| Previous changeset 1:54ce44828e1b (2015-06-01) Next changeset 3:4966079d474b (2015-10-20) |
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Commit message:
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/fuma_galaxy_wrapper commit 3da3fcc0204205d4899763f9fe63edf9aa16d5a2 |
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modified:
fuma.xml test-data/refseq_genes_hg19.bed tool_dependencies.xml |
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added:
README.rst test-data/output_test_1.txt test-data/output_test_2.txt |
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test-data/output.txt |
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| diff -r 54ce44828e1b -r 86526900cb8f README.rst --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.rst Mon Oct 12 04:17:07 2015 -0400 |
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| @@ -0,0 +1,1 @@ +A new generation of tools that identify fusion genes in RNA-seq data is limited in either sensitivity and or specificity. To allow further downstream analysis and to estimate performance, predicted fusion genes from different tools have to be compared. However, several factors complicate genomic location-based matching in a transcriptome context. FusionMatcher (FuMa) is a program that reports identical fusion genes based on gene-name annotations. FuMa automatically compares and summarizes all combinations of two or more datasets in a single run, without additional programming necessary. FuMa uses only one single gene annotation, avoiding mismatches caused by tool specific gene annotations. Furthermore, FuMa accepts intermediate output files that allow a step wise analysis of corresponding tools. \ No newline at end of file |
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| diff -r 54ce44828e1b -r 86526900cb8f fuma.xml --- a/fuma.xml Mon Jun 01 06:45:40 2015 -0400 +++ b/fuma.xml Mon Oct 12 04:17:07 2015 -0400 |
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| b'@@ -1,116 +1,182 @@\n <?xml version="1.0" encoding="UTF-8"?>\n-<tool id="fuma" name="FuMa" version="2.7.1.b">\n-\t<description>FuMa (FusionMatcher) matches detected fusion genes based on gene name subset matching (designed in particular for RNA-Seq).</description>\n-\t\n-\t<requirements>\n-\t\t<requirement type="package" version="2.7.1">fuma</requirement>\n-\t</requirements>\n-\t\n-\t<version_command>fuma --version 2>&1 | head -n 1</version_command><!-- -V also works, but is not GNU standard -->\n-\t\n-\t<command>\n-\t\t#import pipes\n-\t\t\n-\t\t#set $gene_annotations = []\n-\t\t#set $samples = []\n-\t\t#set $links = []\n-\t\t\n-\t\t#for $i, $d in enumerate( $datasets )\n-\t\t\t\n-\t\t\t#set $sample_name = pipes.quote(str($d[\'sample\'].name))\n-\t\t\t\n-\t\t\t#set $gene_annotations = $gene_annotations + [ "ga_" + str($i) + ":" + str($d[\'gene_annotation\'].file_name) ]\n-\t\t\t\n-\t\t\t#set $samples = $samples + [ $sample_name + ":" + str($d[\'format\']) + ":" + str($d[\'sample\'].file_name) ]\n-\t\t\t#set $links = $links + [ $sample_name + ":" + str("ga_") + str($i) ]\n-\t\t#end for\n-\t\t\n-\t\t#set $gene_annotations_str = " ".join(gene_annotations)\n-\t\t#set $samples_str = " ".join(samples)\n-\t\t#set $links_str = " ".join(links)\n-\t\t\n-\t\tfuma \n-\t\t -a\n-\t\t $gene_annotations_str\n-\t\t -s\n-\t\t $samples_str\n-\t\t -l\n-\t\t $links_str\n-\t\t#if $output_format.value == "list_boolean"\n-\t\t -f list\n-\t\t#else\n-\t\t -f $output_format.value\n-\t\t#end if\n-\t\t -o $fuma_overview ; \n-\t\t\n-\t\t\n-\t\t\n-\t\t#if $output_format.value == "list_boolean"\n-\t\t\tfuma-list-to-boolean-list -o tmp.txt $fuma_overview &&\n-\t\t\tmv tmp.txt $fuma_overview\n-\t\t#end if\n-\t</command>\n-\t\n-\t<inputs>\n-\t\t<repeat name="datasets" title="FusionGene Datasets" min="2">\n-\t\t\t<param name="sample" type="data" format="txt,tabular" label="Dataset (RNA-Seq fusion gene detection experiment)" />\n-\t\t\t<param name="format" type="select" label="Format of dataset">\n-\t\t\t\t<option value="chimerascan">ChimeraScan</option>\n-\t\t\t\t<option value="defuse">DeFuse</option>\n-\t\t\t\t<option value="complete-genomics">Complete Genomics</option>\n-\t\t\t\t<option value="fusion-catcher_final">Fusion Catcher (final-list file)</option>\n-\t\t\t\t<option value="fusionmap">FusionMap</option>\n-\t\t\t\t<option value="trinity-gmap">GMAP (As step after Trinity)</option>\n-\t\t\t\t<option value="oncofuse">OncoFuse</option>\n-\t\t\t\t<option value="rna-star_chimeric">STAR (chimeric file)</option>\n-\t\t\t\t<option value="tophat-fusion_pre">Tophat Fusion Pre (fusions.out)</option>\n-\t\t\t\t<option value="tophat-fusion_post_potential_fusion">Tophat Fusion Post (potential_fusion.txt)</option>\n-\t\t\t\t<option value="tophat-fusion_post_result">Tophat Fusion Post (result.txt)</option>\n-\t\t\t</param>\n-\t\t\t<param name="gene_annotation" type="data" format="bed" label="Corresponding gene-name annotation file (BED format)" help="Make use of persistent gene annotations! Gene annotations should only be different if different reference genome builds were used." />\n-\t\t</repeat>\n-\t\t\n-\t\t<param name="output_format" type="select" label="Output format">\n-\t\t\t<option value="list_boolean" selected="true">List (Boolean)</option>\n-\t\t\t<option value="list">List</option>\n-\t\t\t<option value="summary">Count summary</option>\n-\t\t</param>\n-\t</inputs>\n-\t\n-\t<outputs>\n-\t\t<data format="tabular" name="fuma_overview" label="${tool.name} on ${\', \'.join([ str(d[\'sample\'].hid)+\': \'+d[\'sample\'].name for d in $datasets ])}" />\n-\t</outputs>\n-\t\n-\t<tests>\n-\t\t<test>\n-\t\t\t<!