands) on behalf of the Translational +# Research IT (TraIT) project: +# http://www.ctmm.nl/en/programmas/infrastructuren/traitprojecttranslationeleresearch +# +# More tools by the Translational Research IT (TraIT) project can be +# found in the following repository: +# http://toolshed.dtls.nl/ + + +exon_level="true" +filename="" + +# Parse parameters +while getopts e:f: option +do + case "${option}" + in + e) exon_level=${OPTARG};; + f) filename=$OPTARG;; + esac +done + +# Convert the file +if [ $filename == "" ]; then + echo "Usage:" + echo " -e [true, false] true = entry for every exon; false = line for genes first exon" + echo " -f FILENAME from featureCounts" +else + while read line; do + first=${line:0:1} + if [ $first != "#" ]; then + columns=($line) + uid=${columns[@]:0:1} + if [ $uid != "Geneid" ]; then + chr=${columns[@]:1:1} + start=${columns[@]:2:1} + stop=${columns[@]:3:1} + direction=${columns[@]:4:1} + length=${columns[@]:5:1} + count=${columns[@]:6:1} + + chr_splitted=($(echo $chr | tr ";" "\n")) + start_splitted=($(echo $start | tr ";" "\n")) + stop_splitted=($(echo $stop | tr ";" "\n")) + strand_splitted=($(echo $direction | tr ";" "\n")) + + if [ $exon_level == "true" ]; then + n=${#chr_splitted[@]} + else + n=1 + fi + + for (( i=0; i<$n; i++ )) + do + echo ${chr_splitted[@]:$i:1}" "${start_splitted[@]:$i:1}" "${stop_splitted[@]:$i:1}" "$uid" ("$((${stop_splitted[@]:$i:1}-${start_splitted[@]:$i:1}))"/"$length"nt) "$count" "${strand_splitted[@]:$i:1} + done + fi + fi + done < $filename +fi diff -r 000000000000 -r ab0323782bb5 test-data/featureCounts_guide.gff --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/featureCounts_guide.gff Mon May 18 04:49:19 2015 -0400 @@ -0,0 +1,680 @@ +X FlyBase exon 30948 31447 . + . ID=FBti0062706;gene_id=left +X FlyBase exon 32172 32671 . + . ID=FBti0062706;gene_id=right +X FlyBase exon 51312 51811 . + . ID=FBti0062715;gene_id=left +X FlyBase exon 52318 52817 . + . ID=FBti0062715;gene_id=right +X FlyBase exon 53883 54382 . - . ID=FBti0062719;gene_id=left +X FlyBase exon 55280 55779 . - . ID=FBti0062719;gene_id=right +X FlyBase exon 64215 64714 . + . ID=FBti0062738;gene_id=left +X FlyBase exon 65335 65834 . + . ID=FBti0062738;gene_id=right +X FlyBase exon 77479 77978 . - . ID=FBti0063571;gene_id=left +X FlyBase exon 78341 78840 . - . ID=FBti0063571;gene_id=right +X FlyBase exon 79405 79904 . - . ID=FBti0063569;gene_id=left +X FlyBase exon 80154 80653 . - . ID=FBti0063569;gene_id=right +X FlyBase exon 82402 82901 . - . ID=FBti0063568;gene_id=left +X FlyBase exon 83164 83663 . - . ID=FBti0063568;gene_id=right +X FlyBase exon 90012 90511 . + . ID=FBti0062762;gene_id=left +X FlyBase exon 90918 91417 . + . ID=FBti0062762;gene_id=right +X FlyBase exon 92326 92825 . + . ID=FBti0062765;gene_id=left +X FlyBase exon 93238 93737 . + . ID=FBti0062765;gene_id=right +X FlyBase exon 168410 168909 . + . ID=FBti0062766;gene_id=left +X FlyBase exon 169363 169862 . + . ID=FBti0062766;gene_id=right +X FlyBase exon 184346 184845 . - . ID=FBti0062772;gene_id=left +X FlyBase exon 185123 185622 . - . ID=FBti0062772;gene_id=right +X FlyBase exon 186159 186658 . - . ID=FBti0019520;gene_id=left +X FlyBase exon 187028 187527 . - . ID=FBti0019520;gene_id=right +X FlyBase exon 189437 189936 . - . ID=FBti0019521;gene_id=left +X FlyBase exon 197509 198008 . - . ID=FBti0019521;gene_id=right +X FlyBase exon 200157 200656 . - . ID=FBti0062785;gene_id=left +X FlyBase exon 200936 201435 . - . ID=FBti0062785;gene_id=right +X FlyBase exon 212059 212558 . + . ID=FBti0019522;gene_id=left +X FlyBase exon 217588 218087 . + . ID=FBti0019522;gene_id=right +X FlyBase exon 230841 231340 . - . ID=FBti0062869;gene_id=left +X FlyBase exon 231571 232070 . - . ID=FBti0062869;gene_id=right +X FlyBase exon 322007 322506 . + . ID=FBti0019523;gene_id=left +X FlyBase exon 328634 329133 . + . ID=FBti0019523;gene_id=right +X FlyBase exon 445010 445509 . + . ID=FBti0019524;gene_id=left +X FlyBase exon 453015 453514 . + . ID=FBti0019524;gene_id=right +X FlyBase exon 539893 540392 . + . ID=FBti0063323;gene_id=left +X FlyBase exon 540801 541300 . + . ID=FBti0063323;gene_id=right +X FlyBase exon 558910 559409 . - . ID=FBti0063324;gene_id=left +X FlyBase exon 559791 560290 . - . ID=FBti0063324;gene_id=right +X FlyBase exon 577936 578435 . + . ID=FBti0063326;gene_id=left +X FlyBase exon 578752 579251 . + . ID=FBti0063326;gene_id=right +X FlyBase exon 587701 588200 . + . ID=FBti0063332;gene_id=left +X FlyBase exon 588492 588991 . + . ID=FBti0063332;gene_id=right +X FlyBase exon 598742 599241 . + . ID=FBti0063335;gene_id=left +X FlyBase exon 599600 600099 . + . ID=FBti0063335;gene_id=right +X FlyBase exon 604149 604648 . + . ID=FBti0063337;gene_id=left +X FlyBase exon 605153 605652 . + . ID=FBti0063337;gene_id=right +X FlyBase exon 615232 615731 . + . ID=FBti0063351;gene_id=left +X FlyBase exon 616141 616640 . + . ID=FBti0063351;gene_id=right +X FlyBase exon 705855 706354 . + . ID=FBti0019525;gene_id=left +X FlyBase exon 711929 712428 . + . ID=FBti0019525;gene_id=right +X FlyBase exon 721190 721689 . + . ID=FBti0019526;gene_id=left +X FlyBase exon 729424 729923 . + . ID=FBti0019526;gene_id=right +X FlyBase exon 800289 800788 . + . ID=FBti0019527;gene_id=left +X FlyBase exon 802523 803022 . + . ID=FBti0019527;gene_id=right +X FlyBase exon 915767 916266 . + . ID=FBti0019528;gene_id=left +X FlyBase exon 916539 917038 . + . ID=FBti0019528;gene_id=right +X FlyBase exon 926940 927439 . + . ID=FBti0019531;gene_id=left +X FlyBase exon 935016 935515 . + . ID=FBti0019531;gene_id=right +X FlyBase exon 957344 957843 . + . ID=FBti0019532;gene_id=left +X FlyBase exon 966580 967079 . + . ID=FBti0019532;gene_id=right +X FlyBase exon 1407723 1408222 . + . ID=FBti0019536;gene_id=left +X FlyBase exon 1408486 1408985 . + . ID=FBti0019536;gene_id=right +X FlyBase exon 1461250 1461749 . - . ID=FBti0019537;gene_id=left +X FlyBase exon 1463477 1463976 . - . ID=FBti0019537;gene_id=right +X FlyBase exon 1521562 1522061 . - . ID=FBti0019538;gene_id=left +X FlyBase exon 1529473 1529972 . - . ID=FBti0019538;gene_id=right +X FlyBase exon 1630699 1631198 . - . ID=FBti0019539;gene_id=left +X FlyBase exon 1640306 1640805 . - . ID=FBti0019539;gene_id=right +X FlyBase exon 1712287 1712786 . - . ID=FBti0063525;gene_id=left +X FlyBase exon 1713042 1713541 . - . ID=FBti0063525;gene_id=right +X FlyBase exon 1714165 1714664 . + . ID=FBti0063527;gene_id=left +X FlyBase exon 1714987 