| Previous changeset 4:77021ad5037d (2021-10-09) Next changeset 6:7253b367c082 (2021-10-11) |
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Commit message:
"planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit bdefea23247f7d999b96e232ce810e2887338680" |
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modified:
arriba.xml arriba_download_reference.xml arriba_get_filters.xml |
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added:
test-data/cytobands.tsv test-data/protein_domains.gff3 |
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| diff -r 77021ad5037d -r 005b200c8841 arriba.xml --- a/arriba.xml Sat Oct 09 15:41:49 2021 +0000 +++ b/arriba.xml Sun Oct 10 13:00:45 2021 +0000 |
| [ |
| @@ -71,7 +71,9 @@ -t '$tags' #end if -o fusions.tsv +#if $output_fusions_discarded -O fusions.discarded.tsv +#end if #if str($input_params.input_source) == "use_fastq" && samtools sort -@ \${GALAXY_SLOTS:-1} -m 4G -T tmp -O bam Aligned.out.bam > Aligned.sortedByCoord.out.bam && samtools index Aligned.sortedByCoord.out.bam @@ -88,7 +90,7 @@ #if $visualization.cytobands --cytobands='$visualization.cytobands' #end if - #if '$protein_domains' + #if $protein_domains --proteinDomains='$protein_domains' #end if #end if @@ -130,13 +132,14 @@ </conditional> <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="blacklist" argument="-b" type="data" format="tabular,tabular.gz" 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"> + <param name="known_fusions" argument="-k" type="data" format="tabular,tabular.gz" 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." help="This can be the known fusions if that input has a third column with a name"/> + <param name="output_fusions_discarded" type="boolean" truevalue="yes" falsevalue="no" checked="true" label="Output fusions.discarded.tsv"/> <conditional name="visualization"> <param name="do_viz" type="select" label="Generate visualization"> <option value="yes">Yes</option> @@ -147,11 +150,12 @@ </when> <when value="no"/> </conditional> - </inputs> <outputs> <data name="fusions" format="tabular" label="${tool.name} on ${on_string}: fusions.tsv" from_work_dir="fusions.tsv"/> - <data name="discarded" format="tabular" label="${tool.name} on ${on_string}: fusions.discarded.tsv" from_work_dir="fusions.discarded.tsv"/> + <data name="discarded" format="tabular" label="${tool.name} on ${on_string}: fusions.discarded.tsv" from_work_dir="fusions.discarded.tsv"> + <filter> output_fusions_discarded == "yes"</filter> + </data> <data name="aligned_bam" format="bam" label="${tool.name} on ${on_string}: Aligned.bam" from_work_dir="Aligned.sortedByCoord.out.bam"> <filter>input_params['input_source'] == "use_fastq"</filter> </data> @@ -168,8 +172,10 @@ </conditional> <param name="genome_assembly" ftype="fasta" value="genome.fasta"/> <param name="gtf" ftype="gtf" value="genome.gtf"/> + <param name="protein_domains" ftype="gff3" value="protein_domains.gff3"/> <conditional name="visualization"> <param name="do_viz" value="no"/> + <param name="cytobands" ftype="tabular" value="cytobands.tsv"/> </conditional> <output name="fusions"> <assert_contents> @@ -177,6 +183,24 @@ </assert_contents> </output> </test> + <!