| Previous changeset 3:2d32e6c86c48 (2021-10-08) Next changeset 5:005b200c8841 (2021-10-10) |
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Commit message:
"planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 5a62e8a2ec56a8ce00f89c8fbe61b3f1dffbbffd" |
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modified:
arriba.xml arriba_download_reference.xml arriba_get_filters.xml test-data/Aligned.out.sam |
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added:
test-data/fusions.tsv test-data/genome.fasta test-data/genome.gtf test-data/read1.fastq.gz test-data/read2.fastq.gz |
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| diff -r 2d32e6c86c48 -r 77021ad5037d arriba.xml --- a/arriba.xml Fri Oct 08 20:44:25 2021 +0000 +++ b/arriba.xml Sat Oct 09 15:41:49 2021 +0000 |
| [ |
| @@ -20,7 +20,7 @@ #end if ln -f -s '${input_params.right_fq}' ${read2} && #if str($input_params.index.index_source) == "history" - #set $star_index_dir = $input_params.index.star_index.files_path + #set $star_index_dir = $input_params.index.star_index.extra_files_path #end if STAR --runThreadN \${GALAXY_SLOTS:-1} @@ -56,29 +56,31 @@ #end if -a '$genome_assembly' -g '$gtf' - #if '$blacklist' + #if $blacklist -b '$blacklist' + #else + -f 'blacklist' #end if - #if '$protein_domains' + #if $protein_domains -p '$protein_domains' #end if - #if '$known_fusions' + #if $known_fusions -k '$known_fusions' #end if - #if '$tags' + #if $tags -t '$tags' #end if -o fusions.tsv -O fusions.discarded.tsv #if str($input_params.input_source) == "use_fastq" - && samtools sort -@ "$THREADS" -m 4G -T tmp -O bam Aligned.out.bam > Aligned.sortedByCoord.out.bam + && samtools sort -@ \${GALAXY_SLOTS:-1} -m 4G -T tmp -O bam Aligned.out.bam > Aligned.sortedByCoord.out.bam && samtools index Aligned.sortedByCoord.out.bam #elif str($visualization.do_viz) == "yes" - && samtools sort -@ "$THREADS" -m 4G -T tmp -O bam '$input_params.input' > Aligned.sortedByCoord.out.bam + && samtools sort -@ \${GALAXY_SLOTS:-1} -m 4G -T tmp -O bam '$input_params.input' > Aligned.sortedByCoord.out.bam && samtools index Aligned.sortedByCoord.out.bam #end if #if str($visualization.do_viz) == "yes" -draw_fusions.R \ +&& draw_fusions.R --fusions=fusions.tsv --alignments=Aligned.sortedByCoord.out.bam --output=fusions.pdf @@ -87,7 +89,7 @@ --cytobands='$visualization.cytobands' #end if #if '$protein_domains' - --proteinDomains=database/protein_domains_hg19_hs37d5_GRCh37_v2.1.0.gff3 + --proteinDomains='$protein_domains' #end if #end if @@ -129,11 +131,12 @@ <param name="genome_assembly" argument="-a" type="data" format="fasta" label="genome assembly fasta"/> <param name="gtf" argument="-g" type="data" format="gtf" label="GTF file with gene annotation"/> <param name="blacklist" argument="-b" type="data" format="tabular" optional="true" label="File containing blacklisted ranges."/> - <param name="protein_domains" argument="-p" type="data" format="gff3" optional="true" label="File containing blacklisted ranges."/> + <param name="protein_domains" argument="-p" type="data" format="gff3" optional="true" label="File containing protein domains"/> <param name="known_fusions" argument="-k" type="data" format="tabular" optional="true" label="File containing known fusions"> <help><![CDATA[ file two TAB separated columns: five-prime region three-prime region ]]></help> </param> - <param name="tags" argument="-t" type="data" format="tabular" optional="true" label="File containing tag names for a fusion."/> + <param name="tags" argument="-t" type="data" format="tabular" optional="true" label="File containing tag names for a fusion." + help="This can be the known fusions if that input has a third column with a name"/> <conditional name="visualization"> <param name="do_viz" type="select" label="Generate visualization"> <option value="yes">Yes</option> @@ -152,10 +155,29 @@ <data name="aligned_bam" format="bam" label="${tool.name} on ${on_string}: Aligned.bam" from_work_dir="Aligned.sortedByCoord.out.bam"> <filter>input_params['input_source'] == "use_fastq"</filter> </data> - <data name="fusions_png" format="png" label="${tool.name} on ${on_string}: fusions.pdf" from_work_dir="fusions.pdf"> + <data name="fusions_pdf" format="pdf" label="${tool.name} on ${on_string}: fusions.pdf" from_work_dir="fusions.pdf"> <filter>visualization['do_viz'] == "yes"</filter> </data> </outputs> + <tests> + <!