1715486 . + . ID=FBti0063527;gene_id=right +X FlyBase exon 1824125 1824624 . - . ID=FBti0019540;gene_id=left +X FlyBase exon 1832140 1832639 . - . ID=FBti0019540;gene_id=right +X FlyBase exon 1848474 1848973 . - . ID=FBti0019541;gene_id=left +X FlyBase exon 1856857 1857356 . - . ID=FBti0019541;gene_id=right +X FlyBase exon 2025638 2026137 . + . ID=FBti0019542;gene_id=left +X FlyBase exon 2027584 2028083 . + . ID=FBti0019542;gene_id=right +X FlyBase exon 2202381 2202880 . - . ID=FBti0019543;gene_id=left +X FlyBase exon 2211408 2211907 . - . ID=FBti0019543;gene_id=right +X FlyBase exon 2293426 2293925 . + . ID=FBti0019544;gene_id=left +X FlyBase exon 2302221 2302720 . + . ID=FBti0019544;gene_id=right +X FlyBase exon 2319538 2320037 . + . ID=FBti0063994;gene_id=left +X FlyBase exon 2320468 2320967 . + . ID=FBti0063994;gene_id=right +X FlyBase exon 2503973 2504472 . - . ID=FBti0019545;gene_id=left +X FlyBase exon 2511533 2512032 . - . ID=FBti0019545;gene_id=right +X FlyBase exon 2557975 2558474 . - . ID=FBti0019546;gene_id=left +X FlyBase exon 2559561 2560060 . - . ID=FBti0019546;gene_id=right +X FlyBase exon 2717376 2717875 . - . ID=FBti0019547;gene_id=left +X FlyBase exon 2726366 2726865 . - . ID=FBti0019547;gene_id=right +X FlyBase exon 2738488 2738987 . - . ID=FBti0019548;gene_id=left +X FlyBase exon 2746341 2746840 . - . ID=FBti0019548;gene_id=right +X FlyBase exon 2951607 2952106 . - . ID=FBti0019549;gene_id=left +X FlyBase exon 2952293 2952792 . - . ID=FBti0019549;gene_id=right +X FlyBase exon 2963803 2964302 . - . ID=FBti0019550;gene_id=left +X FlyBase exon 2967374 2967873 . - . ID=FBti0019550;gene_id=right +X FlyBase exon 2969222 2969721 . + . ID=FBti0019551;gene_id=left +X FlyBase exon 2974971 2975470 . + . ID=FBti0019551;gene_id=right +X FlyBase exon 3072054 3072553 . + . ID=FBti0019552;gene_id=left +X FlyBase exon 3080162 3080661 . + . ID=FBti0019552;gene_id=right +X FlyBase exon 3112094 3112593 . - . ID=FBti0019553;gene_id=left +X FlyBase exon 3121685 3122184 . - . ID=FBti0019553;gene_id=right +X FlyBase exon 3308606 3309105 . - . ID=FBti0019554;gene_id=left +X FlyBase exon 3315233 3315732 . - . ID=FBti0019554;gene_id=right +X FlyBase exon 3357795 3358294 . - . ID=FBti0019555;gene_id=left +X FlyBase exon 3359641 3360140 . - . ID=FBti0019555;gene_id=right +X FlyBase exon 3386680 3387179 . - . ID=FBti0019556;gene_id=left +X FlyBase exon 3396281 3396780 . - . ID=FBti0019556;gene_id=right +X FlyBase exon 3556511 3557010 . - . ID=FBti0059983;gene_id=left +X FlyBase exon 3557209 3557708 . - . ID=FBti0059983;gene_id=right +X FlyBase exon 3647008 3647507 . - . ID=FBti0019563;gene_id=left +X FlyBase exon 3655006 3655505 . - . ID=FBti0019563;gene_id=right +X FlyBase exon 3679400 3679899 . - . ID=FBti0019564;gene_id=left +X FlyBase exon 3680089 3680588 . - . ID=FBti0019564;gene_id=right +X FlyBase exon 3689927 3690426 . - . ID=FBti0060049;gene_id=left +X FlyBase exon 3690843 3691342 . - . ID=FBti0060049;gene_id=right +X FlyBase exon 3735908 3736407 . - . ID=FBti0019565;gene_id=left +X FlyBase exon 3736594 3737093 . - . ID=FBti0019565;gene_id=right +X FlyBase exon 3833560 3834059 . + . ID=FBti0060050;gene_id=left +X FlyBase exon 3834334 3834833 . + . ID=FBti0060050;gene_id=right +X FlyBase exon 3880451 3880950 . - . ID=FBti0019566;gene_id=left +X FlyBase exon 3888527 3889026 . - . ID=FBti0019566;gene_id=right +X FlyBase exon 4051480 4051979 . + . ID=FBti0019567;gene_id=left +X FlyBase exon 4058958 4059457 . + . ID=FBti0019567;gene_id=right +X FlyBase exon 4178048 4178547 . - . ID=FBti0019568;gene_id=left +X FlyBase exon 4183693 4184192 . - . ID=FBti0019568;gene_id=right +X FlyBase exon 4524542 4525041 . + . ID=FBti0060466;gene_id=left +X FlyBase exon 4525317 4525816 . + . ID=FBti0060466;gene_id=right +X FlyBase exon 4581901 4582400 . + . ID=FBti0060479;gene_id=left +X FlyBase exon 4582662 4583161 . + . ID=FBti0060479;gene_id=right +X FlyBase exon 4593999 4594498 . - . ID=FBti0019569;gene_id=left +X FlyBase exon 4594766 4595265 . - . ID=FBti0019569;gene_id=right +X FlyBase exon 4625418 4625917 . - . ID=FBti0019570;gene_id=left +X FlyBase exon 4630936 4631435 . - . ID=FBti0019570;gene_id=right +X FlyBase exon 4656840 4657339 . + . ID=FBti0019571;gene_id=left +X FlyBase exon 4657771 4658270 . + . ID=FBti0019571;gene_id=right +X FlyBase exon 4683101 4683600 . - . ID=FBti0019572;gene_id=left +X FlyBase exon 4684795 4685294 . - . ID=FBti0019572;gene_id=right +X FlyBase exon 4685985 4686484 . - . ID=FBti0019573;gene_id=left +X FlyBase exon 4686835 4687334 . - . ID=FBti0019573;gene_id=right +X FlyBase exon 4721556 4722055 . - . ID=FBti0019574;gene_id=left +X FlyBase exon 4729370 4729869 . - . ID=FBti0019574;gene_id=right +X FlyBase exon 4989861 4990360 . - . ID=FBti0019578;gene_id=left +X FlyBase exon 4997871 4998370 . - . ID=FBti0019578;gene_id=right +X FlyBase exon 5232315 5232814 . - . ID=FBti0019579;gene_id=left +X FlyBase exon 5233988 5234487 . - . ID=FBti0019579;gene_id=right +X FlyBase exon 5283350 5283849 . - . ID=FBti0019580;gene_id=left +X FlyBase exon 5286897 5287396 . - . ID=FBti0019580;gene_id=right +X FlyBase exon 5374647 5375146 . + . ID=FBti0019581;gene_id=left +X FlyBase exon 5379034 5379533 . + . ID=FBti0019581;gene_id=right +X FlyBase exon 5418429 5418928 . + . ID=FBti0019582;gene_id=left +X FlyBase exon 5422735 5423234 . + . ID=FBti0019582;gene_id=right +X FlyBase exon 5620971 5621470 . + . ID=FBti0019583;gene_id=left +X FlyBase exon 5626192 5626691 . + . ID=FBti0019583;gene_id=right +X FlyBase exon 5767200 5767699 . - . ID=FBti0061115;gene_id=left +X FlyBase exon 5767900 5768399 . - . ID=FBti0061115;gene_id=right +X FlyBase exon 5820682 5821181 . - . ID=FBti0019586;gene_id=left +X FlyBase exon 5826329 5826828 . - . ID=FBti0019586;gene_id=right +X FlyBase exon 6065171 6065670 . - . ID=FBti0019587;gene_id=left +X FlyBase exon 6073047 6073546 . - . ID=FBti0019587;gene_id=right +X FlyBase exon 6228798 6229297 . + . ID=FBti0019588;gene_id=left +X FlyBase exon 6231752 6232251 . + . ID=FBti0019588;gene_id=right +X FlyBase exon 6286459 6286958 . + . ID=FBti0019589;gene_id=left +X FlyBase exon 6291656 6292155 . + . ID=FBti0019589;gene_id=right +X FlyBase exon 6323576 6324075 . - . ID=FBti0019590;gene_id=left +X FlyBase exon 6329246 6329745 . - . ID=FBti0019590;gene_id=right +X FlyBase exon 6338891 6339390 . - . ID=FBti0019591;gene_id=left +X FlyBase exon 6345092 6345591 . - . ID=FBti0019591;gene_id=right +X FlyBase exon 