-- Test 2 - From exisitng BAM with protein_domains and visualization --> + <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="yes"/> + </conditional> + <output name="fusions"> + <assert_contents> + <has_text_matching expression="BCR\tABL1"/> + </assert_contents> + </output> + </test> + </tests> <help><![CDATA[ ** Arriba ** @@ -379,7 +403,10 @@ The file fusions.discarded.tsv (as specified by the parameter -O) contains all events that Arriba classified as an artifact or that are also observed in healthy tissue. It has the same format as the file fusions.tsv. +** VISUALIZATION_ ** + - fusions.pdf + A PDF file with one page for each predicted fusion. Each page depicts the fusion partners, their orientation, the retained exons in the fusion transcript, statistics about the number of supporting reads, and if the column fusion_transcript has a value an excerpt of the sequence around the breakpoint. Code repository: https://github.com/suhrig/arriba @@ -391,6 +418,7 @@ .. _Arriba: https://arriba.readthedocs.io/en/latest/ .. _INPUTS: https://arriba.readthedocs.io/en/latest/input-files/ .. _OUTPUTS: https://arriba.readthedocs.io/en/latest/output-files/ +.. _VISUALIZATION: https://arriba.readthedocs.io/en/latest/visualization/ ]]></help> <expand macro="citations" /> |
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| diff -r 77021ad5037d -r 005b200c8841 arriba_download_reference.xml --- a/arriba_download_reference.xml Sat Oct 09 15:41:49 2021 +0000 +++ b/arriba_download_reference.xml Sun Oct 10 13:00:45 2021 +0000 |
| [ |
| @@ -9,19 +9,19 @@ echo $arriba_reference_name > '$star_index' && BASE_DIR=\$(dirname \$(dirname `which arriba`)) && REF_SCRIPT=`find \$BASE_DIR -name 'download_references.sh'` && + #if $is_test != 'yes' \$REF_SCRIPT '$arriba_reference_name' && cp *.fa* '$genome_fasta' && cp *.gtf* '$genome_gtf' && mv STAR_index_* '$star_index.extra_files_path' + #else + [[ -x \$REF_SCRIPT ]] + #end if ]]></command> <inputs> + <param name="is_test" type="hidden" value="no"/> <param name="arriba_reference_name" type="select" label="Select reference"> - <option value="GRCh37+ENSEMBL87">GRCh37+ENSEMBL87</option> - <option value="GRCh37+GENCODE19">GRCh37+GENCODE19</option> - <option value="GRCh37+RefSeq">GRCh37+RefSeq</option> - <option value="GRCh37viral+ENSEMBL87">GRCh37viral+ENSEMBL87</option> - <option value="GRCh37viral+GENCODE19">GRCh37viral+GENCODE19</option> - <option value="GRCh37viral+RefSeq">GRCh37viral+RefSeq</option> + <option value="GRCh38+ENSEMBL93">GRCh38+ENSEMBL93</option> <option value="GRCh38+GENCODE28">GRCh38+GENCODE28</option> <option value="GRCh38+RefSeq">GRCh38+RefSeq</option> @@ -32,18 +32,24 @@ <option value="GRCm38+RefSeq">GRCm38+RefSeq</option> <option value="GRCm38viral+GENCODEM25">GRCm38viral+GENCODEM25</option> <option value="GRCm38viral+RefSeq">GRCm38viral+RefSeq</option> + <option value="hg38+ENSEMBL93">hg38+ENSEMBL93</option> + <option value="hg38+GENCODE28">hg38+GENCODE28</option> + <option value="hg38+RefSeq">hg38+RefSeq</option> + <option value="hg38viral+ENSEMBL93">hg38viral+ENSEMBL93</option> + <option value="hg38viral+GENCODE28">hg38viral+GENCODE28</option> + <option value="hg38viral+RefSeq">hg38viral+RefSeq</option> + <option value="GRCh37+ENSEMBL87">GRCh37+ENSEMBL87</option> + <option value="GRCh37+GENCODE19">GRCh37+GENCODE19</option> + <option value="GRCh37+RefSeq">GRCh37+RefSeq</option> + <option value="GRCh37viral+ENSEMBL87">GRCh37viral+ENSEMBL87</option> + <option