-- <repeat name="datasets"> -->\n-\t\t\t\t<param name="datasets_0|sample" value="chimerascan.txt" ftype="tabular" />\n-\t\t\t\t<param name="datasets_0|format" value="chimerascan" />\n-\t\t\t\t<param name="datasets_0|gene_annotation" value="refseq_genes_hg19.bed" ftype="bed" />\n-\t\t\t<!-- </repeat> -->\n-\t\t\t<!-- <repeat name="datasets"> -->\n-\t\t\t\t<param name="datasets_1|sample" value="defuse.txt" ftype="tabular" />\n-\t\t\t\t<param name="datasets_1|format" value="defuse" />\n-\t\t\t\t<param name="datasets_1|gene_annotation" value="refseq_genes_hg19.bed" ftype="bed" />\n-\t\t\t<!-- </repeat> -->\n-\t\t\t<!-- <repeat name="datasets"> -->\n-\t\t\t\t<param name="dataset'..b'ets"> -->\n+ <param name="datasets_2|sample" value="fusion-map.txt" ftype="tabular" />\n+ <param name="datasets_2|format" value="fusionmap" />\n+ <param name="datasets_2|gene_annotation" value="refseq_genes_hg19.bed" ftype="bed" />\n+ <!-- </repeat> -->\n+ <!-- <repeat name="datasets"> -->\n+ <param name="datasets_3|sample" value="edgren_tp.txt" ftype="tabular" />\n+ <param name="datasets_3|format" value="fusionmap" />\n+ <param name="datasets_3|gene_annotation" value="refseq_genes_hg19.bed" ftype="bed" />\n+ <!-- </repeat> -->\n+ \n+ <param name="settingsType" value="full" />\n+ \n+ <param name="matching_method" value="subset" />\n+ <param name="strand_specific_matching" value="" />\n+ <param name="acceptor_donor_order_specific_matchig" value="" />\n+ <param name="output_format" value="list_boolean" />\n+ \n+ <output name="fuma_overview" file="output_test_2.txt" />\n+ </test>\n+ </tests>\n+ \n+ <help><![CDATA[\n+============\n Introduction\n ============\n \n@@ -131,6 +197,8 @@\n +-------------------+-----------------------+-------------------------------------+\n |Tools | File | Format string |\n +===================+=======================+=====================================+\n+|Chimera | prettyPrint() output | chimera |\n++-------------------+-----------------------+-------------------------------------+\n |ChimeraScan | chimeras.bedpe | chimerascan |\n +-------------------+-----------------------+-------------------------------------+\n |Complete Genomics | highConfidenceJu*.tsv | complete-genomics |\n@@ -153,19 +221,30 @@\n +-------------------+-----------------------+-------------------------------------+\n |RNA STAR | Chimeric.out.junction | rna-star_chimeric |\n +-------------------+-----------------------+-------------------------------------+\n+|STAR Fusion | _candidates.final | star-fusion_final |\n++-------------------+-----------------------+-------------------------------------+\n |TopHat Fusion pre | fusions.out | tophat-fusion_pre |\n +-------------------+-----------------------+-------------------------------------+\n |TopHat Fusion post | potential_fusion.txt | tophat-fusion_post_potential_fusion |\n +-------------------+-----------------------+-------------------------------------+\n |TopHat Fusion post | result.txt | tophat-fusion_post_result |\n +-------------------+-----------------------+-------------------------------------+\n+|TopHat Fusion post | result.html | tophat-fusion_post_result_html |\n++-------------------+-----------------------+-------------------------------------+\n \n To annotate genes upon the breakpoints you must provide a BED file that contains gene annotations for the user genome build. Make sure **your BED file contains one gene per line**. You should use BED files that contain one exon per line only if you want restrict your analysis to fusion genes detected within exons.\n \n UCSC genome browser provides a very simple way of obtaining BED files with one gene per line by selecting their *RefSeq Genes*-track and *knownGene*-table and putting the export format to BED. Galaxy should have a built-in UCSC table browser.\n \n-\t</help>\n-\t\n-\t<citations>\n-\t</citations>\n+ ]]></help>\n+ \n+ <citations>\n+ <citation type="bibtex">\n+ @unpublished{fuma,\n+ author = {Youri Hoogstrate}, \n+ title = {FuMa: reporting overlap in RNA-seq detected fusion genes},\n+ url = { https://github.com/yhoogstrate/fuma }\n+ }\n+ </citation>\n+ </citations>\n </tool>\n' |