-- Test 1 - From exisitng BAM --> + <test> + <conditional name="input_params"> + <param name="input_source" value="use_star"/> + <param name="input" ftype="sam" value="Aligned.out.sam"/> + </conditional> + <param name="genome_assembly" ftype="fasta" value="genome.fasta"/> + <param name="gtf" ftype="gtf" value="genome.gtf"/> + <conditional name="visualization"> + <param name="do_viz" value="no"/> + </conditional> + <output name="fusions"> + <assert_contents> + <has_text_matching expression="BCR\tABL1"/> + </assert_contents> + </output> + </test> + </tests> <help><![CDATA[ ** Arriba ** |
| b |
| diff -r 2d32e6c86c48 -r 77021ad5037d arriba_download_reference.xml --- a/arriba_download_reference.xml Fri Oct 08 20:44:25 2021 +0000 +++ b/arriba_download_reference.xml Sat Oct 09 15:41:49 2021 +0000 |
| b |
| @@ -12,7 +12,7 @@ \$REF_SCRIPT '$arriba_reference_name' && cp *.fa* '$genome_fasta' && cp *.gtf* '$genome_gtf' && - mv STAR*/* '$star_index.extra_files_path' + mv STAR_index_* '$star_index.extra_files_path' ]]></command> <inputs> <param name="arriba_reference_name" type="select" label="Select reference"> |
| b |
| diff -r 2d32e6c86c48 -r 77021ad5037d arriba_get_filters.xml --- a/arriba_get_filters.xml Fri Oct 08 20:44:25 2021 +0000 +++ b/arriba_get_filters.xml Sat Oct 09 15:41:49 2021 +0000 |
| [ |
| @@ -34,11 +34,21 @@ </param> </inputs> <outputs> - <data name="blacklist" format="tabular" label="${tool.name} ${arriba_reference_name} blacklist"/> - <data name="known_fusions" format="tabular" label="${tool.name} ${arriba_reference_name} known_fusions"/> - <data name="protein_domains" format="tabular" label="${tool.name} ${arriba_reference_name} protein_domains"/> - <data name="cytobands" format="tabular" label="${tool.name} ${arriba_reference_name} cytobands"/> + <data name="blacklist" format="tabular" label="${tool.name} ${arriba_reference_name} blacklist.tsv"/> + <data name="known_fusions" format="tabular" label="${tool.name} ${arriba_reference_name} known_fusions.tsv"/> + <data name="protein_domains" format="gff3" label="${tool.name} ${arriba_reference_name} protein_domains.gff3"/> + <data name="cytobands" format="tabular" label="${tool.name} ${arriba_reference_name} cytobands.tsv"/> </outputs> + <tests> + <test> + <param name="arriba_reference_name" value="GRCh38"/> + <output name="cytobands"> + <assert_contents> + <has_text_matching expression="1\t1\t\d+\tp36.33\tgneg"/> + </assert_contents> + </output> + </test> + </tests> <help><![CDATA[ ** Arriba ** |
| b |
| diff -r 2d32e6c86c48 -r 77021ad5037d test-data/Aligned.out.sam --- a/test-data/Aligned.out.sam Fri Oct 08 20:44:25 2021 +0000 +++ b/test-data/Aligned.out.sam Sat Oct 09 15:41:49 2021 +0000 |
| b |
| b'@@ -1,104 +1,82 @@\n @HD\tVN:1.4\tSO:coordinate\n-@SQ\tSN:1\tLN:248956422\n-@SQ\tSN:2\tLN:242193529\n-@SQ\tSN:3\tLN:198295559\n-@SQ\tSN:4\tLN:190214555\n-@SQ\tSN:5\tLN:181538259\n-@SQ\tSN:6\tLN:170805979\n-@SQ\tSN:7\tLN:159345973\n-@SQ\tSN:8\tLN:145138636\n-@SQ\tSN:9\tLN:138394717\n-@SQ\tSN:10\tLN:133797422\n-@SQ\tSN:11\tLN:135086622\n-@SQ\tSN:12\tLN:133275309\n-@SQ\tSN:13\tLN:114364328\n-@SQ\tSN:14\tLN:107043718\n-@SQ\tSN:15\tLN:101991189\n-@SQ\tSN:16\tLN:90338345\n-@SQ\tSN:17\tLN:83257441\n-@SQ\tSN:18\tLN:80373285\n-@SQ\tSN:19\tLN:58617616\n-@SQ\tSN:20\tLN:64444167\n-@SQ\tSN:21\tLN:46709983\n-@SQ\tSN:22\tLN:50818468\n-@SQ\tSN:X\tLN:156040895\n-@SQ\tSN:Y\tLN:57227415\n-@SQ\tSN:MT\tLN:16569\n-@PG\tID:STAR\tPN:STAR\tVN:2.7.8a\tCL:STAR --runThreadN 12 --genomeDir /panfs/roc/website/galaxy.msi.umn.edu/galaxy/tool-data/rnastar/2.7.4a/GRCh38_canon/GRCh38_canon/dataset_1367616_files --genomeLoad NoSharedMemory --readFilesIn /panfs/roc/galaxy/PRODUCTION/database/files/001/368/dataset_1368710.dat /panfs/roc/galaxy/PRODUCTION/database/files/001/368/dataset_1368711.dat --readFilesCommand zcat --limitBAMsortRAM 122880000000 --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif --outSAMattributes NH