value="GRCh37viral+GENCODE19">GRCh37viral+GENCODE19</option> + <option value="GRCh37viral+RefSeq">GRCh37viral+RefSeq</option> <option value="hg19+ENSEMBL87">hg19+ENSEMBL87</option> <option value="hg19+GENCODE19">hg19+GENCODE19</option> <option value="hg19+RefSeq">hg19+RefSeq</option> <option value="hg19viral+ENSEMBL87">hg19viral+ENSEMBL87</option> <option value="hg19viral+GENCODE19">hg19viral+GENCODE19</option> <option value="hg19viral+RefSeq">hg19viral+RefSeq</option> - <option value="hg38+ENSEMBL93">hg38+ENSEMBL93</option> - <option value="hg38+GENCODE28">hg38+GENCODE28</option> - <option value="hg38+RefSeq">hg38+RefSeq</option> - <option value="hg38viral+ENSEMBL93">hg38viral+ENSEMBL93</option> - <option value="hg38viral+GENCODE28">hg38viral+GENCODE28</option> - <option value="hg38viral+RefSeq">hg38viral+RefSeq</option> <option value="hs37d5+ENSEMBL87">hs37d5+ENSEMBL87</option> <option value="hs37d5+GENCODE19">hs37d5+GENCODE19</option> <option value="hs37d5+RefSeq">hs37d5+RefSeq</option> @@ -61,12 +67,42 @@ <data name="genome_gtf" format="gtf" label="${tool.name} ${arriba_reference_name} GTF"/> <data name="star_index" format="txt" label="${tool.name} ${arriba_reference_name} STAR index"/> </outputs> + <tests> + <!-- Downloading a genome and annotation plus build a STAR index requires too many resources for testing. + Just test that we can locate the script. --> + <test> + <param name="is_test" value="yes"/> + <param name="arriba_reference_name" value="GRCh38+ENSEMBL93"/> + <output name="star_index"> + <assert_contents> + <has_text text="GRCh38+ENSEMBL93"/> + </assert_contents> + </output> + + </test> + </tests> <help><![CDATA[ -** Arriba ** +** Arriba Reference ** Arriba_ is a fast tool to search for aberrant transcripts such as gene fusions. It is based on chimeric alignments found by the STAR RNA-Seq aligner. +**Arriba Reference** downloads a genome sequence fasta and its related annoation GTF, and then build a STAR index for the RNA STAR aligner. + +These datasets will be added to your Galaxy history: + + - genome assembly fasta + - genome annotation GTF + - STAR index + +See Arriba manual pages: + + - https://arriba.readthedocs.io/en/latest/workflow/ + - https://arriba.readthedocs.io/en/latest/input-files/ + + +**NOTE:** This is a resource intensive process, so the results should be copies to new histories as needed rather than running this in each workflow. + .. _Arriba: https://arriba.readthedocs.io/en/latest/ ]]></help> |
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| diff -r 77021ad5037d -r 005b200c8841 arriba_get_filters.xml --- a/arriba_get_filters.xml Sat Oct 09 15:41:49 2021 +0000 +++ b/arriba_get_filters.xml Sun Oct 10 13:00:45 2021 +0000 |
| [ |
| @@ -34,8 +34,8 @@ </param> </inputs> <outputs> - <data name="blacklist" format="tabular" label="${tool.name} ${arriba_reference_name} blacklist.tsv"/> - <data name="known_fusions" format="tabular" label="${tool.name} ${arriba_reference_name} known_fusions.tsv"/> + <data name="blacklist" format="tabular.gz" label="${tool.name} ${arriba_reference_name} blacklist.tsv.gz"/> + <data name="known_fusions" format="tabular.gz" label="${tool.name} ${arriba_reference_name} known_fusions.tsv.gz"/> <data name="protein_domains" format="gff3" label="${tool.name} ${arriba_reference_name} protein_domains.gff3"/> <data