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| diff -r 54ce44828e1b -r 86526900cb8f test-data/output.txt --- a/test-data/output.txt Mon Jun 01 06:45:40 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,23 +0,0 @@ - chimerascan.txt (10914) defuse.txt (258) fusion-map.txt (58) edgren_tp.txt (25) -chimerascan.txt (10914) 32/10914 (0.29%) : 32/258 (12.4%) 17/10914 (0.16%) : 17/58 (29.31%) 18/10914 (0.16%) : 18/25 (72.0%) -defuse.txt (258) 32/258 (12.4%) : 32/10914 (0.29%) 9/258 (3.49%) : 9/58 (15.52%) 17/258 (6.59%) : 17/25 (68.0%) -fusion-map.txt (58) 17/58 (29.31%) : 17/10914 (0.16%) 9/58 (15.52%) : 9/258 (3.49%) 6/58 (10.34%) : 6/25 (24.0%) -edgren_tp.txt (25) 18/25 (72.0%) : 18/10914 (0.16%) 17/25 (68.0%) : 17/258 (6.59%) 6/25 (24.0%) : 6/58 (10.34%) - - - chimerascan.txt (10914) defuse.txt (258) fusion-map.txt (58) edgren_tp.txt (25) -chimerascan.txt & defuse.txt (32) 8/32 (25.0%) : 8/58 (13.79%) 15/32 (46.88%) : 15/25 (60.0%) -chimerascan.txt & fusion-map.txt (17) 8/17 (47.06%) : 8/258 (3.1%) 5/17 (29.41%) : 5/25 (20.0%) -chimerascan.txt & edgren_tp.txt (18) 15/18 (83.33%) : 15/258 (5.81%) 5/18 (27.78%) : 5/58 (8.62%) -defuse.txt & fusion-map.txt (9) 8/9 (88.89%) : 8/10914 (0.07%) 6/9 (66.67%) : 6/25 (24.0%) -defuse.txt & edgren_tp.txt (17) 15/17 (88.24%) : 15/10914 (0.14%) 6/17 (35.29%) : 6/58 (10.34%) -fusion-map.txt & edgren_tp.txt (6) 5/6 (83.33%) : 5/10914 (0.05%) 6/6 (100.0%) : 6/258 (2.33%) - - - chimerascan.txt (10914) defuse.txt (258) fusion-map.txt (58) edgren_tp.txt (25) -chimerascan.txt & defuse.txt & fusion-map.txt (8) 5/8 (62.5%) : 5/25 (20.0%) -chimerascan.txt & defuse.txt & edgren_tp.txt (15) 5/15 (33.33%) : 5/58 (8.62%) -chimerascan.txt & fusion-map.txt & edgren_tp.txt (5) 5/5 (100.0%) : 5/258 (1.94%) -defuse.txt & fusion-map.txt & edgren_tp.txt (6) 5/6 (83.33%) : 5/10914 (0.05%) - - |
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| diff -r 54ce44828e1b -r 86526900cb8f test-data/output_test_1.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_test_1.txt Mon Oct 12 04:17:07 2015 -0400 |
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| b'@@ -0,0 +1,11394 @@\n+Left-genes\tRight-genes\tchimerascan.txt\tdefuse.txt\tfusion-map.txt\tedgren_tp.txt\n+NR_037945:STX16\tRAE1\tTRUE\tFALSE\tFALSE\tFALSE\n+TPD52L2\tDNAJC5\tTRUE\tFALSE\tFALSE\tFALSE\n+C20orf112\tC20orf112\tTRUE\tFALSE\tFALSE\tFALSE\n+PREX1\tCPNE1:NM_001198863:NR_037188\tTRUE\tFALSE\tFALSE\tFALSE\n+AP5S1\tMAVS:NR_037921\tTRUE\tFALSE\tFALSE\tFALSE\n+BCAS4\tNM_001281771:NM_001281772:NM_001281773:NM_001281774:NM_001281775:NM_001281776:NM_001281777:NM_001281778:NM_001281779:NM_001281780:NM_001281781:NM_001281782:NM_001281783:NM_001281784:ZMYND8\tTRUE\tFALSE\tFALSE\tFALSE\n+NR_036633:VAPB\tAPCDD1L-AS1\tTRUE\tFALSE\tFALSE\tFALSE\n+CSNK2A1\tFAM110A:NM_001289145:NM_001289146:NM_001289147\tTRUE\tFALSE\tFALSE\tFALSE\n+NR_109859\tAP5S1\tTRUE\tFALSE\tFALSE\tFALSE\n+FKBP1A:NR_037661:SDCBP2-AS1\tLOC284801\tTRUE\tFALSE\tFALSE\tFALSE\n+ADNP:NM_001282531\tRSPO4\tTRUE\tFALSE\tFALSE\tFALSE\n+LAMA5\tLOC284801\tTRUE\tFALSE\tFALSE\tFALSE\n+OSER1-AS1\tOSER1-AS1\tTRUE\tFALSE\tFALSE\tFALSE\n+ZFP64\tNM_001281507:PHACTR3\tTRUE\tFALSE\tFALSE\tFALSE\n+ARFGAP1:NM_001281482:NM_001281483:NM_001281484:NR_104022:NR_104023\tIFT52:NM_001303458:NM_001303459\tTRUE\tFALSE\tFALSE\tFALSE\n+RAD21L1\tHMGN1\tTRUE\tFALSE\tFALSE\tFALSE\n+VPS16\tPCP4\tTRUE\tFALSE\tFALSE\tFALSE\n+ATP5O\tKIF16B\tTRUE\tFALSE\tFALSE\tFALSE\n+PCNT\tADNP:NM_001282531:NM_001282532\tTRUE\tFALSE\tFALSE\tFALSE\n+SLC2A4RG\tBRWD1\tTRUE\tFALSE\tFALSE\tFALSE\n+LOC400927:NM_001289912\tNR_110051:ZNF217\tTRUE\tFALSE\tFALSE\tFALSE\n+LOC284801\tTUBGCP6\tTRUE\tFALSE\tFALSE\tFALSE\n+ELMO2\tJOSD1\tTRUE\tFALSE\tFALSE\tFALSE\n+RTCB\tSTMN3\tTRUE\tFALSE\tFALSE\tFALSE\n+HIRA\tNM_001282933:NM_001282935:NR_104259:NR_110623:ZNF341\tTRUE\tFALSE\tFALSE\tFALSE\n+DENND6B\tMTRNR2L3:RAE1\tTRUE\tFALSE\tFALSE\tFALSE\n+EWSR1\tNM_001278649:OSBPL2\tTRUE\tFALSE\tFALSE\tFALSE\n+CTSZ\tEP300\tTRUE\tFALSE\tFALSE\tFALSE\n+DYNLRB1:NM_001281727:NM_001281728:NM_001281729:NM_177953:NR_104032\tLARGE\tTRUE\tFALSE\tFALSE\tFALSE\n+ENTPD6\tNM_001287387:SLC25A1\tTRUE\tFALSE\tFALSE\tFALSE\n+SHANK3\tLAMA5\tTRUE\tFALSE\tFALSE\tFALSE\n+ATRN\tNM_001284277:NM_001284278:PITPNB\tTRUE\tFALSE\tFALSE\tFALSE\n+SULF2\tPRICKLE2:PRICKLE2-AS1\tTRUE\tFALSE\tFALSE\tFALSE\n+VPRBP\tNSFL1C\tTRUE\tFALSE\tFALSE\tFALSE\n+MFN1\tMAPRE1\tTRUE\tFALSE\tFALSE\tFALSE\n+PCMTD2\tPAK2\tTRUE\tFALSE\tFALSE\tFALSE\n+CEP63\tDNMT3B\tTRUE\tFALSE\tFALSE\tFALSE\n+RRP9\tCSE1L\tTRUE\tFALSE\tFALSE\tFALSE\n+CP:NR_046371\tCHD6\tTRUE\tFALSE\tFALSE\tFALSE\n+TMEM189:TMEM189-UBE2V1\tGLT8D1:GNL3:NM_001278280:NM_001278281\tTRUE\tFALSE\tFALSE\tFALSE\n+ST6GAL1\tNM_001278649:OSBPL2\tTRUE\tFALSE\tFALSE\tFALSE\n+OXSM\tMAP1LC3A\tTRUE\tFALSE\tFALSE\tFALSE\n+PHF20\tCDC25A\tTRUE\tFALSE\tFALSE\tFALSE\n+GOLIM4:NM_001308155\tGNAS:NM_001309840:NM_001309861\tTRUE\tFALSE\tFALSE\tFALSE\n+SLC25A38\tNM_001301188:NM_001301190:NM_001301193:NM_001301196:NM_001301201:TRIB3\tTRUE\tFALSE\tFALSE\tFALSE\n+ZNFX1\tIQCG\tTRUE\tFALSE\tFALSE\tFALSE\n+SNRK\tLAMA5\tTRUE\tFALSE\tFALSE\tFALSE\n+EYA2\tNR_103507:SLC6A6\tTRUE\tFALSE\tFALSE\tFALSE\n+KIF16B\tCACNA1D\tTRUE\tFALSE\tFALSE\tFALSE\n+SLC9A8\tTNIK\tTRUE\tFALSE\tFALSE\tFALSE\n+NCOA5\tMGLL\tTRUE\tFALSE\tFALSE\tFALSE\n+POLQ\tTGM2\tTRUE\tFALSE\tFALSE\tFALSE\n+FBLN2\tPOFUT1\tTRUE\tFALSE\tFALSE\tFALSE\n+FKBP1A:NR_037661\tATP11B\tTRUE\tFALSE\tFALSE\tFALSE\n+NRSN2\tNM_001195483:SLC12A8\tTRUE\tFALSE\tFALSE\tFALSE\n+FNDC3B\tSOGA1\tTRUE\tFALSE\tFALSE\tFALSE\n+CPNE1:NM_001198863:NR_037188:RBM12\tCHRD:NM_001304472:NM_001304473:NM_001304474:NR_130747\tTRUE\tFALSE\tFALSE\tFALSE\n+C3orf18:HEMK1\tPCNA:PCNA-AS1\tTRUE\tFALSE\tFALSE\tFALSE\n+RYBP\tLAMA5\tTRUE\tFALSE\tFALSE\tFALSE\n+USP19\tGNAS:NM_001309840:NM_001309861\tTRUE\tFALSE\tFALSE\tFALSE\n+SNRPB\tSEC61A1\tTRUE\tFALSE\tFALSE\tFALSE\n+MAVS:NR_037921\tKAT2B\tTRUE\tFALSE\tFALSE\tFALSE\n+GGT7\tCMC1\tTRUE\tFALSE\tFALSE\tFALSE\n+RPS21\tQRICH1\tTRUE\tFALSE\tFALSE\tFALSE\n+KIAA0226\tNM_001278649:OSBPL2\tTRUE\tFALSE\tFALSE\tFALSE\n+CDC25B:NM_001287516:NM_001287517:NM_001287518:NM_001287519:NM_001287520:NM_001287522:NM_001287524\tDNAJC19:NR_033721\tTRUE\tFALSE\tFALSE\tFALSE\n+C5orf34\tGNAS:NM_001309840:NM_001309861\tTRUE\tFALSE\tFALSE\tFALSE\n+DROSHA\tDLGAP4:NR_109939\tTRUE\tFALSE\tFALSE\tFALSE\n+SQSTM1\tEIF6\tTRUE\tFALSE\tFALSE\tFALSE\n+KDM3B\tDYNLRB1:NM_001281727:NM_001281728:NM_001281729:NM_177953:NR_104032\tTRUE\tFALSE\tFALSE\tFALSE\n+CYFIP2:NM_001291721:NM_001291722\tNR_037945:STX16\tTRUE\tFALSE\tFALSE\tFALSE\n+NPR3\tCPNE1:NM_001198863:NR_037188\tTRUE'..b'\tTRUE\tFALSE\tFALSE\n+SMAD2\tRPS23\tFALSE\tTRUE\tFALSE\tFALSE\n+NR_120540\tUBA2\tFALSE\tFALSE\tTRUE\tFALSE\n+NR_024091:ZFP91:ZFP91-CNTF\tLINC00261\tFALSE\tFALSE\tTRUE\tFALSE\n+FAT3\tCASC5\tFALSE\tFALSE\tTRUE\tFALSE\n+FRMD4A\tFRMD4A\tFALSE\tFALSE\tTRUE\tFALSE\n+NM_001291876:NM_001291877:TACC2\tRPLP1\tFALSE\tFALSE\tTRUE\tFALSE\n+EEF1A1\tGHITM\tFALSE\tFALSE\tTRUE\tFALSE\n+NM_001286806:NM_001286807:SLC25A30\tNDE1\tFALSE\tFALSE\tTRUE\tFALSE\n+RYBP\tYAF2\tFALSE\tFALSE\tTRUE\tFALSE\n+GALNT6\tGALNT6\tFALSE\tFALSE\tTRUE\tFALSE\n+NM_001290002:NM_001290004:NR_120486:NR_120487:ZNF385A\tNR_120486:NR_120487:ZNF385A\tFALSE\tFALSE\tTRUE\tFALSE\n+POR\tPUS1\tFALSE\tFALSE\tTRUE\tFALSE\n+NM_001159287:TPI1\tMLLT6\tFALSE\tFALSE\tTRUE\tFALSE\n+NM_001293212:NM_001293213:NM_001293214:NM_001293215:NM_001293216:NR_120608:TUBB\tKRT80\tFALSE\tFALSE\tTRUE\tFALSE\n+EEF1A1\tRPLP0\tFALSE\tFALSE\tTRUE\tFALSE\n+LY6E\tZNF609\tFALSE\tFALSE\tTRUE\tFALSE\n+TEKT4P2\tBRWD1\tFALSE\tFALSE\tTRUE\tFALSE\n+HNRNPK\tAATF\tFALSE\tFALSE\tTRUE\tFALSE\n+PKIA\tRARA\tFALSE\tFALSE\tTRUE\tFALSE\n+MRPL38\tMAP1LC3A\tFALSE\tFALSE\tTRUE\tFALSE\n+MYO19\tSKA2\tFALSE\tFALSE\tTRUE\tFALSE\n+ARHGAP27:NM_001282290\tARHGAP27:NM_001282290\tFALSE\tFALSE\tTRUE\tFALSE\n+BCAS3\tMED13\tFALSE\tFALSE\tTRUE\tFALSE\n+BPTF\tAMZ2:NM_001289054:NM_001289056\tFALSE\tFALSE\tTRUE\tFALSE\n+CARD14\tCARD14\tFALSE\tFALSE\tTRUE\tFALSE\n+PDCD2\tRPL26\tFALSE\tFALSE\tTRUE\tFALSE\n+EIF2A\tMYH11:NDE1\tFALSE\tFALSE\tTRUE\tFALSE\n+GATAD2A\tGATAD2A:NM_001300946\tFALSE\tFALSE\tTRUE\tFALSE\n+PLD3\tNM_001291311:PLD3\tFALSE\tFALSE\tTRUE\tFALSE\n+ARFIP1:NM_001287431:NM_001287432:NM_001287433\tDPY19L3\tFALSE\tFALSE\tTRUE\tFALSE\n+EEF1A1\tZNF317\tFALSE\tFALSE\tTRUE\tFALSE\n+NR_031672:SPTAN1\tBCL2L13:NR_073068:NR_073069\tFALSE\tFALSE\tTRUE\tFALSE\n+HMGN2\tESYT1\tFALSE\tFALSE\tTRUE\tFALSE\n+LOC644961:TMEM222\tACTG1:NR_037688\tFALSE\tFALSE\tTRUE\tFALSE\n+SARS\tME2\tFALSE\tFALSE\tTRUE\tFALSE\n+KISS1\tGOLT1A\tFALSE\tFALSE\tTRUE\tFALSE\n+CC2D1B\tDTYMK\tFALSE\tFALSE\tTRUE\tFALSE\n+SYTL1\tHSP90AB1\tFALSE\tFALSE\tTRUE\tFALSE\n+PAK2\tMAGEA10:MAGEA10-MAGEA5\tFALSE\tFALSE\tTRUE\tFALSE\n+TMCC1\tTMCC1\tFALSE\tFALSE\tTRUE\tFALSE\n+HPS3:NM_001308258:NR_046371\tCP:NR_046371\tFALSE\tFALSE\tTRUE\tFALSE\n+RSRC1\tRSRC1\tFALSE\tFALSE\tTRUE\tFALSE\n+GREB1\tGREB1\tFALSE\tFALSE\tTRUE\tFALSE\n+NR_130784\tNR_037904:SCLY\tFALSE\tFALSE\tTRUE\tFALSE\n+PNKD:TMBIM1\tPNKD:TMBIM1\tFALSE\tFALSE\tTRUE\tFALSE\n+PTMA\tRGL2\tFALSE\tFALSE\tTRUE\tFALSE\n+SLC30A5\tAZIN1:NM_001301668\tFALSE\tFALSE\tTRUE\tFALSE\n+NM_001286052:NM_001286053:NM_001286054:NM_001289931:NR_110527:ZNF595:ZNF718\tPSPH\tFALSE\tFALSE\tTRUE\tFALSE\n+RALGPS1\tRALGPS1\tFALSE\tFALSE\tTRUE\tFALSE\n+SULF2\tARFGEF2\tFALSE\tFALSE\tTRUE\tFALSE\n+NDUFA1\tSYNJ2BP:SYNJ2BP-COX16\tFALSE\tFALSE\tTRUE\tFALSE\n+NEDD8:NEDD8-MDP1\tNEDD8:NEDD8-MDP1\tFALSE\tFALSE\tTRUE\tFALSE\n+YLPM1\tITPK1\tFALSE\tFALSE\tTRUE\tFALSE\n+LAMP1\tMCF2L2\tFALSE\tFALSE\tFALSE\tTRUE\n+NFS1\tPREX1\tFALSE\tFALSE\tFALSE\tTRUE\n+STARD3\tDOK5:NM_177959\tFALSE\tFALSE\tFALSE\tTRUE\n+NM_001272060:RPS6KB1\tVMP1\tFALSE\tFALSE\tFALSE\tTRUE\n+NOS1AP\tC1orf226\tTRUE\tFALSE\tTRUE\tFALSE\n+INIP\tC5\tTRUE\tFALSE\tTRUE\tFALSE\n+FAM208B\tFAM208B\tTRUE\tFALSE\tTRUE\tFALSE\n+MED1\tACSF2:NM_001288968:NM_001288969:NM_001288970:NM_001288971:NM_001288972:NR_110232\tTRUE\tFALSE\tTRUE\tFALSE\n+PPP3R1\tVPS35\tTRUE\tFALSE\tTRUE\tFALSE\n+PPP1R12A\tSEPT10\tTRUE\tFALSE\tFALSE\tTRUE\n+NM_001281771:NM_001281772:NM_001281773:NM_001281774:NM_001281775:NM_001281776:NM_001281777:NM_001281778:NM_001281779:NM_001281780:NM_001281781:NM_001281782:NM_001281783:NM_001281784:ZMYND8\tCEP250\tTRUE\tFALSE\tFALSE\tTRUE\n+ARFGEF2\tSULF2\tTRUE\tFALSE\tFALSE\tTRUE\n+DIDO1\tNM_001303457:TTI1\tTRUE\tFALSE\tFALSE\tTRUE\n+DHX35\tITCH\tTRUE\tFALSE\tFALSE\tTRUE\n+CPNE1:NM_001198863:NR_037188\tPI3\tTRUE\tFALSE\tFALSE\tTRUE\n+CCDC85C\tSETD3\tTRUE\tFALSE\tFALSE\tTRUE\n+CYTH1\tEIF3H\tTRUE\tFALSE\tFALSE\tTRUE\n+RARA\tPKIA\tTRUE\tFALSE\tFALSE\tTRUE\n+BCAS4\tBCAS3\tTRUE\tFALSE\tFALSE\tTRUE\n+NR_036633:VAPB\tIKZF3:NM_001284514:NM_001284515\tTRUE\tFALSE\tFALSE\tTRUE\n+NM_001272060:RPS6KB1\tSNF8\tTRUE\tFALSE\tFALSE\tTRUE\n+SKA2\tMYO19\tTRUE\tFALSE\tFALSE\tTRUE\n+BSG\tNFIX\tTRUE\tFALSE\tFALSE\tTRUE\n+RAB22A\tMYO9B\tTRUE\tFALSE\tFALSE\tTRUE\n+GLB1\tCMTM7\tTRUE\tFALSE\tFALSE\tTRUE\n+NOTCH1\tNUP214\tTRUE\tFALSE\tFALSE\tTRUE\n+WDR67\tZNF704\tTRUE\tFALSE\tFALSE\tTRUE\n+ANKHD1:ANKHD1-EIF4EBP3\tPCDH1\tFALSE\tFALSE\tTRUE\tTRUE\n+TATDN1\tGSDMB\tTRUE\tFALSE\tTRUE\tTRUE\n+ACACA\tSTAC2\tTRUE\tFALSE\tTRUE\tTRUE\n' |
| b |
| diff -r 54ce44828e1b -r 86526900cb8f test-data/output_test_2.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_test_2.txt Mon Oct 12 04:17:07 2015 -0400 |
| b |
| b'@@ -0,0 +1,11248 @@\n+Left-genes\tRight-genes\tchimerascan.txt\tdefuse.txt\tfusion-map.txt\tedgren_tp.txt\n+C20orf112\tC20orf112\tTRUE\tFALSE\tFALSE\tFALSE\n+AP5S1\tMAVS:NR_037921\tTRUE\tFALSE\tFALSE\tFALSE\n+NM_001281771:NM_001281772:NM_001281773:NM_001281774:NM_001281775:NM_001281776:NM_001281777:NM_001281778:NM_001281779:NM_001281780:NM_001281781:NM_001281782:NM_001281783:NM_001281784:ZMYND8\tBCAS4\tTRUE\tFALSE\tFALSE\tFALSE\n+NR_036633:VAPB\tAPCDD1L-AS1\tTRUE\tFALSE\tFALSE\tFALSE\n+CSNK2A1\tFAM110A:NM_001289145:NM_001289146:NM_001289147\tTRUE\tFALSE\tFALSE\tFALSE\n+NR_109859\tAP5S1\tTRUE\tFALSE\tFALSE\tFALSE\n+FKBP1A:NR_037661:SDCBP2-AS1\tLOC284801\tTRUE\tFALSE\tFALSE\tFALSE\n+RSPO4\tADNP:NM_001282531\tTRUE\tFALSE\tFALSE\tFALSE\n+LOC284801\tLAMA5\tTRUE\tFALSE\tFALSE\tFALSE\n+OSER1-AS1\tOSER1-AS1\tTRUE\tFALSE\tFALSE\tFALSE\n+ZFP64\tNM_001281507:PHACTR3\tTRUE\tFALSE\tFALSE\tFALSE\n+IFT52:NM_001303458:NM_001303459\tARFGAP1:NM_001281482:NM_001281483:NM_001281484:NR_104022:NR_104023\tTRUE\tFALSE\tFALSE\tFALSE\n+RAD21L1\tHMGN1\tTRUE\tFALSE\tFALSE\tFALSE\n+VPS16\tPCP4\tTRUE\tFALSE\tFALSE\tFALSE\n+KIF16B\tATP5O\tTRUE\tFALSE\tFALSE\tFALSE\n+ADNP:NM_001282531:NM_001282532\tPCNT\tTRUE\tFALSE\tFALSE\tFALSE\n+SLC2A4RG\tBRWD1\tTRUE\tFALSE\tFALSE\tFALSE\n+NR_110051:ZNF217\tLOC400927:NM_001289912\tTRUE\tFALSE\tFALSE\tFALSE\n+LOC284801\tTUBGCP6\tTRUE\tFALSE\tFALSE\tFALSE\n+ELMO2\tJOSD1\tTRUE\tFALSE\tFALSE\tFALSE\n+STMN3\tRTCB\tTRUE\tFALSE\tFALSE\tFALSE\n+NM_001282933:NM_001282935:NR_104259:NR_110623:ZNF341\tHIRA\tTRUE\tFALSE\tFALSE\tFALSE\n+MTRNR2L3:RAE1\tDENND6B\tTRUE\tFALSE\tFALSE\tFALSE\n+NM_001278649:OSBPL2\tEWSR1\tTRUE\tFALSE\tFALSE\tFALSE\n+CTSZ\tEP300\tTRUE\tFALSE\tFALSE\tFALSE\n+DYNLRB1:NM_001281727:NM_001281728:NM_001281729:NM_177953:NR_104032\tLARGE\tTRUE\tFALSE\tFALSE\tFALSE\n+ENTPD6\tNM_001287387:SLC25A1\tTRUE\tFALSE\tFALSE\tFALSE\n+LAMA5\tSHANK3\tTRUE\tFALSE\tFALSE\tFALSE\n+ATRN\tNM_001284277:NM_001284278:PITPNB\tTRUE\tFALSE\tFALSE\tFALSE\n+SULF2\tPRICKLE2:PRICKLE2-AS1\tTRUE\tFALSE\tFALSE\tFALSE\n+NSFL1C\tVPRBP\tTRUE\tFALSE\tFALSE\tFALSE\n+MAPRE1\tMFN1\tTRUE\tFALSE\tFALSE\tFALSE\n+PCMTD2\tPAK2\tTRUE\tFALSE\tFALSE\tFALSE\n+DNMT3B\tCEP63\tTRUE\tFALSE\tFALSE\tFALSE\n+CSE1L\tRRP9\tTRUE\tFALSE\tFALSE\tFALSE\n+CHD6\tCP:NR_046371\tTRUE\tFALSE\tFALSE\tFALSE\n+TMEM189:TMEM189-UBE2V1\tGLT8D1:GNL3:NM_001278280:NM_001278281\tTRUE\tFALSE\tFALSE\tFALSE\n+NM_001278649:OSBPL2\tST6GAL1\tTRUE\tFALSE\tFALSE\tFALSE\n+MAP1LC3A\tOXSM\tTRUE\tFALSE\tFALSE\tFALSE\n+PHF20\tCDC25A\tTRUE\tFALSE\tFALSE\tFALSE\n+GNAS:NM_001309840:NM_001309861\tGOLIM4:NM_001308155\tTRUE\tFALSE\tFALSE\tFALSE\n+NM_001301188:NM_001301190:NM_001301193:NM_001301196:NM_001301201:TRIB3\tSLC25A38\tTRUE\tFALSE\tFALSE\tFALSE\n+ZNFX1\tIQCG\tTRUE\tFALSE\tFALSE\tFALSE\n+LAMA5\tSNRK\tTRUE\tFALSE\tFALSE\tFALSE\n+EYA2\tNR_103507:SLC6A6\tTRUE\tFALSE\tFALSE\tFALSE\n+KIF16B\tCACNA1D\tTRUE\tFALSE\tFALSE\tFALSE\n+SLC9A8\tTNIK\tTRUE\tFALSE\tFALSE\tFALSE\n+NCOA5\tMGLL\tTRUE\tFALSE\tFALSE\tFALSE\n+TGM2\tPOLQ\tTRUE\tFALSE\tFALSE\tFALSE\n+POFUT1\tFBLN2\tTRUE\tFALSE\tFALSE\tFALSE\n+FKBP1A:NR_037661\tATP11B\tTRUE\tFALSE\tFALSE\tFALSE\n+NRSN2\tNM_001195483:SLC12A8\tTRUE\tFALSE\tFALSE\tFALSE\n+SOGA1\tFNDC3B\tTRUE\tFALSE\tFALSE\tFALSE\n+CPNE1:NM_001198863:NR_037188:RBM12\tCHRD:NM_001304472:NM_001304473:NM_001304474:NR_130747\tTRUE\tFALSE\tFALSE\tFALSE\n+PCNA:PCNA-AS1\tC3orf18:HEMK1\tTRUE\tFALSE\tFALSE\tFALSE\n+LAMA5\tRYBP\tTRUE\tFALSE\tFALSE\tFALSE\n+GNAS:NM_001309840:NM_001309861\tUSP19\tTRUE\tFALSE\tFALSE\tFALSE\n+SNRPB\tSEC61A1\tTRUE\tFALSE\tFALSE\tFALSE\n+MAVS:NR_037921\tKAT2B\tTRUE\tFALSE\tFALSE\tFALSE\n+GGT7\tCMC1\tTRUE\tFALSE\tFALSE\tFALSE\n+RPS21\tQRICH1\tTRUE\tFALSE\tFALSE\tFALSE\n+NM_001278649:OSBPL2\tKIAA0226\tTRUE\tFALSE\tFALSE\tFALSE\n+CDC25B:NM_001287516:NM_001287517:NM_001287518:NM_001287519:NM_001287520:NM_001287522:NM_001287524\tDNAJC19:NR_033721\tTRUE\tFALSE\tFALSE\tFALSE\n+GNAS:NM_001309