HI AS nM ch --outSAMunmapped Within --outSAMprimaryFlag OneBestScore --outSAMmapqUnique 60 --outBAMsortingThreadN 12 --outBAMsortingBinsN 50 --outSAMattrIHstart 1 --winAnchorMultimapNmax 50 --chimSegmentMin 12 --chimOutType WithinBAM Junctions --chimOutJunctionFormat 1 --quantMode GeneCounts --twopass1readsN 50000 --twopassMode Basic\n-@CO\tuser command line: STAR --runThreadN 12 --genomeLoad NoSharedMemory --genomeDir /panfs/roc/website/galaxy.msi.umn.edu/galaxy/tool-data/rnastar/2.7.4a/GRCh38_canon/GRCh38_canon/dataset_1367616_files --readFilesIn /panfs/roc/galaxy/PRODUCTION/database/files/001/368/dataset_1368710.dat /panfs/roc/galaxy/PRODUCTION/database/files/001/368/dataset_1368711.dat --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate --twopassMode Basic --twopass1readsN 50000 --quantMode GeneCounts --outSAMstrandField intronMotif --outSAMattrIHstart 1 --outSAMattributes NH HI AS nM ch --outSAMprimaryFlag OneBestScore --outSAMmapqUnique 60 --outSAMunmapped Within --chimSegmentMin 12 --outBAMsortingThreadN 12 --outBAMsortingBinsN 50 --winAnchorMultimapNmax 50 --limitBAMsortRAM 122880000000 --chimOutType WithinBAM Junctions --chimOutJunctionFormat 1\n-BCR-ABL1-76\t99\t9\t130854061\t60\t24S126M\t=\t130854103\t755\tCAGCCACTGGATTTAAGCAGAGTTCAAAAGCCCTTCAGCGGCCAGTAGCATCTGACTTTGAGCCTCAGGGTCTGAGTGAAGCCGCTCGTTGGAACTCCAAGGAAAACCTTCTCGCTGGACCCAGTGAAAATGACCCCAACCTTTTCGTTG\tCCCGGGGCGGGCGJJJJJGJJJGJJJJJJJJJGJ1JCJJGJGGJJJGJJGGJJJ8GGJJGGGJJ=GGCGGGGGG=GGCCGGG8GC=GGGG=GCGGCGGGGJGG=GGGG=GGGGGGGGCGGGGCCGGGCG=GG(G=GCGCCG1CCGGCGGG\tNH:i:1\tHI:i:1\tAS:i:274\tnM:i:1\tXS:A:+\tNM:i:1\n-BCR-ABL1-64\t99\t9\t130854061\t60\t6S144M\t=\t130854104\t756\tAGAGTTCAAAAGCCCTTCAGCGGCCAGTAGCATCTGACTTTGAGCCTCAGGGTCTGAGTGAAGCCGCTCGTTGGAACTCCAAGGAAAACCTTCTCGCTGGACCCAGTGAAAATGACCCCAACCTTTTCGTTGCACTGTATGATTTTGTGG\tCCCGGGGGCGGGGGJJJGJJJGGJJJJJCJJJJGGJJJGJJGJGJG=GGJG=JJJJCGCCC==JGGCGGGCJG1CCCCGG8CGGGGGGGGCCGC=CGCGGJGGGGCGCGGGGGGGGCCGCGGGG=GCGGGGGGG=GGGGCGGGGGGCCGG\tNH:i:1\tHI:i:1\tAS:i:290\tnM:i:2\tXS:A:+\tNM:i:1\n-BCR-ABL1-54\t99\t9\t130854061\t60\t61S89M\t=\t130854061\t140\tCCGGGGCTCTATGGGTTTCTGAATGTCATCGTCCACTCAGCCACTGGATTTAAGCAGAGTTCAAAAGCCCTTGAGCGGCCAGTAGCATCTGACTTTGAGCCTCAGGGTCTGAGTGAAGCCGCTCGTTGGAACTCCAAGGAAAACCTTCTC\tCCCGGGGGGGGGGGJJJJJGJ=JJJJJJGJJJGGJJJJJJJCJJG8JJJGJJGJ=GG=JJJGGCGGCGGJGC(GGGGGCGC8CGGCGCCGGC=GGGCGGGJG1GGGGGG1CG=GGGGC=1G1CGGGGGCCGGGGCGG=CC=C=CGGGGG8\tNH:i:1\tHI:i:1\tAS:i:219\tnM:i:4\tNM:i:2\n-BCR-ABL1-54\t147\t9\t130854061\t60\t10S140M\t=\t130854061\t-140\tAAGCAGAGTTCAAAAGCCCTTCAGCGGCCAGTAGCATCTGACTTTGAGCCTCAGGGTCTGAGTGAAGCCGCTCGTTGGAACTCCAAGGAAAACGTTCTCGCTGGACCCAGTGAAAATGACCCCAACCTTTTCGTTGCACTGTATGATTTT\t=GGGGGGGCCCCGCCGGG=G(GGGG=CGCGGCGCCGG=GGGGGCJJJ=GC8C1GGGGGCG8GCCGC=GGG1GCCGGJC8GCGGCGCGJGJJJG1CGJGG=CJJJGGGGJG=CJGJJJJCJCJJGGJJJJJGGJGGJJCGGGGGGGGG=CC\tNH:i:1\tHI:i:1\tAS:i:219\tnM:i:4\tNM:i:2\n-BCR-ABL1-'..b'CGC=GGGGGG1JJJGJGJJJCJJCGJJJJJJJJJJCGJJJJJJGGCCJ1JGCGGCGJ8GG(CJGJGJCGGCGG1CC=CG=GCC=GGGGG=GGCGCCG1CGGGGGGG1GGGGGCGGGCGCGGCGG811G8CCGGGGCGGGGGCCG=CGC\tNH:i:1\tHI:i:1\tAS:i:298\tnM:i:0\tNM:i:0\n+BCR-ABL1-16\t83\t9\t275888\t60\t150M\t=\t275840\t-198\tCCCAAACCAAAAATGGCCAAGGCTGGGTCCCAAGCAACTACATCACGCCAGTCAACAGTCTGGAGAAACACTCCTGGTACCATGGGCCTGTGTCCCGCAATGCCGCTGAGTATCTGCTGAGCAGCGGGATCAATGGCAGCTTCTTGGTGC\tCGGGGGG=GGCGGGCGGGGGGGCGGGGCGGGGCCCG=CGGGGGCGGGCCCGG8GCCCGG8GCGGC=GCCCGGGGGGCGGGCGGJGGGCCGGJCGGJJGJGGGGGJJJJGJJGGJJGG=JGGJJGGJ=JGJJJJJJGJC1GGGG=GGG1C1\tNH:i:1\tHI:i:1\tAS:i:296\tnM:i:1\tNM:i:0\n+BCR-ABL1-32\t147\t9\t275894\t60\t150M\t=\t275850\t-194\tCCAAAAATGGCCAAGGCTGGGTCCCAAGCAACTACATCACGCCAGTCAACAGTCTGGAGAAACACTCCTGGTACCATGGGCCTGTGTCCCGCAATGCCGCTGAGTATCTGCTGAGCAGCGGGATCAATGGCAGCTTCTTGGTGCGTGAGA\t8GCCCCGGCGCGC1GGGGCGGCCGGGGCG1(GG=GG=GCGGCGJCJJCGG8=GGGCCGCGGGCGGGGGC=GC1=GGGGGJGGCCGJJCGGGJJJCGGG8CCGGGCJGJGJJGCCGCJJJJJJJJJJGCGJJJGJJGJGGGGGCGGGG=CC\tNH:i:1\tHI:i:1\tAS:i:298\tnM:i:0\tNM:i:0\n+BCR-ABL1-38\t83\t9\t275900\t60\t150M\t=\t275854\t-196\tATGGCCAAGGCTGGGTCCCAAGCAACTACATCACGCCAGTCAACAGTCTGGAGAAACACTCCTGGTACCATGGGCCTGTGTCCCGCAATGCCGCTGAGTATCTGCTGAGCAGCGGGATCAATGGCAGCTTCTTGGTGCGTGAGAGTGAGA\tGCGCCGCGGGCGGGGGGGCGGCGCG8CGCGGGG8GGCGGGCCCCG8CC=JGCGGGGGGCGGGGCGCCGC=GCCCGGJGGGCGGGCJGCCJJGJG=GGCJJJGGJCGJCGCGJJJC=JJGJCJGJGJJGJJJ=JJJ1GGGGGGGGGGGCCC\tNH:i:1\tHI:i:1\tAS:i:298\tnM:i:0\tNM:i:0\n+BCR-ABL1-6\t147\t9\t275903\t60\t150M\t=\t275846\t-207\tGCCAAGGCTGGGTCCCAAGCAACTACATCACGCCAGTCAACAGTCTGGAGAAACACTCCTGGTACCATGGGCCTGTGTCCCGCAATGCCGCTGAGTATCTGCTGAGCAGCGGGATCAATGGCAGCTTCTTGGTGCGTGAGAGTGAGAGCA\tCG8GCGGGCCCCGGCGCGGGGCCGGGCGG8CG=G=GCCGCGG=1CJ8JCCGCGGGGGCGGGGGGCGG=G=8GCGJG=GGGGGGJGCCGGJJGG=G=CJ8=JJJJGG=JJJJJGJJGJGJJGJJJJJCCCJJJGGJJJG1GGG1GGGGCCC\tNH:i:1\tHI:i:1\tAS:i:298\tnM:i:0\tNM:i:0\n+BCR-ABL1-70\t83\t9\t275911\t60\t150M\t=\t275874\t-187\tTGGGTCCCAAGCAACTACATCACGCCAGTCAACAGTCTGGAGAAACACTCCTGGTACCATGGGCCTGTGTCCCGCAATGCCGCTGAGTATCTGCTGAGCAGCGGGATCAATGGCAGCTTCTTGGTGCGTGAGAGTGAGAGCAGTCCTGGC\tCGGGCGGGCGGGCCGGGG=GGG8GCGGG8GGCGGGCGGCGGGCGGGGG=JGGGGGCGCGGGGGCGGGGCGCG1GGGGCJC8GG=JGGJJCCCJJGGGGJGJGJGGJJGGJJJJJGCJJJJGGJJGJJGJJJGGGJJJGGGGCGGGGG=CC\tNH:i:1\tHI:i:1\tAS:i:298\tnM:i:0\tNM:i:0\n+BCR-ABL1-36\t147\t9\t275919\t60\t150M\t=\t275872\t-197\tAAGCAACTACATCACGCCAGTCAACAGTCTGGAGAAACACTCCTGGTACCATGGGCCTGTGTCCCGCAATGCCGCTGAGTATCTGCTGAGCAGCGGGATCAATGGCAGCTTCTTGGTGCGTGAGAGTGAGAGCAGTCCTGGCCAGAGGTC\tC=GGGGGGCCGGGGGGGGG=GGCCGCGGGC1GCGC1GCGGCCGJJ(CCG8GCCGGGCCGGGC=CC1CG=CGCCGGG=CGGGGGGGGCGGGGGJ==JJJJJ1CJJJGJGGJCGCJGJGJGJJJJ=GG1CJJCGJG1GC=GGGCGCGGGCCC\tNH:i:1\tHI:i:1\tAS:i:298\tnM:i:0\tNM:i:0\n+BCR-ABL1-56\t147\t9\t275928\t60\t150M\t=\t275885\t-193\tCATCACGCCAGTCAACAGTCTGGAGAAACACTCCTGGTACCATGGGCCTGTGTCCCGCAATGCCGCTGAGTATCTGCTGAGCAGCGGGATCAATGGCAGCTTCTTGGTGCGTGAGAGTGAGAGCAGTCCTGGCCAGAGGTCCATCTCGCT\tCCGGGCGCGCGGGCG=CCCGGCGCGGGGC=CGGCGGCCGCGGGJJJJCCGCCG(GCCCCCGGCCGGG=G8GGGGGGCC=C=CGGJGJJJGC=JGGJJJGJGJ1JJJGC=JJJG=JCJJJJJJJ=JJGGGJJJCGJJJGGGGGCGG=GCCC\tNH:i:1\tHI:i:1\tAS:i:298\tnM:i:0\tNM:i:0\n BCR-ABL1-74\t77\t*\t0\t0\t*\t*\t0\t0\tTCATTTTCACTGGGTCCAGCGAGAAGGTTTTCCTTGGAGTTCCAACGAGCGGCTTCACTCAGACCCTGAGGCTCAAAGTCAGATGCTACTGGCCGCTGAAGGGCTTTTGAACTCTGCTTAAATCCAGTGGCTGAGTGGACGATGACATTC\tCC11GGGGGGGGGGCCJJJGCGJJGJJJJJGGGGGGJJJGGJG==GCJCJ=GGJJGGJJGGCJGG=GGGGGJGGJGC=GC=GGGCGGGCGGGGCCGCGGGJCGC=GGC8CGCGCGGGGGGCGCC1GGCGCC=GCCGCGGC8GCGGGCCCG\tNH:i:0\tHI:i:0\tAS:i:155\tnM:i:2\tuT:A:1\n BCR-ABL1-74\t141\t*\t0\t0\t*\t*\t0\t0\tCATTCCGCTGACCATCAATAAGGAAGATGATGAGTCTCCGGGGCTCTATGGGTTTCTGAATGTCATCGTCCACTCAGCCACTGGATTTAGGCAGAGTTCAAAAGCCCTTCAGCGGCCAGTAGCATCTGACTTTGAGCCTCAGGGTCTGAG\tCCCGGGGGGCGCGJGGJJGGJGJJJGJGGJJGGJGJJ1=JCJJGGGJJJJGGGJGCCJGGJGG=J1JG8JGCGGGJG=GC1CGCCGGCG(GGCGGCGGGGGCJC1CCGC==CCGGGGCGGCGGGCCGGCGCGC8CCCCGGG=GGGC=GGG\tNH:i:0\tHI:i:0\tAS:i:155\tnM:i:2\tuT:A:1\n BCR-ABL1-66\t77\t*\t0\t0\t*\t*\t0\t0\tTCCAGCGAGAAGGTTTTCCTTGGAGTTCCAACGAGCGGCTTCACTCAGACCCTGAGGCTCAAAGTCAGATGCTACTGGCCGCTGAAGGGCTTTTGAACTCTGCTTAAATCCAGTGGCTGAGTGGACGATGACATTCAGAAACCCATAGAG\tCCC=GGGGCGGGGJJJJJGJJJJ=JJJGJJ1GJJGJJJJJGJJJJJGGGGCGJJGGGJJJGGCGGGGJGCGG1JCGGG=GCCGCG=GC=G=GCCGGGGG8JGGGGGGGGGGGG=GGCGGC8GGCCGGGC=GGGGGGGGG=CGG=8GGCCG\tNH:i:0\tHI:i:0\tAS:i:159\tnM:i:0\tuT:A:1\n' |
| b |
| diff -r 2d32e6c86c48 -r 77021ad5037d test-data/fusions.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fusions.tsv Sat Oct 09 15:41:49 2021 +0000 |
| b |
| @@ -0,0 +1,2 @@ +#gene1 gene2 strand1(gene/fusion) strand2(gene/fusion) breakpoint1 breakpoint2 site1 site2 type split_reads1 split_reads2 discordant_mates coverage1 coverage2 confidence reading_frame tags retained_protein_domains closest_genomic_breakpoint1 closest_genomic_breakpoint2 gene_id1 gene_id2 transcript_id1 transcript_id2 direction1 direction2 filters fusion_transcript peptide_sequence read_identifiers +BCR ABL1 +/+ +/+ 22:23632600 9:133729451 CDS/splice-site CDS/splice-site translocation 4 7 0 4 12 high in-frame Mitelman Bcr-Abl_oncoprotein_oligomerisation_domain(100%),C2_domain(100%),PH_domain(100%),RhoGEF_domain(100%)|F-actin_binding(100%),Protein_kinase_domain(100%),SH2_domain(100%),SH3_domain(100%),Variant_SH3_domain(100%) . . ENSG00000186716.15 ENSG00000097007.13 ENST00000305877.8 ENST00000372348.2 downstream upstream . AGCTTCTCCCTGACATCCGTGGAGCTGCAGATGCTGACCAACTCGTGTGTGAAACTCCAGACTGTCCACAGCATTCCGCTGACCATCAATAAGGAAG___ATGATGAGTCTCCGGGGCTCTATGGGTTTCTGAATGTCATCGTCCACTCAGCCACTGGATTTAAGCAGAGTTCAA|AAGCCCTTCAGCGGCCAGTAGCATCTGACTTTGAGCCTCAGGGTCTGAGTGAAGCCGCTCGTTGGAACTCCAAGGAAAACCTTCTCGCTGGACCCAGTGAAAATGACCCCAACCTTTTCGTTGCACTGTATGATTTTGTGGCCAGTGGAGATAACACTCTAAGCATAACTAAAG___GTGAAAAGCTCCGGG SFSLTSVELQMLTNSCVKLQTVHSIPLTINKEDDESPGLYGFLNVIVHSATGFKQSS|kALQRPVASDFEPQGLSEAARWNSKENLLAGPSENDPNLFVALYDFVASGDNTLSITKGEKLR BCR-ABL1-10,BCR-ABL1-2,BCR-ABL1-24,BCR-ABL1-28,BCR-ABL1-58,BCR-ABL1-60,BCR-ABL1-76,BCR-ABL1-12,BCR-ABL1-18,BCR-ABL1-4,BCR-ABL1-66 |