name="cytobands" format="tabular" label="${tool.name} ${arriba_reference_name} cytobands.tsv"/> </outputs> @@ -50,12 +50,21 @@ </test> </tests> <help><![CDATA[ -** Arriba ** +**Arriba Get Filters** Arriba_ is a fast tool to search for aberrant transcripts such as gene fusions. It is based on chimeric alignments found by the STAR RNA-Seq aligner. +The **Arriba Get Filters** tool adds the following Arriba distribution input_files_ to your galaxy history: + + - blacklist + - known_fusions + - protein_domains + - cytobands + + .. _Arriba: https://arriba.readthedocs.io/en/latest/ +.. _input_files: https://arriba.readthedocs.io/en/latest/input-files/ ]]></help> <expand macro="citations" /> |
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| diff -r 77021ad5037d -r 005b200c8841 test-data/cytobands.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cytobands.tsv Sun Oct 10 13:00:45 2021 +0000 |
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| @@ -0,0 +1,5 @@ +contig start end name giemsa +22 1 40586 q11.22 gpos25 +22 40586 269079 q11.23 gneg +9 1 21036 q34.11 gneg +9 21036 515509 q34.12 gpos25 |
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| diff -r 77021ad5037d -r 005b200c8841 test-data/protein_domains.gff3 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/protein_domains.gff3 Sun Oct 10 13:00:45 2021 +0000 |
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| b'@@ -0,0 +1,83 @@\n+9\tpfam\tprotein_domain\t33502\t33541\t0\t+\t.\tName=KH domain;color=#808080;gene_id=ENSG00000107164;gene_name=FUBP3;protein_domain_id=PF00013\n+9\tpfam\tprotein_domain\t33992\t34063\t0\t+\t.\tName=KH domain;color=#808080;gene_id=ENSG00000107164;gene_name=FUBP3;protein_domain_id=PF00013\n+9\tpfam\tprotein_domain\t35324\t35381\t0\t+\t.\tName=KH domain;color=#808080;gene_id=ENSG00000107164;gene_name=FUBP3;protein_domain_id=PF00013\n+9\tpfam\tprotein_domain\t37391\t37409\t0\t+\t.\tName=KH domain;color=#808080;gene_id=ENSG00000107164;gene_name=FUBP3;protein_domain_id=PF00013\n+9\tpfam\tprotein_domain\t37479\t37553\t0\t+\t.\tName=KH domain;color=#808080;gene_id=ENSG00000107164;gene_name=FUBP3;protein_domain_id=PF00013\n+9\tpfam\tprotein_domain\t38833\t38931\t0\t+\t.\tName=KH domain;color=#808080;gene_id=ENSG00000107164;gene_name=FUBP3;protein_domain_id=PF00013\n+9\tpfam\tprotein_domain\t41390\t41413\t0\t+\t.\tName=KH domain;color=#808080;gene_id=ENSG00000107164;gene_name=FUBP3;protein_domain_id=PF00013\n+9\tpfam\tprotein_domain\t41489\t41494\t0\t+\t.\tName=KH domain;color=#808080;gene_id=ENSG00000107164;gene_name=FUBP3;protein_domain_id=PF00013\n+9\tpfam\tprotein_domain\t43744\t43846\t0\t+\t.\tName=KH domain;color=#808080;gene_id=ENSG00000107164;gene_name=FUBP3;protein_domain_id=PF00013\n+9\tpfam\tprotein_domain\t44647\t44729\t0\t+\t.\tName=KH domain;color=#808080;gene_id=ENSG00000107164;gene_name=FUBP3;protein_domain_id=PF00013\n+9\tpfam\tprotein_domain\t47496\t47541\t0\t+\t.\tName=KH domain;color=#808080;gene_id=ENSG00000107164;gene_name=FUBP3;protein_domain_id=PF00013\n+9\tpfam\tprotein_domain\t51664\t51812\t0\t+\t.\tName=KH domain;color=#808080;gene_id=ENSG00000107164;gene_name=FUBP3;protein_domain_id=PF00013\n+9\tpfam\tprotein_domain\t102331\t102396\t0\t+\t.