840:NM_001309861\tC5orf34\tTRUE\tFALSE\tFALSE\tFALSE\n+DLGAP4:NR_109939\tDROSHA\tTRUE\tFALSE\tFALSE\tFALSE\n+EIF6\tSQSTM1\tTRUE\tFALSE\tFALSE\tFALSE\n+DYNLRB1:NM_001281727:NM_001281728:NM_001281729:NM_177953:NR_104032\tKDM3B\tTRUE\tFALSE\tFALSE\tFALSE\n+NR_037945:STX16\tCYFIP2:NM_001291721:NM_001291722\tTRUE\tFALSE\tFALSE\tFALSE\n+CPNE1:NM_001198863:NR_037188\tNPR3\tTRUE\tFALSE\tFALSE\tFALSE\n+ACSS2\tHMGCR\tTRUE\tFALSE\tFALSE\tFALSE\n+CTSZ\tCCT5:NM_001306153:NM_001306154:NM_001306155:NM_001306156\tTRUE\tFALSE\tFALSE\tFALSE\n+L'..b'0004:NR_120486:NR_120487:ZNF385A\tNR_120486:NR_120487:ZNF385A\tFALSE\tFALSE\tTRUE\tFALSE\n+PUS1\tPOR\tFALSE\tFALSE\tTRUE\tFALSE\n+NM_001159287:TPI1\tMLLT6\tFALSE\tFALSE\tTRUE\tFALSE\n+KRT80\tNM_001293212:NM_001293213:NM_001293214:NM_001293215:NM_001293216:NR_120608:TUBB\tFALSE\tFALSE\tTRUE\tFALSE\n+RPLP0\tEEF1A1\tFALSE\tFALSE\tTRUE\tFALSE\n+ZNF609\tLY6E\tFALSE\tFALSE\tTRUE\tFALSE\n+AATF\tHNRNPK\tFALSE\tFALSE\tTRUE\tFALSE\n+MRPL38\tMAP1LC3A\tFALSE\tFALSE\tTRUE\tFALSE\n+BPTF\tAMZ2:NM_001289054:NM_001289056\tFALSE\tFALSE\tTRUE\tFALSE\n+CARD14\tCARD14\tFALSE\tFALSE\tTRUE\tFALSE\n+RPL26\tPDCD2\tFALSE\tFALSE\tTRUE\tFALSE\n+MYH11:NDE1\tEIF2A\tFALSE\tFALSE\tTRUE\tFALSE\n+GATAD2A\tGATAD2A:NM_001300946\tFALSE\tFALSE\tTRUE\tFALSE\n+PLD3\tNM_001291311:PLD3\tFALSE\tFALSE\tTRUE\tFALSE\n+DPY19L3\tARFIP1:NM_001287431:NM_001287432:NM_001287433\tFALSE\tFALSE\tTRUE\tFALSE\n+ZNF317\tEEF1A1\tFALSE\tFALSE\tTRUE\tFALSE\n+BCL2L13:NR_073068:NR_073069\tNR_031672:SPTAN1\tFALSE\tFALSE\tTRUE\tFALSE\n+LOC644961:TMEM222\tACTG1:NR_037688\tFALSE\tFALSE\tTRUE\tFALSE\n+SARS\tME2\tFALSE\tFALSE\tTRUE\tFALSE\n+SYTL1\tHSP90AB1\tFALSE\tFALSE\tTRUE\tFALSE\n+PAK2\tMAGEA10:MAGEA10-MAGEA5\tFALSE\tFALSE\tTRUE\tFALSE\n+TMCC1\tTMCC1\tFALSE\tFALSE\tTRUE\tFALSE\n+HPS3:NM_001308258:NR_046371\tCP:NR_046371\tFALSE\tFALSE\tTRUE\tFALSE\n+RSRC1\tRSRC1\tFALSE\tFALSE\tTRUE\tFALSE\n+GREB1\tGREB1\tFALSE\tFALSE\tTRUE\tFALSE\n+NR_130784\tNR_037904:SCLY\tFALSE\tFALSE\tTRUE\tFALSE\n+PNKD:TMBIM1\tPNKD:TMBIM1\tFALSE\tFALSE\tTRUE\tFALSE\n+PTMA\tRGL2\tFALSE\tFALSE\tTRUE\tFALSE\n+SLC30A5\tAZIN1:NM_001301668\tFALSE\tFALSE\tTRUE\tFALSE\n+NM_001286052:NM_001286053:NM_001286054:NM_001289931:NR_110527:ZNF595:ZNF718\tPSPH\tFALSE\tFALSE\tTRUE\tFALSE\n+RALGPS1\tRALGPS1\tFALSE\tFALSE\tTRUE\tFALSE\n+SYNJ2BP:SYNJ2BP-COX16\tNDUFA1\tFALSE\tFALSE\tTRUE\tFALSE\n+NEDD8:NEDD8-MDP1\tNEDD8:NEDD8-MDP1\tFALSE\tFALSE\tTRUE\tFALSE\n+YLPM1\tITPK1\tFALSE\tFALSE\tTRUE\tFALSE\n+LAMP1\tMCF2L2\tFALSE\tFALSE\tFALSE\tTRUE\n+NFS1\tPREX1\tFALSE\tFALSE\tFALSE\tTRUE\n+VMP1\tNM_001272060:RPS6KB1\tFALSE\tFALSE\tFALSE\tTRUE\n+FEN1\tFADS2:NM_001281501:NM_001281502\tTRUE\tTRUE\tFALSE\tFALSE\n+MCF2L\tLAMP1\tTRUE\tTRUE\tFALSE\tFALSE\n+GCN1L1\tMSI1\tTRUE\tTRUE\tFALSE\tFALSE\n+TNFRSF1A\tSCNN1A\tTRUE\tTRUE\tFALSE\tFALSE\n+RAE1\tNR_037945:STX16\tTRUE\tTRUE\tFALSE\tFALSE\n+TPD52L2\tDNAJC5\tTRUE\tTRUE\tFALSE\tFALSE\n+CPNE1:NM_001198863:NR_037188\tPREX1\tTRUE\tTRUE\tFALSE\tFALSE\n+SYNRG\tTOB1\tTRUE\tTRUE\tFALSE\tFALSE\n+MED1\tSTXBP4\tTRUE\tTRUE\tFALSE\tFALSE\n+SUMF1\tLRRFIP2:NM_001282691\tTRUE\tTRUE\tFALSE\tFALSE\n+NM_001165931:RRM2\tC2orf48\tTRUE\tTRUE\tFALSE\tFALSE\n+VAMP8\tVAMP5\tTRUE\tTRUE\tFALSE\tFALSE\n+TMEM120A\tSTYXL1\tTRUE\tTRUE\tFALSE\tFALSE\n+NCOA2\tZNF704\tTRUE\tTRUE\tFALSE\tFALSE\n+FAM208B\tFAM208B\tTRUE\tFALSE\tTRUE\tFALSE\n+YAF2\tRYBP\tTRUE\tFALSE\tTRUE\tFALSE\n+ARHGAP27:NM_001282290\tARHGAP27:NM_001282290\tTRUE\tFALSE\tTRUE\tFALSE\n+VPS35\tPPP3R1\tTRUE\tFALSE\tTRUE\tFALSE\n+NOS1AP\tC1orf226\tTRUE\tFALSE\tTRUE\tFALSE\n+KISS1\tGOLT1A\tTRUE\tFALSE\tTRUE\tFALSE\n+CC2D1B\tDTYMK\tTRUE\tFALSE\tTRUE\tFALSE\n+HMGN2\tESYT1\tTRUE\tFALSE\tTRUE\tFALSE\n+INIP\tC5\tTRUE\tFALSE\tTRUE\tFALSE\n+PPP1R12A\tSEPT10\tTRUE\tFALSE\tFALSE\tTRUE\n+ITCH\tDHX35\tTRUE\tFALSE\tFALSE\tTRUE\n+CPNE1:NM_001198863:NR_037188\tPI3\tTRUE\tFALSE\tFALSE\tTRUE\n+SETD3\tCCDC85C\tTRUE\tFALSE\tFALSE\tTRUE\n+ZNF704\tWDR67\tTRUE\tFALSE\tFALSE\tTRUE\n+STARD3\tDOK5:NM_177959\tFALSE\tTRUE\tFALSE\tTRUE\n+TEKT4P2\tBRWD1\tTRUE\tTRUE\tTRUE\tFALSE\n+MED1\tACSF2:NM_001288968:NM_001288969:NM_001288970:NM_001288971:NM_001288972:NR_110232\tTRUE\tTRUE\tTRUE\tFALSE\n+BCAS3\tMED13\tTRUE\tTRUE\tTRUE\tFALSE\n+BSG\tNFIX\tTRUE\tTRUE\tFALSE\tTRUE\n+MYO9B\tRAB22A\tTRUE\tTRUE\tFALSE\tTRUE\n+NUP214\tNOTCH1\tTRUE\tTRUE\tFALSE\tTRUE\n+CMTM7\tGLB1\tTRUE\tTRUE\tFALSE\tTRUE\n+CEP250\tNM_001281771:NM_001281772:NM_001281773:NM_001281774:NM_001281775:NM_001281776:NM_001281777:NM_001281778:NM_001281779:NM_001281780:NM_001281781:NM_001281782:NM_001281783:NM_001281784:ZMYND8\tTRUE\tTRUE\tFALSE\tTRUE\n+NM_001303457:TTI1\tDIDO1\tTRUE\tTRUE\tFALSE\tTRUE\n+CYTH1\tEIF3H\tTRUE\tTRUE\tFALSE\tTRUE\n+BCAS3\tBCAS4\tTRUE\tTRUE\tFALSE\tTRUE\n+IKZF3:NM_001284514:NM_001284515\tNR_036633:VAPB\tTRUE\tTRUE\tFALSE\tTRUE\n+SNF8\tNM_001272060:RPS6KB1\tTRUE\tTRUE\tFALSE\tTRUE\n+ANKHD1:ANKHD1-EIF4EBP3\tPCDH1\tFALSE\tTRUE\tTRUE\tTRUE\n+SULF2\tARFGEF2\tTRUE\tTRUE\tTRUE\tTRUE\n+GSDMB\tTATDN1\tTRUE\tTRUE\tTRUE\tTRUE\n+RARA\tPKIA\tTRUE\tTRUE\tTRUE\tTRUE\n+ACACA\tSTAC2\tTRUE\tTRUE\tTRUE\tTRUE\n+MYO19\tSKA2\tTRUE\tTRUE\tTRUE\tTRUE\n' |