| b |
| diff -r 2d32e6c86c48 -r 77021ad5037d test-data/genome.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/genome.fasta Sat Oct 09 15:41:49 2021 +0000 |
| b |
| b'@@ -0,0 +1,4 @@\n+>22\n+TAAAGAGACTTAGCACATTTATTCACTCACAGAGGTGAATGAAGGGCTCAGGGTTTGAACTCGATGACACTGATGGCGATCCGGGCTGCCCGCTGTAAGGCTTCGGCCACTTGAGGCTTTTCGTAAGTCTCCACCTCCATGGCACGGAAAGTGGGCACGTGCGTCTGCAGGGCCTTGCGGCCCTCGGGGGCCTCTGCCAGCATGGTAAGGGCCTTGGTGGCATTCAGGCGCGCTATGGTCATGGGGGAGTGCAGCAGCTCCAGGAGCAGGCCGATGGCTTGTGCCTCCAGGGCCGCATACTTCCCTGCAGGCCACCAACACAAGGCGTTCCAAACAGCCCAAGGGGCCCTCTTCTCACCCCCTCTCACCCTAGCCCTCTCCTGACCCTCCTCCTTGTGCAGTCTCAAGGGGTTTATGCCTGGTTTATGCCCCACCAACATGCCCTCACCCTCAGGGCTCTTGCACCTTCGCTGAGTCCGGCCTGGGCCTGGCCTCTTCATCTCCTGCCTTTCCGGCCTCAACTGGCTCCTCTCCATCCACCCTCGTATCCTGCCCAGGAGTTCAAGACCAGCCTGGGCAACATAATGAGATTCCATCTCTACAAAAATTTAAAAATTATCCAGATGTAGTGACAGGTGCCTACAGTCCCAGCTACTCAGGAGACTGAGCGGGGAGGATCACTAGAGCCTGGGAGTTTGAGGCTGCAGTGATCGTGACATCGTACTCTAGCCTGGGTGACACACTGAGACACTGGCTCTTTAAAAAAAGTAAGCCCAGCTGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCTGGTGGATCACGAGGTCAGGAGATTGTGACCATCCTGGCTAACACAGTGAAACCCCGTCTCTATTAAAAATACAAAAAATTAGCCGGGCATGGTGGCGGGCGCCTGTAGTCCCAGCTACTCAGGAGGCTGAGGCAGGAGAATGCGTGAACCTGGGAGGCGGAGCTTGCAGTGAGCCAAGATGGTGCCACTGCACTCCAGCCTGGGCGACAGAGCGAGACTCCATCTCAAAAAAAAAAAAAAAGTAAACCCAATAGTTCATATATGTTGCCAATATTTCTTGAGCACCTACTCTGCACAAAACACACATGGTTCCTGAGAGATGCCCTCCTCAACCATTCGCTGCCCCTTTCTGCTGTCCTTGCCGGCCCTATGCTCCTGCAGTGCCCAGTGGACTCTCCCCTTTGCTGGTGGAACCTCTCAGCCTGGGCCCTGCCAACTCCCATTGTCCTTGGGATTGATCCCAAGCCCTTCCCAGAGGCGACTTGTCCCCTGTGTTTGCCCCACCCATGCTGGGCTTCTCCTCCACATCCCTCATCACTGCCTCCCAGGGCCTGGCACGTGGCAGGGGCTTCAGGACCCTCAGCTGGAGTGCCAGCTTGGGAATAAGTGGCCTCATCTCCCTGGGTCTCAGCCTCTTGTGTCTCGAGCCCCGTGGCCCTCCAAGCACTCCTACAGAAAGCCTGGACCGAGAAGGACACTGGGCTGAGGCTGCCCCAAGATAAACACGCAGGGGGAGCCCCTGCCACCGTGCAGTCAGCATCCTGACTACACCAGTAAAAGGAGGGGCTGTGGACTCCAAGAAAGCCCCAACCTCTCCCATCTGCATACCTCAAGCAGCATTAGGGTCAGGTGTGCAGGGCCTGGGAGGACCTGTCTTTGGGAGGCTGATTGCAAATCCAAGCCCAGATGGTCCTCCATGGAACTCAAAGGAAGCACAGGGCCCCAGGCTGGTGGGTGTGTAGGGGCCAGAGGGAAAGTCAAATGCTTTCAGGGGTCCTGGGAGTGCCACGCCCCAGTCTGCCAGGTGTGGAAACAGCCCAGGGTTCTTCCATGAGCCCAGGGTTGGGTGACTTAGAGGGGAAGCCTGACTGGCTGGGAGTCCCAAGGTAGGGGGCTCGGGGGAGATAATTCTGAATTTGCCCCCTCCTCCAGTTTAAGAAAAATAATTAGGATGAATAAACACCATAGAGTCAAGGGCTCCAGGGTTTGCTTAGACCTCAGGGTAACAGAATCATGGATGGCAAACTAATCAACCCTTGAGTCACAGCTCACAAGGGGCCTGGGTGGGAGGCGGGAATTCCAGGCCCAGGGAACAGACTGGTGCGAAGGCACAGAGGTCCTAATGTGAGTGACTGGTGAGGGGCCACTGTGCTGGGGAGAAGAGGGAGGGCTGGGCCTTGGACCCAACCTTGAAAGGACATCAGTGATAGGCCAAGGGGAGGTTTTTTTTTTTTTTGCAAAGTGTGGAGTTTGGGGGACGATACCCAGCCCCTGAGTACAGAAAGCTCATCACGGCTGCTAGCCTGCTAGGGTCTCCCTCCCTGCGGCACCCCCCACCGCCTCACCTTCAGTGATCACTGTGGCGAACATCAGGGCACCGGCAGCGTTAGACTTCACATGCTCCACTGGGTCTTTCAGCAGATGGACCAGGATGGGGATGACGTCAAAATGACACACCTGTTTCTTGCCCTCTCGAGATATGCTGGGGCAGAGAGGGAACAGAGAGGGGCTCTGCTTGGAAGGGAGAAGAGGCGCAAGGCCCAGGAGTGCCCCAGGGAGACACAAAAGAAATAATTGTGTGGGGGCTACCCCAGGTAGTCCCAGGACTGGTCCCCATGATCCAGGACTGGTCATGGCAGGGATGCTGGGCTGCAGAGGAGCATTGGTGTGAACGCGGCCCACTGCCAGTGAAGACCACGGGGTGACAGGGCCTCACTCTGAGCCAGCACACAGAAAAGAAATAGGGCATGTTCTCCGTGGCCCCAAAATGGGGAACAGCAGGACCCAGGGGTGTCAACCACAGGGAGACCTGTTTTGACTTTGCCTAAGAGCCAGAGCTGACAGTGATGGGCCAAGCTGCCCCCAACAGCAGCAGCTGCCGGGCACTGGGCAACTGCAGCTAAGGACTCAGACCAGGTAACTTTTAGGCCACTTACTCTGGCACTGAATGAAGTTGTGGAAATGAGGATGATGAACTCCCCAAAAGTTTCCTGAGAGAGGGTCAATTCTGTCCCCTAAAAAGAAAGGGCTCCCTGGGCCAGGAAACACTGTTCACAAGCCCCACAGGAATGCCACAGTGCAAAGACCCCTGTGTCACTTAGTTTAATCAACCTTTCCCAAATGTAGCCACCAAAGAACCCTCATTTTTGTAGAGCTCTTAATGACCTCAAAGACACAGGTGTTCCCTGGGAACACAGATTGGGAAATGAGGTTGGCCAGCCACTAGCTGTGACACTGGGAGCCTTTCAGGGCAGTGGGCCTCAACCCCGAAGCCCATGATCAAAGTTGCAGAGTCCTGGGCCCCACATGCAGGGATTCCCTGATTCGTTCACACAGCAAGACACTGAGACAAGAGCGATGCAGGGATTCCCCGATTTGTTCACAAGAGTGGGGACAAGAGCAGGGTTTCTCCAGCTCAGTGTTCTTTAGGGCCAGATAATTCTCAACTGGGAGCCAAAGCTCCCCCGCTGCAAACCCTGGGTTTAGGGCAGCAAACAGAGGAAAGCCCTGTCCTCAGGAGCTCCCCTCGGGGATGACACACAAAGTAACGGCAGGGATGGTGGTCACAGTGGACATGGGAGGACAGGGGACAGCAGGGAGGTTACAGTTTCAGAGAGAGAGAGCTCTCTCCTGGAAAGCCACTCTCATGGTCCCACAGAAAGGGGACCTCTGAGCAGACCTAAGAATGATGGGGCTGGGACAGGGCCCAGGAATCTGCATTTTCACAAACCTCCCGGTGGCTTGGGTCCGGGGCCCCACTTGCAGAAATACTGGCCTGAGCCTCTAGTGAGACTCTCAGAAGAGAAGCCAGGACTTAGGGAAGGCAAGAGGGTCTCCACTAAAGAGACATAGCCACAGCTAAGGCAGAGACTCTGGGGTTCGGTGACCAGCCTGTCCTCGTGAAAAGGGGCCCAGTGTGAGAACACAC'..b'GCAGGGCCTTGGCTCCCCTCTGCCTTCTCTTGCACACTGGCTCAGTGCTTGCAGCTGCTTGCCCAGGAAATCCAGGGCCTCGGGGATCCCAGGGGCCCAGTGGAATCCTGTGGGGTTAGAAGCAGCCACTTGGGGCTGGGCATGGTGGCTCATGCCTGCAATCCCAGCACTTTGGGAGGCCAAGGCGGGTGGATCACTGGAGGTCAGGAGTTTGAGACCAGCCTGACCAACATGGTGAAACCCTGTCTCTACAAAAAATACAAAAATTAGGCAAGGCGTGGTGGCTCACACCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGCAGATCACCTGAGGTCAGGAGTTTGAGACCAGCCTGGCCAACGTGGTGAAACCCTGTCTCTACTAAAAATACAAAAAAATTAGCGGAGCATGGTGGCAGGCACCTGTAATCCCAGATACTCGGGAGGCTGAGGCAGGAGAATCGCTTGAACCTGAGGCCACAGTAAGCTGAGATCGTACCACTGCACTCCAGCCTGGACAACAGAGCGAGACTCCGTCTCAATAAATAAATAAATGCATCCATCCATCCATACATACATACAAAAATTAGCTGGGCATGGTGGTGTGGGCCTGTGGTTTACCCCAGTGATTGCCCACATCCAGGCCCACAGGCGGCATCTGTAAACGTGTGCTGTCAGTGAATTGAGCCAGCATGTTCAAGCTGGCAAAAATCACAGGGGCCTTTCTCCCACACTGTTTTGTAAATGAGTAAACTAAGACTCAGAGAGGACTCACCTGAGGCCTTCTTTTTTAACAATAATAGTAAAACCATCAACAAAAATGACATTTGTCAAGTGCCACCCAGGAGGATGTTCTAGAGTCTGCCCATGGGCCCGTTGGGATGCTATGGGTCCTCACCCACCTCCCAGCCCTTCTGCTCCCCATCTTTCCCTGGTGGATGGTGGGCCATTGGAATCCTGGGAGGCCTGAGCTGGGGAGAGGCTCAGGGGCTGGGAGGTGCCCTGGGGCCTGCAGGGCTGCTGGCTCACAGTGAGGCTGTTTGTGCCCCACCACAGGGTCGCTGGACACCCATCAAGCCCCAGCCCAGGCCCTGAACGAGACTCAGTGGGCACTAGAACGCCTGAGGCTGCAGCTGGGCTCCCCGGGGTCCTTGCAGAGGAAACTCAGTCTGCTGGAGCAGGAATCCCAGCAGCAGGAGCTGCAGATCCAGGGCTTCGAGAGTGACCTCGCCGAGATCCGCGCCGACAAACAGAACCTGGAGGCCATTCTGCACAGCCTGCCCGAGAACTGTGCCAGCTGGCAGTGAGGGCTGCCCAGATCCCCGGCACACACTCCCCCACCTGCTGTTTACATGACCCAGGGGGTGCACACTACCCCACAGGTGTGCCCATACAGACATTCCCCGGAGCCGGCTGCTGTGAACTCGCCCCCGTGTGGATAGTCACTCCCTGCCGATTCTGTCTGTGGCTTCTTCCCTGCCAGCAGGACTGAGTGTGCGTACCCAGTTCACCTGGACATGAGTGCACACTCTCACCCCTGCACATGCATAAACGGGCACACCCCAGTGTCAATAACATACACACGTGAGGGTGCATGTCTGTGTGTATGACCCACACGTGTTCAAGTCTAATCCATCCAGTCAGCAGCTTACGGTCCACACACATTACAGTCCACAGCTGTTGTGAGAGCCACCTGTGTGCTGGACACCCTCTGGATGTTGGGCAAGTTGTTACATGAGATGCCCTGGGGTGCTACATCCACTCACTCCAGATAGCAGGGAGGTCTCAGCAGATCTGCAGAGATCAAGGGGGTCAGCAACAGCCAAAGCCCCTAGTCCCAGAGCTGGCTGCCCTCTGTTTCACAGCAGCTCCCTGACCTGTGTTGCTGCGTGCACTCCCTACAGCTCGACACAGCCAGGGGACCAACAGGCCAAGAAATGCAAGATCCCGGGAGGGTTCTTAGCAGCAGAATCTGAGGCCCAGAGACCCTGAGGCCGTGGCCAGGCCTGCTAGTCTGGCTAGAGCAAGGCCCATTCCTGGCGGGGGTGTCATTGCCTTCACCGGACGCTTCCCTCTCAGGGTCCTGGGACTGCACCAGATGCCCTGAGGGAATGGCCCACCCTGGCCTGTACCCACTTCAGCCTGTGATCTATCCAAAGAGCCAGGCCCAAAAGCGCCTAGGTCAGGGTGCTCAGGCTACCAGGAGCACGCCTCTGTGCCCCCGGCAACCCAGTTGACCTTTAATTGACGCTTTCCAGACCAGCCCTGCGGCACCACTTGCCATGCGGGAGGCCACCAGGGTGTGCAAGCCTGGCTGCCATTCCAGTCTGTCCTGTCTGGGAATCGCCCTGTGGCCAGGCCCGCATGCTGGCCTCTGCCCAGGACTCCTCAGCATTTCCTCTTGGCATCCCTCCCCTCTCCCAGACCCTCTTCCAGCAGATGGCAAGGCCTCGGCATTGGGAAGTCAGGCACCTCTGCGGGCCCAGCCCCCTCCCGTGGCTCCCCTGACAGGGGCAGGGGTAGGGCAGCAGCACAGACCAATTCCGTTGAACGTGGAAATAAAGGACCCTTTCACTGGGCAGGGTGGTGTGCCTCACCCTCCCCGGCTGGTGGGCAGCCAGGGCCCTGGCTGTGGGTGTGCATATGACACACCTAGTAGGTGGCCAGCATGTGGACCGGACGTTGGTAGGAAGGTGGCAAAAGCCGAGCTCGTGGCTGGGCCAGTACCTCCCATTAGAGGGCTTTGCTGGGGTTGTGTGATCACAGGTACCTACCCTGTCCTCTCAGGCACTTACCACGTAAAGCCTAGGAGCTGGTGAGTTGGAGGGGTGGGGTGCGGAGAGGCCCTCAGCTGACCTCTGGTTCAGGCTCGAGACGAACTCACAGCCAAGTGTCCGAGGATGGTGAGGAGCAGGGAGGGGCGCCATCCAGGAGGGGGATGGTGTGGGTGGGGCCTTGAAGGGTGGGGAGGCAGAGAAGGAAGCATTCCAGGCAAGAGGGTGGACAACAGTCCGGGGCCCGCAGGGTTGGGGCTCGGCCAGCTTGCATCACTCCAGGACCCCAGGTTGAATGGGGTGGGATGTTGGAGCTGCTCAGTCAGGGCTCTTGGCCGCAGGCCTCAAACCCCTCCTGAGGTGGTTTCAGCAGAAAAGGGGTGTTGGGAGGGTCGCTTGGAACCCTGGAGTAAAAACGGCTGCCACGTGTTGGAGATAGCCTAGGGAGGGGAGCCTGAGGCTTCCGGGATAGGTTGGCTTCCCTCTTCCCCCCTCCCGCCTCTCTTCTTGGTCTGTGTCTCTGCTCTCCTCTCCTGTATCTGCTTCGTTCTTTTCTCTTTATTTATTGATTTTTTTTGAGATGGAGTCTCGCTCTGTTGCCCAGGCTGGAGTGCAGTGGCATGATCTCTGCCCACTGCATCCTCCACCTCCCAGGTTTAAGCAATTCTCCTGCCTCAGCCTCCCGAGTAGCTAGGACTACAGGTGCTTGCCACCATGCCCAGCTAATTTTGGTATTTTTAGTAGAGACAGGGTTTCACCACGTTGGTCAGGCTGGTCTCAAACTCCTGACCTCAGATGATATACCTGCATTGGCCTCTTAAAGTTCTGGGATTTCAGGCATGAGCCACTGCAACCGGCCCATTCTTTTCTCTTTGCAGAGTGGCTTTCTTTGTTTTTCTTGTGCCTGATAGGAGAGGACACCCACCCCTACCGCCATCCCCCATAATGGCCCCAGGTGTACATGTCATCAGGTCCAGTGCTTGCAAGAGACAAGCTGGTGACTCTGTCCTGATTCCAGCTTCTCAGCTTAGGTGAAGTCCCACCAACCCCCGTTCAGGATAATGAGGATCTCTGGATCTAAGGCCAATAATGGATGACCGGTGCCACCCCCCAACCTAATGGGAGATGGTGTTCAGAGAAGAGGTGTGCTCCTCCACAGAAAACTGTAAAATCAAGGCTACGGTGGGGGATTGACATGATTAAACTGAGCTAGGAGTGA\n' |