\tName=Zinc finger%2C C2H2 type;color=#80FF00;gene_id=ENSG00000130711;gene_name=PRDM12;protein_domain_id=PF00096\n+9\tpfam\tprotein_domain\t102412\t102480\t0\t+\t.\tName=C2H2-type zinc finger;color=#80FF80;gene_id=ENSG00000130711;gene_name=PRDM12;protein_domain_id=PF13894\n+9\tpfam\tprotein_domain\t114903\t114949\t0\t+\t.\tName=Exosome complex exonuclease RRP4 N-terminal region;color=#FF0000;gene_id=ENSG00000130713;gene_name=EXOSC2;protein_domain_id=PF14382\n+9\tpfam\tprotein_domain\t116528\t116596\t0\t+\t.\tName=Exosome complex exonuclease RRP4 N-terminal region;color=#FF0000;gene_id=ENSG00000130713;gene_name=EXOSC2;protein_domain_id=PF14382\n+9\tpfam\tprotein_domain\t121951\t121971\t0\t+\t.\tName=KH domain;color=#000080;gene_id=ENSG00000130713;gene_name=EXOSC2;protein_domain_id=PF15985\n+9\tpfam\tprotein_domain\t123179\t123300\t0\t+\t.\tName=KH domain;color=#000080;gene_id=ENSG00000130713;gene_name=EXOSC2;protein_domain_id=PF15985\n+9\tpfam\tprotein_domain\t275219\t275273\t0\t+\t.\tName=SH3 domain;color=#FF0000;gene_id=ENSG00000097007;gene_name=ABL1;protein_domain_id=PF00018\n+9\tpfam\tprotein_domain\t275837\t275922\t0\t+\t.\tName=SH3 domain;color=#FF0000;gene_id=ENSG00000097007;gene_name=ABL1;protein_domain_id=PF00018\n+9\tpfam\tprotein_domain\t275962\t276132\t0\t+\t.\tName=SH2 domain;color=#80FFFF;gene_id=ENSG00000097007;gene_name=ABL1;protein_domain_id=PF00017\n+9\tpfam\tprotein_domain\t283799\t283855\t0\t+\t.\tName=SH2 domain;color=#80FFFF;gene_id=ENSG00000097007;gene_name=ABL1;protein_domain_id=PF00017\n+9\tpfam\tprotein_domain\t283973\t284071\t0\t+\t.\tName=Protein kinase domain;color=#80FF00;gene_id=ENSG00000097007;gene_name=ABL1;protein_domain_id=PF00069\n+9\tpfam\tprotein_domain\t293165\t293249\t0\t+\t.\tName=Protein kinase domain;color=#80FF00;gene_id=ENSG00000097007;gene_name=ABL1;protein_domain_id=PF00069\n+9\tpfam\tprotein_domain\t293896\t294073\t0\t+\t.\tName=Protein kinase domain;color=#80FF00;gene_id=ENSG00000097007;gene_name=ABL1;protein_domain_id=PF00069\n+9\tpfam\tprotein_domain\t295904\t296088\t0\t+\t.\tName=Protein kinase domain;color=#80FF00;gene_id=ENSG00000097007;gene_name=ABL1;protein_domain_id=PF00069\n+9\tpfam\tprotein_domain\t299451\t299603\t0\t+\t.\tName=Protein kinase domain;color=#80FF00;gene_id=ENSG00000097007;gene_name=ABL1;protein_domain_id=PF00069\n+9\tpfam\tprotein_domain\t301104\t301156\t0\t+\t.\tName=Protein kinase domain;color=#80FF00;gene_id=ENSG00000097007;ge'..b'd=PF00053\n+9\tpfam\tprotein_domain\t489945\t490067\t0\t+\t.\tName=Laminin EGF domain;color=#FFFFFF;gene_id=ENSG00000050555;gene_name=LAMC3;protein_domain_id=PF00053\n+9\tpfam\tprotein_domain\t490710\t490856\t0\t+\t.\tName=Laminin EGF domain;color=#FFFFFF;gene_id=ENSG00000050555;gene_name=LAMC3;protein_domain_id=PF00053\n+22\tpfam\tprotein_domain\t2420\t2524\t0\t-\t.\tName=Armadillo/beta-catenin-like repeat;color=#000080;gene_id=ENSG00000100218;gene_name=RSPH14;protein_domain_id=PF00514\n+22\tpfam\tprotein_domain\t36321\t37004\t0\t+\t.\tName=G-protein alpha subunit;color=#80FFFF;gene_id=ENSG00000128266;gene_name=GNAZ;protein_domain_id=PF00503\n+22\tpfam\tprotein_domain\t63673\t63981\t0\t+\t.\tName=G-protein alpha subunit;color=#80FFFF;gene_id=ENSG00000128266;gene_name=GNAZ;protein_domain_id=PF00503\n+22\tpfam\tprotein_domain\t90736\t90740\t0\t+\t.\tName=Ras family;color=#80FFFF;gene_id=ENSG00000100228;gene_name=RAB36;protein_domain_id=PF00071\n+22\tpfam\tprotein_domain\t93060\t93112\t0\t+\t.\tName=Ras family;color=#80FFFF;gene_id=ENSG00000100228;gene_name=RAB36;protein_domain_id=PF00071\n+22\tpfam\tprotein_domain\t93619\t93720\t0\t+\t.\tName=Ras family;color=#80FFFF;gene_id=ENSG00000100228;gene_name=RAB36;protein_domain_id=PF00071\n+22\tpfam\tprotein_domain\t96554\t96622\t0\t+\t.\tName=Ras family;color=#80FFFF;gene_id=ENSG00000100228;gene_name=RAB36;protein_domain_id=PF00071\n+22\tpfam\tprotein_domain\t98578\t98629\t0\t+\t.\tName=Ras family;color=#80FFFF;gene_id=ENSG00000100228;gene_name=RAB36;protein_domain_id=PF00071\n+22\tpfam\tprotein_domain\t99484\t99565\t0\t+\t.\tName=Ras family;color=#80FFFF;gene_id=ENSG00000100228;gene_name=RAB36;protein_domain_id=PF00071\n+22\tpfam\tprotein_domain\t99749\t99839\t0\t+\t.\tName=Ras family;color=#80FFFF;gene_id=ENSG00000100228;gene_name=RAB36;protein_domain_id=PF00071\n+22\tpfam\tprotein_domain\t101465\t101502\t0\t+\t.\tName=Ras family;color=#80FFFF;gene_id=ENSG00000100228;gene_name=RAB36;protein_domain_id=PF00071\n+22\tpfam\tprotein_domain\t121553\t121771\t0\t+\t.\tName=Bcr-Abl oncoprotein oligomerisation domain;color=#FF0000;gene_id=ENSG00000186716;gene_name=BCR;protein_domain_id=PF09036\n+22\tpfam\tprotein_domain\t201581\t201640\t0\t+\t.\tName=RhoGEF domain;color=#000000;gene_id=ENSG00000186716;gene_name=BCR;protein_domain_id=PF00621\n+22\tpfam\tprotein_domain\t201941\t202126\t0\t+\t.\tName=RhoGEF domain;color=#000000;gene_id=ENSG00000186716;gene_name=BCR;protein_domain_id=PF00621\n+22\tpfam\tprotein_domain\t208994\t209101\t0\t+\t.\tName=RhoGEF domain;color=#000000;gene_id=ENSG00000186716;gene_name=BCR;protein_domain_id=PF00621\n+22\tpfam\tprotein_domain\t212118\t212178\t0\t+\t.\tName=RhoGEF domain;color=#000000;gene_id=ENSG00000186716;gene_name=BCR;protein_domain_id=PF00621\n+22\tpfam\tprotein_domain\t213667\t213719\t0\t+\t.\tName=RhoGEF domain;color=#000000;gene_id=ENSG00000186716;gene_name=BCR;protein_domain_id=PF00621\n+22\tpfam\tprotein_domain\t214220\t214312\t0\t+\t.\tName=RhoGEF domain;color=#000000;gene_id=ENSG00000186716;gene_name=BCR;protein_domain_id=PF00621\n+22\tpfam\tprotein_domain\t230954\t230999\t0\t+\t.\tName=C2 domain;color=#00FF00;gene_id=ENSG00000186716;gene_name=BCR;protein_domain_id=PF00168\n+22\tpfam\tprotein_domain\t233127\t233224\t0\t+\t.\tName=C2 domain;color=#00FF00;gene_id=ENSG00000186716;gene_name=BCR;protein_domain_id=PF00168\n+22\tpfam\tprotein_domain\t235610\t235741\t0\t+\t.\tName=C2 domain;color=#00FF00;gene_id=ENSG00000186716;gene_name=BCR;protein_domain_id=PF00168\n+22\tpfam\tprotein_domain\t250010\t250018\t0\t+\t.\tName=C2 domain;color=#00FF00;gene_id=ENSG00000186716;gene_name=BCR;protein_domain_id=PF00168\n+22\tpfam\tprotein_domain\t252302\t252422\t0\t+\t.\tName=RhoGAP domain;color=#FFFFFF;gene_id=ENSG00000186716;gene_name=BCR;protein_domain_id=PF00620\n+22\tpfam\tprotein_domain\t253473\t253607\t0\t+\t.\tName=RhoGAP domain;color=#FFFFFF;gene_id=ENSG00000186716;gene_name=BCR;protein_domain_id=PF00620\n+22\tpfam\tprotein_domain\t254554\t254659\t0\t+\t.\tName=RhoGAP domain;color=#FFFFFF;gene_id=ENSG00000186716;gene_name=BCR;protein_domain_id=PF00620\n+22\tpfam\tprotein_domain\t255138\t255228\t0\t+\t.\tName=RhoGAP domain;color=#FFFFFF;gene_id=ENSG00000186716;gene_name=BCR;protein_domain_id=PF00620\n' |