| b |
| diff -r 54ce44828e1b -r 86526900cb8f test-data/refseq_genes_hg19.bed --- a/test-data/refseq_genes_hg19.bed Mon Jun 01 06:45:40 2015 -0400 +++ b/test-data/refseq_genes_hg19.bed Mon Oct 12 04:17:07 2015 -0400 |
| b |
| b'@@ -1,11072 +1,12261 @@\n-chr1\t66999824\t67210768\tNM_032291\n-chr1\t48998526\t50489626\tNM_032785\n-chr1\t16767166\t16786584\tNM_001145277\n-chr1\t16767166\t16786584\tNM_001145278\n-chr1\t16767166\t16786584\tNM_018090\n-chr1\t25071759\t25170815\tNM_013943\n-chr1\t33546713\t33585995\tNM_052998\n-chr1\t8384389\t8404227\tNM_001080397\n-chr1\t92145899\t92371559\tNM_001195684\n-chr1\t92145899\t92351836\tNM_001195683\n-chr1\t92145899\t92351836\tNM_003243\n-chr1\t100652477\t100715409\tNM_001918\n-chr1\t92145899\t92351836\tNR_036634\n+chr1\t66999638\t67216822\tSGIP1\n+chr1\t66999251\t67216822\tNM_001308203\n+chr1\t33547778\t33586132\tNM_001301825\n+chr1\t8378144\t8404227\tSLC45A1\n+chr1\t16767166\t16786584\tNECAP2\n+chr1\t16767166\t16786584\tNECAP2\n+chr1\t33547778\t33567493\tNR_126031\n+chr1\t16767166\t16786584\tNECAP2\n+chr1\t33546713\t33586132\tADC\n+chr1\t25071759\t25170815\tCLIC4\n+chr1\t33546713\t33586132\tNM_001293562\n+chr1\t33546729\t33586132\tNM_001301824\n+chr1\t33546729\t33586132\tNM_001301823\n+chr1\t33547778\t33567493\tNM_001301826\n+chr1\t48998526\t50489626\tAGBL4\n+chr1\t92145899\t92351836\tTGFBR3\n+chr1\t92145899\t92351836\tTGFBR3\n+chr1\t92145899\t92371559\tTGFBR3\n+chr1\t92145899\t92351836\tTGFBR3\n+chr1\t100652477\t100715409\tDBT\n+chr1\t175913961\t176176380\tRFWD2\n+chr1\t175913961\t176176380\tRFWD2\n+chr1\t150980866\t151008189\tNM_001303242\n chr1\t175913961\t176176380\tNM_001286644\n-chr1\t175913961\t176176380\tNM_022457\n-chr1\t184356149\t184598155\tNM_030806\n-chr1\t150980972\t151008189\tNM_021222\n-chr1\t175913961\t176176380\tNM_001001740\n-chr1\t226418849\t226497204\tNM_001270409\n-chr1\t226418849\t226497204\tNM_173083\n-chr1\t226418849\t226497449\tNM_001270410\n-chr1\t2985741\t3355185\tNM_199454\n-chr1\t2985741\t3355185\tNM_022114\n-chr1\t2005424\t2116834\tNM_001242874\n-chr1\t6845383\t7829766\tNM_015215\n-chr1\t6281252\t6296044\tNM_012405\n-chr1\t1017197\t1051736\tNM_017891\n-chr1\t2036154\t2116834\tNM_001033582\n-chr1\t2005085\t2116834\tNM_001033581\n-chr1\t1981908\t2116834\tNM_002744\n-chr1\t22004791\t22109688\tNM_032236\n-chr1\t20959947\t20978004\tNM_032409\n-chr1\t23037330\t23241823\tNM_017449\n-chr1\t23037330\t23241823\tNM_004442\n+chr1\t150980866\t151008189\tPRUNE\n+chr1\t150980866\t151008189\tNM_001303243\n+chr1\t150980866\t151008189\tNM_001303229\n+chr1\t184356149\t184598155\tC1orf21\n+chr1\t150980866\t151008189\tNR_130132\n+chr1\t150980866\t151008189\tNR_130131\n+chr1\t150980866\t151008189\tNR_130130\n+chr1\t150980866\t151008189\tNR_130135\n+chr1\t226418849\t226497449\tLIN9\n+chr1\t226418849\t226497204\tLIN9\n+chr1\t226418849\t226497204\tLIN9\n+chr1\t1017197\t1051736\tC1orf159\n+chr1\t2036154\t2116834\tPRKCZ\n+chr1\t6845383\t7829766\tCAMTA1\n+chr1\t2005424\t2116834\tPRKCZ\n+chr1\t2985741\t3355185\tPRDM16\n+chr1\t2005085\t2116834\tPRKCZ\n+chr1\t6281252\t6296044\tICMT\n+chr1\t1981908\t2116834\tPRKCZ\n+chr1\t2985741\t3355185\tPRDM16\n+chr1\t13629924\t13635299\tPRAMEF10\n+chr1\t13328195\t13698405\tPRAMEF19\n+chr1\t13629931\t13635299\tNM_001291381\n+chr1\t20959947\t20978004\tPINK1\n+chr1\t23037330\t23247993\tEPHB2\n chr1\t20969149\t20978686\tNR_046507\n-chr1\t29213602\t29446558\tNM_001166005\n-chr1\t32479294\t32509482\tNM_001271878\n-chr1\t29213602\t29446558\tNM_004437\n-chr1\t27248212\t27273362\tNM_006600\n-chr1\t28296854\t28415148\tNM_001990\n-chr1\t29241087\t29391733\tNM_001166006\n+chr1\t22004791\t22109688\tUSP48\n+chr1\t23037330\t23247993\tEPHB2\n+chr1\t23037330\t23247993\tNM_001309193\n+chr1\t23037330\t23247993\tNM_001309192\n+chr1\t29213602\t29446558\tEPB41\n+chr1\t29241087\t29391733\tEPB41\n+chr1\t29213602\t29446558\tEPB41\n+chr1\t26210676\t26232993\tSTMN1\n+chr1\t31404352\t31538564\tPUM1\n+chr1\t28296854\t28415148\tNM_001282562\n chr1\t28296854\t28415148\tNM_001282561\n-chr1\t29213602\t29446558\tNM_001166007\n-chr1\t31404352\t31538564\tNM_014676\n-chr1\t28296854\t28415148\tNM_001282562\n-chr1\t32479294\t32509482\tNM_006559\n-chr1\t26210676\t26232993\tNM_001145454\n chr1\t28303783\t28415148\tNM_001282560\n-chr1\t29213602\t29446558\tNM_203343\n+chr1\t28296854\t28415148\tEYA3\n+chr1\t31404352\t31538564\tPUM1\n chr1\t32479294\t32526460\tNR_073499\n