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| diff -r 2d32e6c86c48 -r 77021ad5037d test-data/genome.gtf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/genome.gtf Sat Oct 09 15:41:49 2021 +0000 |
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| b'@@ -0,0 +1,860 @@\n+#!genome-build GRCh38.p12\n+#!genome-version GRCh38\n+#!genome-date 2013-12\n+#!genome-build-accession NCBI:GCA_000001405.27\n+#!genebuild-last-updated 2018-01\n+9\tensembl_havana\tgene\t1\t59388\t.\t+\t.\tgene_id "ENSG00000107164"; gene_version "15"; gene_name "FUBP3"; gene_source "ensembl_havana"; gene_biotype "protein_coding";\n+9\thavana\ttranscript\t1\t3122\t.\t+\t.\tgene_id "ENSG00000107164"; gene_version "15"; transcript_id "ENST00000467100"; transcript_version "1"; gene_name "FUBP3"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "FUBP3-203"; transcript_source "havana"; transcript_biotype "processed_transcript"; transcript_support_level "2";\n+9\thavana\texon\t1\t800\t.\t+\t.\tgene_id "ENSG00000107164"; gene_version "15"; transcript_id "ENST00000467100"; transcript_version "1"; exon_number "1"; gene_name "FUBP3"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "FUBP3-203"; transcript_source "havana"; transcript_biotype "processed_transcript"; exon_id "ENSE00001817525"; exon_version "1"; transcript_support_level "2";\n+9\thavana\texon\t1695\t3122\t.\t+\t.\tgene_id "ENSG00000107164"; gene_version "15"; transcript_id "ENST00000467100"; transcript_version "1"; exon_number "2"; gene_name "FUBP3"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "FUBP3-203"; transcript_source "havana"; transcript_biotype "processed_transcript"; exon_id "ENSE00001916817"; exon_version "1"; transcript_support_level "2";\n+9\tensembl_havana\ttranscript\t642\t59388\t.\t+\t.\tgene_id "ENSG00000107164"; gene_version "15"; transcript_id "ENST00000319725"; transcript_version "9"; gene_name "FUBP3"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "FUBP3-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS43893"; tag "basic"; transcript_support_level "1";\n+9\tensembl_havana\texon\t642\t800\t.\t+\t.\tgene_id "ENSG00000107164"; gene_version "15"; transcript_id "ENST00000319725"; transcript_version "9"; exon_number "1"; gene_name "FUBP3"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "FUBP3-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS43893"; exon_id "ENSE00001809698"; exon_version "1"; tag "basic"; transcript_support_level "1";\n+9\tensembl_havana\tCDS\t717\t800\t.\t+\t0\tgene_id "ENSG00000107164"; gene_version "15"; transcript_id "ENST00000319725"; transcript_version "9"; exon_number "1"; gene_name "FUBP3"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "FUBP3-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS43893"; protein_id "ENSP00000318177"; protein_version "9"; tag "basic"; transcript_support_level "1";\n+9\tensembl_havana\tstart_codon\t717\t719\t.\t+\t0\tgene_id "ENSG00000107164"; gene_version "15"; transcript_id "ENST00000319725"; transcript_version "9"; exon_number "1"; gene_name "FUBP3"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "FUBP3-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS43893"; tag "basic"; transcript_support_level "1";\n+9\tensembl_havana\texon\t16519\t16624\t.\t+\t.\tgene_id "ENSG00000107164"; gene_version "15"; transcript_id "ENST00000319725"; transcript_version "9"; exon_number "2"; gene_name "FUBP3"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "FUBP3-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS43893"; exon_id "ENSE00003666938"; exon_version "1"; tag "basic"; transcript_support_level "1";\n+9\tensembl_havana\tCDS\t16519\t16624\t.\t+\t0\tgene_id "ENSG00000107164"; gene_version "15"; transcript_id "ENST00000319725"; transcript_version "9"; exon_number "2"; gene_name "FUBP3"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "FUBP3-201"; transcript_source "e'..b'NA";\n+22\tensembl\ttranscript\t202368\t202657\t.