6456406 6456905 . - . ID=FBti0019592;gene_id=left +X FlyBase exon 6465332 6465831 . - . ID=FBti0019592;gene_id=right +X FlyBase exon 6499064 6499563 . - . ID=FBti0019593;gene_id=left +X FlyBase exon 6502529 6503028 . - . ID=FBti0019593;gene_id=right +X FlyBase exon 6649313 6649812 . + . ID=FBti0019594;gene_id=left +X FlyBase exon 6650237 6650736 . + . ID=FBti0019594;gene_id=right +X FlyBase exon 6908350 6908849 . - . ID=FBti0061617;gene_id=left +X FlyBase exon 6909099 6909598 . - . ID=FBti0061617;gene_id=right +X FlyBase exon 6917189 6917688 . + . ID=FBti0019596;gene_id=left +X FlyBase exon 6925022 6925521 . + . ID=FBti0019596;gene_id=right +X FlyBase exon 7018834 7019333 . + . ID=FBti0019597;gene_id=left +X FlyBase exon 7028435 7028934 . + . ID=FBti0019597;gene_id=right +X FlyBase exon 7374377 7374876 . - . ID=FBti0019598;gene_id=left +X FlyBase exon 7376310 7376809 . - . ID=FBti0019598;gene_id=right +X FlyBase exon 7596495 7596994 . + . ID=FBti0019599;gene_id=left +X FlyBase exon 7597374 7597873 . + . ID=FBti0019599;gene_id=right +X FlyBase exon 7677833 7678332 . - . ID=FBti0019600;gene_id=left +X FlyBase exon 7678566 7679065 . - . ID=FBti0019600;gene_id=right +X FlyBase exon 7739314 7739813 . - . ID=FBti0019601;gene_id=left +X FlyBase exon 7741247 7741746 . - . ID=FBti0019601;gene_id=right +X FlyBase exon 7925028 7925527 . - . ID=FBti0019602;gene_id=left +X FlyBase exon 7929763 7930262 . - . ID=FBti0019602;gene_id=right +X FlyBase exon 8186836 8187335 . + . ID=FBti0019603;gene_id=left +X FlyBase exon 8190317 8190816 . + . ID=FBti0019603;gene_id=right +X FlyBase exon 8206413 8206912 . + . ID=FBti0062566;gene_id=left +X FlyBase exon 8207205 8207704 . + . ID=FBti0062566;gene_id=right +X FlyBase exon 8258438 8258937 . + . ID=FBti0019604;gene_id=left +X FlyBase exon 8259269 8259768 . + . ID=FBti0019604;gene_id=right +X FlyBase exon 8353372 8353871 . - . ID=FBti0019605;gene_id=left +X FlyBase exon 8354476 8354975 . - . ID=FBti0019605;gene_id=right +X FlyBase exon 8815918 8816417 . + . ID=FBti0019606;gene_id=left +X FlyBase exon 8816778 8817277 . + . ID=FBti0019606;gene_id=right +X FlyBase exon 8842347 8842846 . + . ID=FBti0019608;gene_id=left +X FlyBase exon 8850299 8850798 . + . ID=FBti0019608;gene_id=right +X FlyBase exon 9401726 9402225 . + . ID=FBti0019609;gene_id=left +X FlyBase exon 9403665 9404164 . + . ID=FBti0019609;gene_id=right +X FlyBase exon 9469379 9469878 . + . ID=FBti0019610;gene_id=left +X FlyBase exon 9470146 9470645 . + . ID=FBti0019610;gene_id=right +X FlyBase exon 9692111 9692610 . - . ID=FBti0019611;gene_id=left +X FlyBase exon 9699606 9700105 . - . ID=FBti0019611;gene_id=right +X FlyBase exon 10031803 10032302 . + . ID=FBti0019614;gene_id=left +X FlyBase exon 10039744 10040243 . + . ID=FBti0019614;gene_id=right +X FlyBase exon 10160891 10161390 . - . ID=FBti0019615;gene_id=left +X FlyBase exon 10170483 10170982 . - . ID=FBti0019615;gene_id=right +X FlyBase exon 10242387 10242886 . + . ID=FBti0019616;gene_id=left +X FlyBase exon 10250397 10250896 . + . ID=FBti0019616;gene_id=right +X FlyBase exon 10339131 10339630 . - . ID=FBti0063412;gene_id=left +X FlyBase exon 10339856 10340355 . - . ID=FBti0063412;gene_id=right +X FlyBase exon 10418659 10419158 . + . ID=FBti0019617;gene_id=left +X FlyBase exon 10426155 10426654 . + . ID=FBti0019617;gene_id=right +X FlyBase exon 10444444 10444943 . + . ID=FBti0019618;gene_id=left +X FlyBase exon 10446350 10446849 . + . ID=FBti0019618;gene_id=right +X FlyBase exon 10579639 10580138 . - . ID=FBti0019619;gene_id=left +X FlyBase exon 10585218 10585717 . - . ID=FBti0019619;gene_id=right +X FlyBase exon 10989586 10990085 . + . ID=FBti0019620;gene_id=left +X FlyBase exon 10997131 10997630 . + . ID=FBti0019620;gene_id=right +X FlyBase exon 11077839 11078338 . - . ID=FBti0019621;gene_id=left +X FlyBase exon 11083358 11083857 . - . ID=FBti0019621;gene_id=right +X FlyBase exon 11134085 11134584 . + . ID=FBti0019623;gene_id=left +X FlyBase exon 11134999 11135498 . + . ID=FBti0019623;gene_id=right +X FlyBase exon 11162151 11162650 . + . ID=FBti0019624;gene_id=left +X FlyBase exon 11164086 11164585 . + . ID=FBti0019624;gene_id=right +X FlyBase exon 11205652 11206151 . - . ID=FBti0019625;gene_id=left +X FlyBase exon 11213441 11213940 . - . ID=FBti0019625;gene_id=right +X FlyBase exon 11428629 11429128 . - . ID=FBti0019626;gene_id=left +X FlyBase exon 11435542 11436041 . - . ID=FBti0019626;gene_id=right +X FlyBase exon 11465040 11465539 . + . ID=FBti0019627;gene_id=left +X FlyBase exon 11465726 11466225 . + . ID=FBti0019627;gene_id=right +X FlyBase exon 11499223 11499722 . + . ID=FBti0064037;gene_id=left +X FlyBase exon 11500111 11500610 . + . ID=FBti0064037;gene_id=right +X FlyBase exon 11527005 11527504 . - . ID=FBti0019628;gene_id=left +X FlyBase exon 11534518 11535017 . - . ID=FBti0019628;gene_id=right +X FlyBase exon 11637155 11637654 . + . ID=FBti0019630;gene_id=left +X FlyBase exon 11644744 11645243 . + . ID=FBti0019630;gene_id=right +X FlyBase exon 11799400 11799899 . - . ID=FBti0064040;gene_id=left +X FlyBase exon 11800359 11800858 . - . ID=FBti0064040;gene_id=right +X FlyBase exon 12057077 12057576 . + . ID=FBti0059925;gene_id=left +X FlyBase exon 12057840 12058339 . + . ID=FBti0059925;gene_id=right +X FlyBase exon 12061726 12062225 . + . ID=FBti0019631;gene_id=left +X FlyBase exon 12067596 12068095 . + . ID=FBti0019631;gene_id=right +X FlyBase exon 12195551 12196050 . - . ID=FBti0019632;gene_id=left +X FlyBase exon 12197292 12197791 . - . ID=FBti0019632;gene_id=right +X FlyBase exon 12275459 12275958 . - . ID=FBti0019633;gene_id=left +X FlyBase exon 12279804 12280303 . - . ID=FBti0019633;gene_id=right +X FlyBase exon 12639971 12640470 . + . ID=FBti0060433;gene_id=left +X FlyBase exon 12640732 12641231 . + . ID=FBti0060433;gene_id=right +X FlyBase exon 12824166 12824665 . - . ID=FBti0019635;gene_id=left +X FlyBase exon 12831723 12832222 . - . ID=FBti0019635;gene_id=right +X FlyBase exon 13295077 13295576 . + . ID=FBti0019045;gene_id=left +X FlyBase exon 13295869 13296368 . + . ID=FBti0019045;gene_id=right +X FlyBase exon 13323052 13323551 . + . ID=FBti0019046;gene_id=left +X FlyBase exon 13324640 13325139 . + . ID=FBti0019046;gene_id=right +X FlyBase exon 13357233 13357732 . + . ID=FBti0019047;gene_id=left +X FlyBase exon 13363253 13363752 . + . ID=FBti0019047;gene_id=right +X FlyBase exon 13831569 13832068 . - . ID=FBti0019048;gene_id=left +X FlyBase exon 13835275 13835774 . - . ID=FBti0019048;gene_id=right +X FlyBase exon 13924339 13924838 . + . ID=FBti0019050;gene_id=left +X FlyBase exon 13929368 13929867 . + . ID=FBti0019050;gene_id=right +X FlyBase exon 13998611 13999110 . + . ID=FBti0019051;gene_id=left +X FlyBase exon 14008204 14008703 . + . ID=FBti0019051;gene_id=right +X FlyBase exon 14051181 14051680 . - . ID=FBti0019052;gene_id=left +X FlyBase exon 14057281 14057780 . - . ID=FBti0019052;gene_id=right +X FlyBase exon 14197670 14198169 . + . ID=FBti0019053;gene_id=left +X FlyBase exon 14204324 14204823 . + . ID=FBti0019053;gene_id=right +X FlyBase exon 14309904 14310403 . - . ID=FBti0019054;gene_id=left +X FlyBase exon 14315102 14315601 . - . ID=FBti0019054;gene_id=right +X FlyBase exon 14445232 14445731 . - . ID=FBti0019055;gene_id=left +X FlyBase exon 14453336 14453835 . - . ID=FBti0019055;gene_id=right +X FlyBase exon 14476735 14477234 . - . ID=FBti0061060;gene_id=left +X FlyBase exon 14477470 14477969 . - . ID=FBti0061060;gene_id=right +X FlyBase exon 14483263 14483762 . + . ID=FBti0019056;gene_id=left +X FlyBase exon 14483949 14484448 . + . ID=FBti0019056;gene_id=right +X FlyBase exon 14530058 14530557 . - . ID=FBti0019057;gene_id=left +X FlyBase exon 14535929 14536428 . - . ID=FBti0019057;gene_id=right +X FlyBase exon 14612714 14613213 . + . ID=FBti0061076;gene_id=left +X FlyBase exon 14613704 14614203 . + . ID=FBti0061076;gene_id=right +X FlyBase exon 14660004 14660503 . - . ID=FBti0061085;gene_id=left +X FlyBase exon 14660980 14661479 . - . ID=FBti0061085;gene_id=right +X FlyBase exon 14664006 14664505 . + . ID=FBti0061087;gene_id=left +X FlyBase exon 14664761 14665260 . + . ID=FBti0061087;gene_id=right +X FlyBase exon 14671630 14672129 . - . ID=FBti0019058;gene_id=left +X FlyBase exon 14676851 14677350 . - . ID=FBti0019058;gene_id=right +X FlyBase exon 14709104 14709603 . - . ID=FBti0061103;gene_id=left +X FlyBase exon 14709807 14710306 . - . ID=FBti0061103;gene_id=right +X FlyBase exon 14712353 14712852 . - . ID=FBti0019059;gene_id=left +X FlyBase exon 14717999 14718498 . - . ID=FBti0019059;gene_id=right +X FlyBase exon 14830448 14830947 . + . ID=FBti0019060;gene_id=left +X FlyBase exon 14840147 14840646 . + . ID=FBti0019060;gene_id=right +X FlyBase exon 14916699 14917198 . + . ID=FBti0061129;gene_id=left +X FlyBase exon 14917704 14918203 . + . ID=FBti0061129;gene_id=right +X FlyBase exon 14927680 14928179 . + . ID=FBti0019061;gene_id=left +X FlyBase exon 14935650 14936149 . + . ID=FBti0019061;gene_id=right +X FlyBase exon 14941525 14942024 . - . ID=FBti0019636;gene_id=left +X FlyBase exon 14942635 14943134 . - . ID=FBti0019636;gene_id=right +X FlyBase exon 14970356 14970855 . + . ID=FBti0019062;gene_id=left +X FlyBase exon 14971399 14971898 . + . ID=FBti0019062;gene_id=right +X FlyBase exon 15167294 15167793 . - . ID=FBti0019637;gene_id=left +X FlyBase exon 15168901 15169400 . - . ID=FBti0019637;gene_id=right +X FlyBase exon 15220273 15220772 . + . ID=FBti0019063;gene_id=left +X FlyBase exon 15220961 15221460 . + . ID=FBti0019063;gene_id=right +X FlyBase exon 15306642 15307141 . + . ID=FBti0019064;gene_id=left +X FlyBase exon 15311368 15311867 . + . ID=FBti0019064;gene_id=right +X FlyBase exon 15315507 15316006 . - . ID=FBti0019065;gene_id=left +X FlyBase exon 15317463 15317962 . - . ID=FBti0019065;gene_id=right +X FlyBase exon 15326753 15327252 . - . ID=FBti0061584;gene_id=left +X FlyBase exon 15327674 15328173 . - . ID=FBti0061584;gene_id=right +X FlyBase exon 15329260 15329759 . + . ID=FBti0019066;gene_id=left +X FlyBase exon 15330136 15330635 . + . ID=FBti0019066;gene_id=right +X FlyBase exon 15375323 15375822 . + . ID=FBti0061582;gene_id=left +X FlyBase exon 15376160 15376659 . + . ID=FBti0061582;gene_id=right +X FlyBase exon 15448269 15448768 . - . ID=FBti0061585;gene_id=left +X FlyBase exon 15449038 15449537 . - . ID=FBti0061585;gene_id=right +X FlyBase exon 15449888 15450387 . - . ID=FBti0061588;gene_id=left +X FlyBase exon 15450644 15451143 . - . ID=FBti0061588;gene_id=right +X FlyBase exon 15468199 15468698 . - . ID=FBti0061589;gene_id=left +X FlyBase exon 15468936 15469435 . - . ID=FBti0061589;gene_id=right +X FlyBase exon 15469456 15469955 . - . ID=FBti0061590;gene_id=left +X FlyBase exon 15470210 15470709 . - . ID=FBti0061590;gene_id=right +X FlyBase exon 15730527 15731026 . + . ID=FBti0061604;gene_id=left +X FlyBase exon 15731253 15731752 . + . ID=FBti0061604;gene_id=right +X FlyBase exon 15734786 15735285 . + . ID=FBti0061606;gene_id=left +X FlyBase exon 15735653 15736152 . + . ID=FBti0061606;gene_id=right +X FlyBase exon 16116366 16116865 . - . ID=FBti0019067;gene_id=left +X FlyBase exon 16125158 16125657 . - . ID=FBti0019067;gene_id=right +X FlyBase exon 16234256 16234755 . - . ID=FBti0019068;gene_id=left +X FlyBase exon 16243855 16244354 . - . ID=FBti0019068;gene_id=right +X FlyBase exon 16386234 16386733 . - . ID=FBti0019069;gene_id=left +X FlyBase exon 16392254 16392753 . - . ID=FBti0019069;gene_id=right +X FlyBase exon 16435015 16435514 . + . ID=FBti0062240;gene_id=left +X FlyBase exon 16436011 16436510 . + . ID=FBti0062240;gene_id=right +X FlyBase exon 16441298 16441797 . + . ID=FBti0062241;gene_id=left +X FlyBase exon 16442176 16442675 . + . ID=FBti0062241;gene_id=right +X FlyBase exon 16829597 16830096 . + . ID=FBti0019070;gene_id=left +X FlyBase exon 16830437 16830936 . + . ID=FBti0019070;gene_id=right +X FlyBase exon 16951522 16952021 . - . ID=FBti0019071;gene_id=left +X FlyBase exon 16952208 16952707 . - . ID=FBti0019071;gene_id=right +X FlyBase exon 17007337 17007836 . - . ID=FBti0019072;gene_id=left +X FlyBase exon 17013408 17013907 . - . ID=FBti0019072;gene_id=right +X FlyBase exon 17088792 17089291 . - . ID=FBti0019073;gene_id=left +X FlyBase exon 17094321 17094820 . - . ID=FBti0019073;gene_id=right +X FlyBase exon 17125391 17125890 . + . ID=FBti0062273;gene_id=left +X FlyBase exon 17126253 17126752 . + . ID=FBti0062273;gene_id=right +X FlyBase exon 17141025 17141524 . - . ID=FBti0062274;gene_id=left +X FlyBase exon 17141719 17142218 . - . ID=FBti0062274;gene_id=right +X FlyBase exon 17155869 17156368 . - . ID=FBti0019074;gene_id=left +X FlyBase exon 17156585 17157084 . - . ID=FBti0019074;gene_id=right +X FlyBase exon 17174503 17175002 . - . ID=FBti0062286;gene_id=left +X FlyBase exon 17175194 17175693 . - . ID=FBti0062286;gene_id=right +X FlyBase exon 17324955 17325454 . - . ID=FBti0019075;gene_id=left +X FlyBase exon 17325723 17326222 . - . ID=FBti0019075;gene_id=right +X FlyBase exon 17450531 17451030 . + . ID=FBti0019076;gene_id=left +X FlyBase exon 17451476 17451975 . + . ID=FBti0019076;gene_id=right +X FlyBase exon 17686539 17687038 . + . ID=FBti0019077;gene_id=left +X FlyBase exon 17690280 17690779 . + . ID=FBti0019077;gene_id=right +X FlyBase exon 17787185 17787684 . - . ID=FBti0019078;gene_id=left +X FlyBase exon 17790414 17790913 . - . ID=FBti0019078;gene_id=right +X FlyBase exon 18024852 18025351 . - . ID=FBti0019639;gene_id=left +X FlyBase exon 18026037 18026536 . - . ID=FBti0019639;gene_id=right +X FlyBase exon 18087657 18088156 . - . ID=FBti0019079;gene_id=left +X FlyBase exon 18088631 18089130 . - . ID=FBti0019079;gene_id=right +X FlyBase exon 18213198 18213697 . - . ID=FBti0062998;gene_id=left +X FlyBase exon 18213981 18214480 . - . ID=FBti0062998;gene_id=right +X FlyBase exon 18250193 18250692 . + . ID=FBti0062977;gene_id=left +X FlyBase exon 18251156 18251655 . + . ID=FBti0062977;gene_id=right +X FlyBase exon 18308377 18308876 . + . ID=FBti0063008;gene_id=left +X FlyBase exon 18309258 18309757 . + . ID=FBti0063008;gene_id=right +X FlyBase exon 18323082 18323581 . + . ID=FBti0019080;gene_id=left +X FlyBase exon 18328836 18329335 . + . ID=FBti0019080;gene_id=right +X FlyBase exon 18448967 18449466 . + . ID=FBti0019081;gene_id=left +X FlyBase exon 18450931 18451430 . + . ID=FBti0019081;gene_id=right +X FlyBase exon 18513283 18513782 . - . ID=FBti0063024;gene_id=left +X FlyBase exon 18514106 18514605 . - . ID=FBti0063024;gene_id=right +X FlyBase exon 18647925 18648424 . + . ID=FBti0059782;gene_id=left +X FlyBase exon 18652033 18652532 . + . ID=FBti0059782;gene_id=right +X FlyBase exon 18677415 18677914 . - . ID=FBti0019082;gene_id=left +X FlyBase exon 18679822 18680321 . - . ID=FBti0019082;gene_id=right +X FlyBase exon 18706010 18706509 . + . ID=FBti0063036;gene_id=left +X FlyBase exon 18706909 18707408 . + . ID=FBti0063036;gene_id=right +X FlyBase exon 18850658 18851157 . - . ID=FBti0019083;gene_id=left +X FlyBase exon 18859763 18860262 . - . ID=FBti0019083;gene_id=right +X FlyBase exon 18954002 18954501 . - . ID=FBti0019084;gene_id=left +X FlyBase exon 18959220 18959719 . - . ID=FBti0019084;gene_id=right +X FlyBase exon 19001351 19001850 . - . ID=FBti0019085;gene_id=left +X FlyBase exon 19003021 19003520 . - . ID=FBti0019085;gene_id=right +X FlyBase exon 19015489 19015988 . - . ID=FBti0063617;gene_id=left +X FlyBase exon 19016439 19016938 . - . ID=FBti0063617;gene_id=right +X FlyBase exon 19030140 19030639 . + . ID=FBti0019086;gene_id=left +X FlyBase exon 19037502 19038001 . + . ID=FBti0019086;gene_id=right +X FlyBase exon 19085704 19086203 . - . ID=FBti0063635;gene_id=left +X FlyBase exon 19086396 19086895 . - . ID=FBti0063635;gene_id=right +X FlyBase exon 19224162 19224661 . - . ID=FBti0063656;gene_id=left +X FlyBase exon 19224877 19225376 . - . ID=FBti0063656;gene_id=right +X FlyBase exon 19250578 19251077 . - . ID=FBti0059696;gene_id=left +X FlyBase exon 19252457 19252956 . - . ID=FBti0059696;gene_id=right +X FlyBase exon 19265090 19265589 . - . ID=FBti0063669;gene_id=left +X FlyBase exon 19265851 19266350 . - . ID=FBti0063669;gene_id=right +X FlyBase exon 19273743 19274242 . - . ID=FBti0019087;gene_id=left +X FlyBase exon 19274429 19274928 . - . ID=FBti0019087;gene_id=right +X FlyBase exon 19330858 19331357 . - . ID=FBti0019088;gene_id=left +X FlyBase exon 19338819 19339318 . - . ID=FBti0019088;gene_id=right +X FlyBase exon 19365718 19366217 . - . ID=FBti0019089;gene_id=left +X FlyBase exon 19366720 19367219 . - . ID=FBti0019089;gene_id=right +X FlyBase exon 19396008 19396507 . + . ID=FBti0063678;gene_id=left +X FlyBase exon 19397006 19397505 . + . ID=FBti0063678;gene_id=right +X FlyBase exon 19489665 19490164 . - . ID=FBti0063729;gene_id=left +X FlyBase exon 19490703 19491202 . - . ID=FBti0063729;gene_id=right +X FlyBase exon 19559764 19560263 . + . ID=FBti0063712;gene_id=left +X FlyBase exon 19560880 19561379 . + . ID=FBti0063712;gene_id=right +X FlyBase exon 19567246 19567745 . - . ID=FBti0063694;gene_id=left +X FlyBase exon 19568106 19568605 . - . ID=FBti0063694;gene_id=right +X FlyBase exon 19588853 19589352 . + . ID=FBti0019090;gene_id=left +X FlyBase exon 19590977 19591476 . + . ID=FBti0019090;gene_id=right +X FlyBase exon 19603659 19604158 . - . ID=FBti0019091;gene_id=left +X FlyBase exon 19605890 19606389 . - . ID=FBti0019091;gene_id=right +X FlyBase exon 19690936 19691435 . - . ID=FBti0019646;gene_id=left +X FlyBase exon 19698692 19699191 . - . ID=FBti0019646;gene_id=right +X FlyBase exon 19703442 19703941 . - . ID=FBti0063736;gene_id=left +X FlyBase exon 19704288 19704787 . - . ID=FBti0063736;gene_id=right +X FlyBase exon 19766215 19766714 . - . ID=FBti0063738;gene_id=left +X FlyBase exon 19767103 19767602 . - . ID=FBti0063738;gene_id=right +X FlyBase exon 19819597 19820096 . - . ID=FBti0062904;gene_id=left +X FlyBase exon 19820338 19820837 . - . ID=FBti0062904;gene_id=right +X FlyBase exon 19829825 19830324 . - . ID=FBti0062915;gene_id=left +X FlyBase exon 19830834 19831333 . - . ID=FBti0062915;gene_id=right +X FlyBase exon 19854295 19854794 . - . ID=FBti0062889;gene_id=left +X FlyBase exon 19854979 19855478 . - . ID=FBti0062889;gene_id=right +X FlyBase exon 19892332 19892831 . - . ID=FBti0062891;gene_id=left +X FlyBase exon 19893117 19893616 . - . ID=FBti0062891;gene_id=right +X FlyBase exon 19926904 19927403 . + . ID=FBti0019648;gene_id=left +X FlyBase exon 19930967 19931466 . + . ID=FBti0019648;gene_id=right +X FlyBase exon 19986996 19987495 . - . ID=FBti0062899;gene_id=left +X FlyBase exon 19987927 19988426 . - . ID=FBti0062899;gene_id=right +X FlyBase exon 19990109 19990608 . + . ID=FBti0062945;gene_id=left +X FlyBase exon 19990790 19991289 . + . ID=FBti0062945;gene_id=right +X FlyBase exon 19993521 19994020 . - . ID=FBti0019649;gene_id=left +X FlyBase exon 19997026 19997525 . - . ID=FBti0019649;gene_id=right +X FlyBase exon 20004574 20005073 . + . ID=FBti0062946;gene_id=left +X FlyBase exon 20005534 20006033 . + . ID=FBti0062946;gene_id=right +X FlyBase exon 20033920 20034419 . - . ID=FBti0062979;gene_id=left +X FlyBase exon 20034692 20035191 . - . ID=FBti0062979;gene_id=right +X FlyBase exon 20037228 20037727 . + . ID=FBti0062965;gene_id=left +X FlyBase exon 20038171 20038670 . + . ID=FBti0062965;gene_id=right +X FlyBase exon 20073287 20073786 . + . ID=FBti0019650;gene_id=left +X FlyBase exon 20075498 20075997 . + . ID=FBti0019650;gene_id=right +X FlyBase exon 20081159 20081658 . + . ID=FBti0019651;gene_id=left +X FlyBase exon 20083385 20083884 . + . ID=FBti0019651;gene_id=right +X FlyBase exon 20088846 20089345 . + . ID=FBti0019652;gene_id=left +X FlyBase exon 20091057 20091556 . + . ID=FBti0019652;gene_id=right +X FlyBase exon 20096706 20097205 . + . ID=FBti0019653;gene_id=left +X FlyBase exon 20098932 20099431 . + . ID=FBti0019653;gene_id=right +X FlyBase exon 20129221 20129720 . + . ID=FBti0062966;gene_id=left +X FlyBase exon 20130117 20130616 . + . ID=FBti0062966;gene_id=right +X FlyBase exon 20214636 20215135 . - . ID=FBti0062995;gene_id=left +X FlyBase exon 20215401 20215900 . - . ID=FBti0062995;gene_id=right +X FlyBase exon 20235565 20236064 . + . ID=FBti0063000;gene_id=left +X FlyBase exon 20236412 20236911 . + . ID=FBti0063000;gene_id=right +X FlyBase exon 20238464 20238963 . + . ID=FBti0063502;gene_id=left +X FlyBase exon 20239208 20239707 . + . ID=FBti0063502;gene_id=right +X FlyBase exon 20247900 20248399 . + . ID=FBti0019654;gene_id=left +X FlyBase exon 20249806 20250305 . + . ID=FBti0019654;gene_id=right +X FlyBase exon 20267464 20267963 . - . ID=FBti0019656;gene_id=left +X FlyBase exon 20269069 20269568 . - . ID=FBti0019656;gene_id=right +X FlyBase exon 20316429 20316928 . + . ID=FBti0063003;gene_id=left +X FlyBase exon 20317218 20317717 . + . ID=FBti0063003;gene_id=right +X FlyBase exon 20331167 20331666 . - . ID=FBti0063472;gene_id=left +X FlyBase exon 20331922 20332421 . - . ID=FBti0063472;gene_id=right +X FlyBase exon 20351467 20351966 . - . ID=FBti0063476;gene_id=left +X FlyBase exon 20352275 20352774 . - . ID=FBti0063476;gene_id=right +X FlyBase exon 20374707 20375206 . + . ID=FBti0019657;gene_id=left +X FlyBase exon 20376670 20377169 . + . ID=FBti0019657;gene_id=right +X FlyBase exon 20397489 20397988 . + . ID=FBti0063522;gene_id=left +X FlyBase exon 20398465 20398964 . + . ID=FBti0063522;gene_id=right +X FlyBase exon 20446575 20447074 . + . ID=FBti0063531;gene_id=left +X FlyBase exon 20447556 20448055 . + . ID=FBti0063531;gene_id=right +X FlyBase exon 20485359 20485858 . - . ID=FBti0063532;gene_id=left +X FlyBase exon 20486219 20486718 . - . ID=FBti0063532;gene_id=right +X FlyBase exon 20503414 20503913 . - . ID=FBti0063542;gene_id=left +X FlyBase exon 20504167 20504666 . - . ID=FBti0063542;gene_id=right +X FlyBase exon 20676657 20677156 . - . ID=FBti0063596;gene_id=left +X FlyBase exon 20677500 20677999 . - . ID=FBti0063596;gene_id=right +X FlyBase exon 20707308 20707807 . + . ID=FBti0019658;gene_id=left +X FlyBase exon 20715353 20715852 . + . ID=FBti0019658;gene_id=right +X FlyBase exon 20727409 20727908 . - . ID=FBti0063600;gene_id=left +X FlyBase exon 20728116 20728615 . - . ID=FBti0063600;gene_id=right +X FlyBase exon 20750652 20751151 . - . ID=FBti0063602;gene_id=left +X FlyBase exon 20751646 20752145 . - . ID=FBti0063602;gene_id=right +X FlyBase exon 20765308 20765807 . - . ID=FBti0063606;gene_id=left +X FlyBase exon 20766073 20766572 . - . ID=FBti0063606;gene_id=right +X FlyBase exon 20811305 20811804 . - . ID=FBti0019659;gene_id=left +X FlyBase exon 20813211 20813710 . - . ID=FBti0019659;gene_id=right +X FlyBase exon 20872979 20873478 . + . ID=FBti0063639;gene_id=left +X FlyBase exon 20873960 20874459 . + . ID=FBti0063639;gene_id=right +X FlyBase exon 20874984 20875483 . - . ID=FBti0063640;gene_id=left +X FlyBase exon 20875962 20876461 . - . ID=FBti0063640;gene_id=right +X FlyBase exon 20876509 20877008 . - . ID=FBti0063641;gene_id=left +X FlyBase exon 20877360 20877859 . - . ID=FBti0063641;gene_id=right +X FlyBase exon 20904331 20904830 . + . ID=FBti0019664;gene_id=left +X FlyBase exon 20905526 20906025 . + . ID=FBti0019664;gene_id=right +X FlyBase exon 20907486 20907985 . + . ID=FBti0063642;gene_id=left +X FlyBase exon 20908317 20908816 . + . ID=FBti0063642;gene_id=right +X FlyBase exon 20932446 20932945 . - . ID=FBti0019665;gene_id=left +X FlyBase exon 20933374 20933873 . - . ID=FBti0019665;gene_id=right +X FlyBase exon 20956729 20957228 . - . ID=FBti0019666;gene_id=left +X FlyBase exon 20958184 20958683 . - . ID=FBti0019666;gene_id=right +X FlyBase exon 20970376 20970875 . + . ID=FBti0064085;gene_id=left +X FlyBase exon 20971290 20971789 . + . ID=FBti0064085;gene_id=right +X FlyBase exon 20996038 20996537 . + . ID=FBti0064087;gene_id=left +X FlyBase exon 20996897 20997396 . + . ID=FBti0064087;gene_id=right +X FlyBase exon 21019641 21020140 . - . ID=FBti0019669;gene_id=left +X FlyBase exon 21020880 21021379 . - . ID=FBti0019669;gene_id=right +X FlyBase exon 21046284 21046783 . + . ID=FBti0064103;gene_id=left +X FlyBase exon 21047030 21047529 . + . ID=FBti0064103;gene_id=right +X FlyBase exon 21047881 21048380 . - . ID=FBti0064157;gene_id=left +X FlyBase exon 21049038 21049537 . - . ID=FBti0064157;gene_id=right +X FlyBase exon 21051404 21051903 . - . ID=FBti0064105;gene_id=left +X FlyBase exon 21052363 21052862 . - . ID=FBti0064105;gene_id=right +X FlyBase exon 21061792 21062291 . + . ID=FBti0064107;gene_id=left +X FlyBase exon 21062834 21063333 . + . ID=FBti0064107;gene_id=right +X FlyBase exon 21086568 21087067 . - . ID=FBti0064109;gene_id=left +X FlyBase exon 21087529 21088028 . - . ID=FBti0064109;gene_id=right +X FlyBase exon 21125285 21125784 . + . ID=FBti0019677;gene_id=left +X FlyBase exon 21126313 21126812 . + . ID=FBti0019677;gene_id=right +X FlyBase exon 21153965 21154464 . + . ID=FBti0064194;gene_id=left +X FlyBase exon 21154739 21155238 . + . ID=FBti0064194;gene_id=right +X FlyBase exon 21171043 21171542 . + . ID=FBti0064205;gene_id=left +X FlyBase exon 21171792 21172291 . + . ID=FBti0064205;gene_id=right +X FlyBase exon 21180050 21180549 . - . ID=FBti0064206;gene_id=left +X FlyBase exon 21181012 21181511 . - . ID=FBti0064206;gene_id=right +X FlyBase exon 21185984 21186483 . - . ID=FBti0064207;gene_id=left +X FlyBase exon 21186897 21187396 . - . ID=FBti0064207;gene_id=right +X FlyBase exon 21291889 21292388 . + . ID=FBti0064220;gene_id=left +X FlyBase exon 21292891 21293390 . + . ID=FBti0064220;gene_id=right +X FlyBase exon 21304742 21305241 . - . ID=FBti0064222;gene_id=left +X FlyBase exon 21305490 21305989 . - . ID=FBti0064222;gene_id=right +X FlyBase exon 21322696 21323195 . + . ID=FBti0064223;gene_id=left +X FlyBase exon 21323624 21324123 . + . ID=FBti0064223;gene_id=right +X FlyBase exon 21329282 21329781 . - . ID=FBti0019678;gene_id=left +X FlyBase exon 21335152 21335651 . - . ID=FBti0019678;gene_id=right +X FlyBase exon 21339280 21339779 . + . ID=FBti0064224;gene_id=left +X FlyBase exon 21339991 21340490 . + . ID=FBti0064224;gene_id=right +X FlyBase exon 21344984 21345483 . + . ID=FBti0019679;gene_id=left +X FlyBase exon 21345795 21346294 . + . ID=FBti0019679;gene_id=right +X FlyBase exon 21376449 21376948 . + . ID=FBti0060042;gene_id=left +X FlyBase exon 21377583 21378082 . + . ID=FBti0060042;gene_id=right +X FlyBase exon 21455828 21456327 . + . ID=FBti0019697;gene_id=left +X FlyBase exon 21456886 21457385 . + . ID=FBti0019697;gene_id=right +X FlyBase exon 21457944 21458443 . - . ID=FBti0060048;gene_id=left +X FlyBase exon 21458705 21459204 . - . ID=FBti0060048;gene_id=right +X FlyBase exon 21474559 21475058 . - . ID=FBti0060061;gene_id=left +X FlyBase exon 21475408 21475907 . - . ID=FBti0060061;gene_id=right +X FlyBase exon 21494393 21494892 . - . ID=FBti0060088;gene_id=left +X FlyBase exon 21495636 21496135 . - . ID=FBti0060088;gene_id=right +X FlyBase exon 21497479 21497978 . + . ID=FBti0019699;gene_id=left +X FlyBase exon 21499277 21499776 . + . ID=FBti0019699;gene_id=right +X FlyBase exon 21685998 21686497 . + . ID=FBti0060594;gene_id=left +X FlyBase exon 21687344 21687843 . + . ID=FBti0060594;gene_id=right +X FlyBase exon 21860031 21860530 . + . ID=FBti0019720;gene_id=left +X FlyBase exon 21861994 21862493 . + . ID=FBti0019720;gene_id=right +X FlyBase exon 21874192 21874691 . + . ID=FBti0019721;gene_id=left +X FlyBase exon 21875323 21875822 . + . ID=FBti0019721;gene_id=right +X FlyBase exon 21877985 21878484 . - . ID=FBti0061140;gene_id=left +X FlyBase exon 21879005 21879504 . - . ID=FBti0061140;gene_id=right +X FlyBase exon 21886041 21886540 . + . ID=FBti0061141;gene_id=left +X FlyBase exon 21886904 21887403 . + . ID=FBti0061141;gene_id=right +X FlyBase exon 21887574 21888073 . + . ID=FBti0061142;gene_id=left +X FlyBase exon 21888567 21889066 . + . ID=FBti0061142;gene_id=right +X FlyBase exon 21889900 21890399 . - . ID=FBti0019722;gene_id=left +X FlyBase exon 21890892 21891391 . - . ID=FBti0019722;gene_id=right +X FlyBase exon 21891428 21891927 . - . ID=FBti0061299;gene_id=left +X FlyBase exon 21892197 21892696 . - . ID=FBti0061299;gene_id=right +X FlyBase exon 21895770 21896269 . + . ID=FBti0061144;gene_id=left +X FlyBase exon 21896836 21897335 . + . ID=FBti0061144;gene_id=right +X FlyBase exon 21907764 21908263 . + . ID=FBti0061147;gene_id=left +X FlyBase exon 21908793 21909292 . + . ID=FBti0061147;gene_id=right +X FlyBase exon 21909599 21910098 . - . ID=FBti0061148;gene_id=left +X FlyBase exon 21910516 21911015 . - . ID=FBti0061148;gene_id=right +X FlyBase exon 21912243 21912742 . - . ID=FBti0061150;gene_id=left +X FlyBase exon 21913162 21913661 . - . ID=FBti0061150;gene_id=right +X FlyBase exon 21914659 21915158 . + . ID=FBti0061152;gene_id=left +X FlyBase exon 21915445 21915944 . + . ID=FBti0061152;gene_id=right +X FlyBase exon 21946675 21947174 . + . ID=FBti0061166;gene_id=left +X FlyBase exon 21947617 21948116 . + . ID=FBti0061166;gene_id=right +X FlyBase exon 21966395 21966894 . + . ID=FBti0019733;gene_id=left +X FlyBase exon 21971918 21972417 . + . ID=FBti0019733;gene_id=right +X FlyBase exon 21974809 21975308 . - . ID=FBti0061271;gene_id=left +X FlyBase exon 21976502 21977001 . - . ID=FBti0061271;gene_id=right +X FlyBase exon 21987500 21987999 . - . ID=FBti0061169;gene_id=left +X FlyBase exon 21988186 21988685 . - . ID=FBti0061169;gene_id=right +X FlyBase exon 21993503 21994002 . - . ID=FBti0061171;gene_id=left +X FlyBase exon 21994450 21994949 . - . ID=FBti0061171;gene_id=right +X FlyBase exon 21997723 21998222 . - . ID=FBti0061189;gene_id=left +X FlyBase exon 21998648 21999147 . - . ID=FBti0061189;gene_id=right +X FlyBase exon 22001309 22001808 . - . ID=FBti0061190;gene_id=left +X FlyBase exon 22002053 22002552 . - . ID=FBti0061190;gene_id=right +X FlyBase exon 22003324 22003823 . + . ID=FBti0061191;gene_id=left +X FlyBase exon 22004349 22004848 . + . ID=FBti0061191;gene_id=right +X FlyBase exon 22021878 22022377 . + . ID=FBti0019735;gene_id=left +X FlyBase exon 22028589 22029088 . + . ID=FBti0019735;gene_id=right +X FlyBase exon 22030491 22030990 . + . ID=FBti0061193;gene_id=left +X FlyBase exon 22031375 22031874 . + . ID=FBti0061193;gene_id=right +X FlyBase exon 22034624 22035123 . + . ID=FBti0061194;gene_id=left +X FlyBase exon 22035583 22036082 . + . ID=FBti0061194;gene_id=right +X FlyBase exon 22036925 22037424 . + . ID=FBti0061195;gene_id=left +X FlyBase exon 22038220 22038719 . + . ID=FBti0061195;gene_id=right +X FlyBase exon 22039357 22039856 . - . ID=FBti0061196;gene_id=left +X FlyBase exon 22040352 22040851 . - . ID=FBti0061196;gene_id=right +X FlyBase exon 22043411 22043910 . - . ID=FBti0061198;gene_id=left +X FlyBase exon 22044257 22044756 . - . ID=FBti0061198;gene_id=right +X FlyBase exon 22048433 22048932 . + . ID=FBti0061330;gene_id=left +X FlyBase exon 22049279 22049778 . + . ID=FBti0061330;gene_id=right +X FlyBase exon 22057124 22057623 . + . ID=FBti0061333;gene_id=left +X FlyBase exon 22057985 22058484 . + . ID=FBti0061333;gene_id=right +X FlyBase exon 22082873 22083372 . + . ID=FBti0019737;gene_id=left +X FlyBase exon 22090779 22091278 . + . ID=FBti0019737;gene_id=right +X FlyBase exon 22095242 22095741 . - . ID=FBti0061335;gene_id=left +X FlyBase exon 22096103 22096602 . - . ID=FBti0061335;gene_id=right +X FlyBase exon 22131802 22132301 . - . ID=FBti0019743;gene_id=left +X FlyBase exon 22133042 22133541 . - . ID=FBti0019743;gene_id=right +X FlyBase exon 22139935 22140434 . + . ID=FBti0019744;gene_id=left +X FlyBase exon 22140885 22141384 . + . ID=FBti0019744;gene_id=right +X FlyBase exon 22143032 22143531 . - . ID=FBti0061353;gene_id=left +X FlyBase exon 22144129 22144628 . - . ID=FBti0061353;gene_id=right +X FlyBase exon 22145369 22145868 . - . ID=FBti0061354;gene_id=left +X FlyBase exon 22146581 22147080 . - . ID=FBti0061354;gene_id=right +X FlyBase exon 22158980 22159479 . - . ID=FBti0060518;gene_id=left +X FlyBase exon 22159740 22160239 . - . ID=FBti0060518;gene_id=right +X FlyBase exon 22177427 22177926 . - . ID=FBti0061357;gene_id=left +X FlyBase exon 22178135 22178634 . - . ID=FBti0061357;gene_id=right +X FlyBase exon 22181659 22182158 . - . ID=FBti0061667;gene_id=left +X FlyBase exon 22182560 22183059 . - . ID=FBti0061667;gene_id=right +X FlyBase exon 22185911 22186410 . - . ID=FBti0019746;gene_id=left +X FlyBase exon 22186943 22187442 . - . ID=FBti0019746;gene_id=right +X FlyBase exon 22190019 22190518 . - . ID=FBti0061670;gene_id=left +X FlyBase exon 22191085 22191584 . - . ID=FBti0061670;gene_id=right +X FlyBase exon 22195806 22196305 . + . ID=FBti0061671;gene_id=left +X FlyBase exon 22196925 22197424 . + . ID=FBti0061671;gene_id=right +X FlyBase exon 22223174 22223673 . + . ID=FBti0061781;gene_id=left +X FlyBase exon 22225997 22226496 . + . ID=FBti0061781;gene_id=right +X FlyBase exon 22234403 22234902 . - . ID=FBti0060517;gene_id=left +X FlyBase exon 22235245 22235744 . - . ID=FBti0060517;gene_id=right +X FlyBase exon 22239374 22239873 . + . ID=FBti0061674;gene_id=left +X FlyBase exon 22240389 22240888 . + . ID=FBti0061674;gene_id=right +X FlyBase exon 22243264 22243763 . + . ID=FBti0019748;gene_id=left +X FlyBase exon 22245337 22245836 . + . ID=FBti0019748;gene_id=right +X FlyBase exon 22250617 22251116 . - . ID=FBti0061812;gene_id=left +X FlyBase exon 22251644 22252143 . - . ID=FBti0061812;gene_id=right +X FlyBase exon 22256814 22257313 . - . ID=FBti0061813;gene_id=left +X FlyBase exon 22257959 22258458 . - . ID=FBti0061813;gene_id=right +X FlyBase exon 22271776 22272275 . - . ID=FBti0061846;gene_id=left +X FlyBase exon 22272465 22272964 . - . ID=FBti0061846;gene_id=right +X FlyBase exon 22276936 22277435 . + . ID=FBti0061848;gene_id=left +X FlyBase exon 22277765 22278264 . + . ID=FBti0061848;gene_id=right +X FlyBase exon 22283375 22283874 . + . ID=FBti0062474;gene_id=left +X FlyBase exon 22285380 22285879 . + . ID=FBti0062474;gene_id=right +X FlyBase exon 22289776 22290275 . + . ID=FBti0062436;gene_id=left +X FlyBase exon 22290575 22291074 . + . ID=FBti0062436;gene_id=right +X FlyBase exon 22326110 22326609 . - . ID=FBti0062440;gene_id=left +X FlyBase exon 22327885 22328384 . - . ID=FBti0062440;gene_id=right +X FlyBase exon 22336396 22336895 . - . ID=FBti0062416;gene_id=left +X FlyBase exon 22337937 22338436 . - . ID=FBti0062416;gene_id=right +X FlyBase exon 22339332 22339831 . + . ID=FBti0061912;gene_id=left +X FlyBase exon 22340231 22340730 . + . ID=FBti0061912;gene_id=right +X FlyBase exon 22385377 22385876 . + . ID=FBti0061942;gene_id=left +X FlyBase exon 22386134 22386633 . + . ID=FBti0061942;gene_id=right +X FlyBase exon 22397699 22398198 . + . ID=FBti0062347;gene_id=left +X FlyBase exon 22405375 22405874 . + . ID=FBti0062347;gene_id=right +X FlyBase exon 22406838 22407337 . + . ID=FBti0062442;gene_id=left +X FlyBase exon 22408770 22409269 . + . ID=FBti0062442;gene_id=right +X FlyBase exon 22412656 22413155 . - . ID=FBti0061946;gene_id=left +X FlyBase exon 22413523 22414022 . - . ID=FBti0061946;gene_id=right diff -r 000000000000 -r ab0323782bb5 test-data/featureCounts_input1.bam Binary file test-data/featureCounts_input1.bam has changed diff -r 000000000000 -r ab0323782bb5 test-data/featureCounts_input2.bam Binary file test-data/featureCounts_input2.bam has changed diff -r 000000000000 -r ab0323782bb5 test-data/output.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output.tab Mon May 18 04:49:19 2015 -0400 @@ -0,0 +1,3 @@ +Geneid 1: featureCounts_input1.bam 2: featureCounts_input2.bam Length +left 92 72 170000 +right 66 63 170000 diff -r 000000000000 -r ab0323782bb5 test-data/output_summary.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_summary.tab Mon May 18 04:49:19 2015 -0400 @@ -0,0 +1,12 @@ +Status 1: featureCounts_input1.bam 2: featureCounts_input2.bam +Assigned 158 135 +Unassigned_Ambiguity 0 0 +Unassigned_MultiMapping 0 0 +Unassigned_NoFeatures 6078 6344 +Unassigned_Unmapped 0 0 +Unassigned_MappingQuality 0 0 +Unassigned_FragementLength 0 0 +Unassigned_Chimera 0 0 +Unassigned_Secondary 0 0 +Unassigned_Nonjunction 0 0 +Unassigned_Duplicate 0 0 diff -r 000000000000 -r ab0323782bb5 tool-data/gene_sets.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/gene_sets.loc.sample Mon May 18 04:49:19 2015 -0400 @@ -0,0 +1,39 @@ +# This is a sample file distributed with Galaxy that enables tools +# to use gene/exon annotations in the GFF/GTF format. You will need +# to add all the gene set annotations in this configuration file. +# Because of this file, galaxy tools are able to access gene annotations +# provided as GFF / GTF files by selecting on: +# - Priorty (defined by the order in the file) +# - Provider +# - dbkey (reference genome id) +# +# The gene_sets.loc file syntax is: +# +# *optional +# +# Please ensure maximally one TAB (\t) between two columns! +# --------------------------------------------------------- +# +# In case you have TWO or MORE providers PER dbkey, the one mentioned +# first in the file, should have the "default" priority. +# + + + +# [UCSC - UCSC Genes: knownGene] + +#hg19.UCSC knownGene (mm/'yy) hg19 /depot/data2/galaxy/hg19/gene_sets/Homo_sapiens.GRCh37.74.gtf ucsc http://genome.ucsc.edu/ +#hg18.UCSC knownGene (mm/'yy) hg18 /depot/data2/galaxy/hg18/gene_sets/Homo_sapiens.NCBI36.54.gtf ucsc http://genome.ucsc.edu/ + + + +# [RefSeq Genes: RefGene] +# link: ftp://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/RefSeqGene/ + + + +# [ Ensembl] +# link: http://www.ensembl.org/info/data/ftp/index.html + +#Homo_sapiens.GRCh37.74 hg19 /depot/data2/galaxy/hg19/gene_sets/Homo_sapiens.GRCh37.74.gtf ensembl ftp://ftp.ensembl.org/pub/release-74/gtf/homo_sapiens/Homo_sapiens.GRCh37.74.gtf.gz +#Homo_sapiens.NCBI36.54 hg18 /depot/data2/galaxy/hg18/gene_sets/Homo_sapiens.NCBI36.54.gtf ensembl ftp://ftp.ensembl.org/pub/release-54/gtf/homo_sapiens/Homo_sapiens.NCBI36.54.gtf.gz diff -r 000000000000 -r ab0323782bb5 tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Mon May 18 04:49:19 2015 -0400 @@ -0,0 +1,8 @@ + + + + + name, dbkey, value, provider, reference + +

+ \ No newline at end of file diff -r 000000000000 -r ab0323782bb5 tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Mon May 18 04:49:19 2015 -0400 @@ -0,0 +1,36 @@ + + + + + + wget http://garr.dl.sourceforge.net/project/subread/subread-1.4.6-p1/subread-1.4.6-p1-source.tar.gz && tar -zxvf subread-1.4.6-p1-source.tar.gz && cd subread-1.4.6-p1-source/src/ && make -f Makefile.Linux && cd ../../ + + ../subread-1.4.6-p1-source/bin/featureCounts + $INSTALL_DIR/bin/ + + + $INSTALL_DIR/bin + + + + + + Downloads and installs featureCounts; requires WGET, GNU AUTOTOOLS and TAR to be installed. + + + + + + + mkdir $INSTALL_DIR/bin ; cp $REPOSITORY_INSTALL_DIR/featurecounts2bed.sh $INSTALL_DIR/bin/ + + $INSTALL_DIR/bin/featurecounts2bed.sh + + + $INSTALL_DIR/bin + $REPOSITORY_INSTALL_DIR + + + + +