chr1\t32479294\t32509482\tNR_073498\n-chr1\t29213602\t29446558\tNM_203342\n-chr1\t31404352\t31538564\tNM_001020658\n-chr1\t39549838\t39952810\tNM_012090\n-chr1\t36690016\t36770957\tNM_005119\n-chr1\t35649200\t35658743\tNM_005066\n+chr1\t32479294\t32509482\tKHDRBS1\n+chr1\t32479294\t32509482\tKHDRBS1\n+chr1\t2724821'..b'\n-chr17_ctg5_hap1\t1407998\t1410253\tNR_026901\n-chr17_ctg5_hap1\t1450905\t1513884\tNM_016632\n+chr17_ctg5_hap1\t197705\t240669\tLRRC37A4P\n+chr17_ctg5_hap1\t330260\t380553\tNSFP1\n+chr17_ctg5_hap1\t266211\t380618\tNSFP1\n+chr17_ctg5_hap1\t266211\t380618\tNSF\n+chr17_ctg5_hap1\t415626\t458604\tLRRC37A\n+chr17_ctg5_hap1\t592235\t595386\tKANSL1-AS1\n+chr17_ctg5_hap1\t891433\t894424\tMAPT-IT1\n+chr17_ctg5_hap1\t790688\t791133\tSTH\n+chr17_ctg5_hap1\t943101\t945284\tSPPL2C\n+chr17_ctg5_hap1\t954314\t1005883\tCRHR1\n+chr17_ctg5_hap1\t954314\t1005883\tCRHR1\n+chr17_ctg5_hap1\t954314\t1005883\tCRHR1\n+chr17_ctg5_hap1\t954314\t1005883\tCRHR1\n+chr17_ctg5_hap1\t954314\t1005883\tNM_001303020\n+chr17_ctg5_hap1\t954314\t1005883\tNM_001303018\n+chr17_ctg5_hap1\t1147639\t1150972\tCRHR1-IT1\n+chr17_ctg5_hap1\t1143725\t1150972\tCRHR1-IT1\n+chr17_ctg5_hap1\t1151951\t1170468\tMGC57346\n+chr17_ctg5_hap1\t1151951\t1170182\tMGC57346\n+chr17_ctg5_hap1\t1188958\t1190710\tLOC644172\n+chr17_ctg5_hap1\t1486976\t1513884\tARL17A\n+chr17_ctg5_hap1\t1450905\t1513884\tARL17A\n chr17_ctg5_hap1\t1461295\t1513884\tNM_001288813\n-chr17_ctg5_hap1\t1486976\t1513884\tNM_001113738\n-chr17_ctg5_hap1\t1481376\t1489848\tNR_002940\n chr17_ctg5_hap1\t1461295\t1513884\tNM_001288811\n-chr1_gl000191_random\t36272\t50281\tNM_006625\n-chr1_gl000191_random\t38911\t50281\tNM_001191005\n-chr1_gl000191_random\t36272\t50281\tNM_001191009\n-chr1_gl000191_random\t36272\t50281\tNM_001191006\n-chr1_gl000191_random\t38911\t50281\tNM_054016\n-chr1_gl000191_random\t36272\t50281\tNR_034035\n-chr1_gl000191_random\t36272\t50281\tNM_001191007\n+chr17_ctg5_hap1\t1481376\t1489848\tLRRC37A4P\n+chr1_gl000191_random\t34172\t50281\tSRSF10\n+chr1_gl000191_random\t34172\t50281\tSRSF10\n+chr1_gl000191_random\t34172\t50281\tSRSF10\n+chr1_gl000191_random\t34172\t50281\tSRSF10\n+chr1_gl000191_random\t34172\t50281\tSRSF10\n+chr1_gl000191_random\t34172\t50281\tSRSF10\n+chr1_gl000191_random\t34172\t50281\tSRSF10\n+chr1_gl000191_random\t34172\t50281\tNM_001300937\n+chr1_gl000191_random\t34172\t50281\tNM_001300936\n chr1_gl000192_random\t132568\t407510\tNR_103556\n-chr4_gl000193_random\t49162\t88375\tNR_038377\n-chr4_gl000194_random\t53588\t115071\tNR_046441\n-chr4_gl000194_random\t53588\t115071\tNR_046440\n-chr4_gl000194_random\t61659\t115071\tNR_046442\n-chr4_gl000194_random\t53588\t115071\tNR_046439\n-chr7_gl000195_random\t42937\t86719\tNM_001242480\n-chr17_gl000205_random\t116622\t119732\tNR_003682\n-chr19_gl000209_random\t21910\t36449\tNM_014219\n+chr1_gl000192_random\t429709\t468683\tNR_120328\n+chr4_gl000193_random\t49162\t88375\tMGC39584\n+chr4_gl000194_random\t61659\t115073\tMAFIP\n+chr4_gl000194_random\t53588\t115073\tMAFIP\n+chr4_gl000194_random\t53588\t115073\tMAFIP\n+chr4_gl000194_random\t53588\t115073\tMAFIP\n+chr7_gl000195_random\t42937\t86719\tLOC389831\n+chr17_gl000205_random\t116622\t119732\tMGC70870\n chr19_gl000209_random\t86690\t96155\tNM_020535\n+chr19_gl000209_random\t98134\t112667\tKIR2DS5\n+chr19_gl000209_random\t70070\t84658\tNM_001282170\n+chr19_gl000209_random\t21910\t36449\tKIR2DL2\n+chr19_gl000209_random\t98111\t113132\tKIR2DS5\n+chr19_gl000209_random\t57208\t68123\tLOC100287534\n+chr19_gl000209_random\t57208\t68123\tKIR2DL4\n+chr19_gl000209_random\t57208\t68123\tLOC100287534\n+chr19_gl000209_random\t86745\t96246\tKIR2DL5B\n+chr19_gl000209_random\t115098\t129113\tKIR2DS1\n chr19_gl000209_random\t70070\t84658\tNM_001282171\n-chr19_gl000209_random\t115098\t129113\tNM_014512\n-chr19_gl000209_random\t57208\t68123\tNM_002255\n-chr19_gl000209_random\t57208\t68123\tNM_001080770\n-chr19_gl000209_random\t98134\t112667\tNM_012313\n-chr19_gl000209_random\t57208\t68123\tNM_001080772\n-chr19_gl000209_random\t98111\t113132\tNM_014513\n-chr19_gl000209_random\t46645\t68123\tNM_001258383\n-chr19_gl000209_random\t86745\t96246\tNM_001018081\n-chr19_gl000209_random\t70070\t84658\tNM_001282170\n-chr19_gl000209_random\t70070\t84658\tNM_001083539\n-chr19_gl000209_random\t131432\t145745\tNM_012312\n+chr19_gl000209_random\t70070\t84658\tKIR3DS1\n+chr19_gl000209_random\t21904\t129563\tNM_001291700\n+chr19_gl000209_random\t131432\t145743\tKIR2DS2\n+chr19_gl000209_random\t131432\t145743\tNM_001291695\n+chr19_gl000209_random\t131432\t145743\tNM_001291696\n+chr19_gl000209_random\t131432\t145743\tNM_001291701\n+chr19_gl000209_random\t131432\t145743\tNM_001291700\n' |
| b |
| diff -r 54ce44828e1b -r 86526900cb8f tool_dependencies.xml --- a/tool_dependencies.xml Mon Jun 01 06:45:40 2015 -0400 +++ b/tool_dependencies.xml Mon Oct 12 04:17:07 2015 -0400 |
| b |
| @@ -1,6 +1,9 @@ <?xml version="1.0"?> <tool_dependency> - <package name="fuma" version="2.7.1"> - <repository changeset_revision="d728db4c0214" name="package_fuma_2_7_1" owner="yhoogstrate" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> + <package name="python" version="2.7"> + <repository changeset_revision="ed2fa0e530f3" name="package_python_2_7" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <package name="fuma" version="2.10.0"> + <repository changeset_revision="48783f711368" name="package_fuma_2_10_0" owner="yhoogstrate" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> </tool_dependency> |