\t-\t.\tgene_id "ENSG00000240160"; gene_version "3"; transcript_id "ENST00000467969"; transcript_version "3"; gene_name "RN7SL263P"; gene_source "ensembl"; gene_biotype "misc_RNA"; transcript_name "RN7SL263P-201"; transcript_source "ensembl"; transcript_biotype "misc_RNA"; tag "basic"; transcript_support_level "NA";\n+22\tensembl\texon\t202368\t202657\t.\t-\t.\tgene_id "ENSG00000240160"; gene_version "3"; transcript_id "ENST00000467969"; transcript_version "3"; exon_number "1"; gene_name "RN7SL263P"; gene_source "ensembl"; gene_biotype "misc_RNA"; transcript_name "RN7SL263P-201"; transcript_source "ensembl"; transcript_biotype "misc_RNA"; exon_id "ENSE00001875334"; exon_version "3"; tag "basic"; transcript_support_level "NA";\n+22\thavana\tgene\t203353\t205591\t.\t+\t.\tgene_id "ENSG00000230701"; gene_version "2"; gene_name "FBXW4P1"; gene_source "havana"; gene_biotype "processed_pseudogene";\n+22\thavana\ttranscript\t203353\t205591\t.\t+\t.\tgene_id "ENSG00000230701"; gene_version "2"; transcript_id "ENST00000426721"; transcript_version "2"; gene_name "FBXW4P1"; gene_source "havana"; gene_biotype "processed_pseudogene"; transcript_name "FBXW4P1-201"; transcript_source "havana"; transcript_biotype "processed_pseudogene"; tag "basic"; transcript_support_level "NA";\n+22\thavana\texon\t203353\t205591\t.\t+\t.\tgene_id "ENSG00000230701"; gene_version "2"; transcript_id "ENST00000426721"; transcript_version "2"; exon_number "1"; gene_name "FBXW4P1"; gene_source "havana"; gene_biotype "processed_pseudogene"; transcript_name "FBXW4P1-201"; transcript_source "havana"; transcript_biotype "processed_pseudogene"; exon_id "ENSE00001782951"; exon_version "2"; tag "basic"; transcript_support_level "NA";\n+22\thavana\tgene\t263129\t263513\t.\t-\t.\tgene_id "ENSG00000214526"; gene_version "3"; gene_name "AP000343.1"; gene_source "havana"; gene_biotype "processed_pseudogene";\n+22\thavana\ttranscript\t263129\t263513\t.\t-\t.\tgene_id "ENSG00000214526"; gene_version "3"; transcript_id "ENST00000440602"; transcript_version "1"; gene_name "AP000343.1"; gene_source "havana"; gene_biotype "processed_pseudogene"; transcript_name "AP000343.1-201"; transcript_source "havana"; transcript_biotype "processed_pseudogene"; tag "basic"; transcript_support_level "NA";\n+22\thavana\texon\t263129\t263513\t.\t-\t.\tgene_id "ENSG00000214526"; gene_version "3"; transcript_id "ENST00000440602"; transcript_version "1"; exon_number "1"; gene_name "AP000343.1"; gene_source "havana"; gene_biotype "processed_pseudogene"; transcript_name "AP000343.1-201"; transcript_source "havana"; transcript_biotype "processed_pseudogene"; exon_id "ENSE00001526946"; exon_version "2"; tag "basic"; transcript_support_level "NA";\n+22\thavana\tgene\t267202\t269079\t.\t+\t.\tgene_id "ENSG00000236611"; gene_version "1"; gene_name "LINC02556"; gene_source "havana"; gene_biotype "lincRNA";\n+22\thavana\ttranscript\t267202\t269079\t.\t+\t.\tgene_id "ENSG00000236611"; gene_version "1"; transcript_id "ENST00000450776"; transcript_version "1"; gene_name "LINC02556"; gene_source "havana"; gene_biotype "lincRNA"; transcript_name "LINC02556-201"; transcript_source "havana"; transcript_biotype "lincRNA"; tag "basic"; transcript_support_level "3";\n+22\thavana\texon\t267202\t267377\t.\t+\t.\tgene_id "ENSG00000236611"; gene_version "1"; transcript_id "ENST00000450776"; transcript_version "1"; exon_number "1"; gene_name "LINC02556"; gene_source "havana"; gene_biotype "lincRNA"; transcript_name "LINC02556-201"; transcript_source "havana"; transcript_biotype "lincRNA"; exon_id "ENSE00001785308"; exon_version "1"; tag "basic"; transcript_support_level "3";\n+22\thavana\texon\t268910\t269079\t.\t+\t.\tgene_id "ENSG00000236611"; gene_version "1"; transcript_id "ENST00000450776"; transcript_version "1"; exon_number "2"; gene_name "LINC02556"; gene_source "havana"; gene_biotype "lincRNA"; transcript_name "LINC02556-201"; transcript_source "havana"; transcript_biotype "lincRNA"; exon_id "ENSE00001710203"; exon_version "1"; tag "basic"; transcript_support_level "3";\n' |
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