Mercurial > repos > iuc > star_fusion
changeset 0:93704f98f56e draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/star_fusion commit ec27c2abb7c8ba0bcbcb2f26cca9ef1109f7a3a2
| author | iuc |
|---|---|
| date | Tue, 06 Sep 2016 04:55:21 -0400 |
| parents | |
| children | 0b44456754e2 |
| files | star_fusion.xml test-data/test1-test1.blastn.tabular test-data/test1.fa test-data/test1.fastqsanger test-data/test1.gtf test-data/test1.tabular tool-data/all_fasta.loc.sample tool_data_table_conf.xml.sample tool_dependencies.xml |
| diffstat | 9 files changed, 661 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/star_fusion.xml Tue Sep 06 04:55:21 2016 -0400 @@ -0,0 +1,249 @@ +<tool id="star_fusion" name="STAR-Fusion" version="0.5.4-2" profile="16.07"> + <description>detect fusion genes in RNA-Seq data</description> + <requirements> + <!-- Bio-conda --> + <requirement type="package" version="0.5.4">star-fusion</requirement> + </requirements> + + <stdio> + <regex match="command not found" source="stderr" level="fatal"/> + <regex match="EXITING because of INPUT ERROR" source="stderr" level="fatal"/> + <regex match="FATAL ERROR" source="stderr" level="fatal"/> + + <regex match="Warning:" source="stderr" level="warning"/> + <regex match="CMD:" source="stderr" level="warning"/> + + <regex match="-done creating index file:" source="stderr" level="warning"/> + <regex match="-parsing GTF file:" source="stderr" level="warning"/> + <regex match="-building interval tree" source="stderr" level="warning"/> + <regex match="-parsing fusion evidence:" source="stderr" level="warning"/> + <regex match="-mapping reads to genes" source="stderr" level="warning"/> + <regex match="-outputting fusion candidates to file:" source="stderr" level="warning"/> + + <regex match="Process complete" source="stderr" level="warning"/> + </stdio> + + <version_command>STAR-Fusion --version 2>&1 | grep version | grep -o -E "software version.*?"</version_command> + + <command><![CDATA[ + ## 1. ensure the blastn file is provided as *.gz + if file --mime-type '${blast_pairs}' | grep -q /gzip\$; then + gzip_suffix='' ; + else + ## Older versions of gzip do not support the -k option to keep + ## the original file - this should be an universion solution + + gzip -1 -c -- '${blast_pairs}' > '${blast_pairs}.gz' && + gzip_suffix='.gz' ; + fi && + + ## 2. create reference index - using \$(pwd) is necessary, probably because the perl script changes work directory + ## - @todo once write a decent STAR and STAR Fusion data manager + prep_genome_lib.pl + --genome_fa '${fasta_type.ownFile}' + --gtf '${geneModel}' + --blast_pairs "${blast_pairs}\$gzip_suffix" + --CPU \${GALAXY_SLOTS:-1} + --output_dir "\$(pwd)/tmp_star_fusion_genome_dir" + && + + ## 3. Run STAR-Fusion + STAR-Fusion + #if str($input_params.input_source) == "use_chimeric": + --chimeric_junction '${input_params.chimeric_junction}' + #else: + --left_fq '${input_params.left_fq}' + #if $input_params.right_fq: + --right_fq '${input_params.right_fq}' + #end if + #end if + + --genome_lib_dir "\$(pwd)/tmp_star_fusion_genome_dir" + + #if str($params.settingsType) == "full": + --min_junction_reads $params.min_junction_reads + --min_sum_frags $params.min_sum_frags + --max_promiscuity $params.max_promiscuity + --min_novel_junction_support $params.min_novel_junction_support + --min_alt_pct_junction $params.min_alt_pct_junction + --aggregate_novel_junction_dist $params.aggregate_novel_junction_dist + --E $params.E + #end if + ]]></command> + + <inputs> + <conditional name="input_params"> + <param name="input_source" + type="select" + label="Use output from earlier STAR run or let STAR Fusion control running STAR"> + <option value="use_chimeric">Use output from earlier STAR</option> + <option value="use_fastq">Let STAR Fusion control running STAR</option> + </param> + <when value="use_chimeric"> + <param name="chimeric_junction" + type="data" + format="interval" + argument="--chimeric_junction" + label="Chimeric junction file from STAR (with STAR-Fusion settings)"/> + </when> + <when value="use_fastq"> + <param name="left_fq" + type="data" + format="fastqsanger" + argument="--left_fq" + label="left.fq file"/> + <param name="right_fq" + type="data" + format="fastqsanger" + optional="true" + argument="--right_fq" + label="right.fq file (actually optional, but highly recommended)"/> + </when> + </conditional> + + <!-- Genome source. --> + <conditional name="fasta_type"> + <param name="fasta_type_selector" type="select" label="Source for sequence to search"> + <option value="cached">Locally Cached sequences</option> + <option value="history" selected="true">Sequences from your history</option> + </param> + <when value="cached"> + <param name="ownFile" + type="select" label="Genome to search"> + <options from_data_table="all_fasta"> + <column name="dbkey" index="1"/> + <column name="name" index="2"/> + <column name="value" index="3"/> + </options> + </param> + </when> + <when value="history"> + <param name="ownFile" + type="data" + format="fasta" + metadata_name="dbkey" + label="Select the reference genome (FASTA file)"/> + </when> + </conditional> + + <param name="geneModel" + type="data" + format="gff3,gtf" + label="Gene model (gff3,gtf) file for splice junctions and fusion gene detection"/> + <param name="blast_pairs" + type="data" + format="tabular" + label="Result of BLAST+-blastn of the reference fasta sequence with itself" + help="Run blastn with '-outputfmt 6' or choose 'Tabular (standard 12 columns)' in the Galaxy wrapper. For human data it is recommended to obtain it from here: https://data.broadinstitute.org/Trinity/CTAT_RESOURCE_LIB/"/> + + <conditional name="params"> + <param name="settingsType" type="select" label="Settings to use" help="You can use the default settings or set custom values for any STAR Fusion parameter."> + <option value="default" selected="true">Use Defaults</option> + <option value="full">Full parameter list</option> + </param> + <when value="default" /> + <when value="full"><!-- Full/advanced params. --> + <param name="min_junction_reads" + type="integer" value="1" + label="minimum number of junction-spanning reads required." + argument="--min_junction_reads"/> + <param name="min_sum_frags" + type="integer" + value="2" + label="minimum fusion support = (#junction_reads + #spanning_frags)" + argument="--min_sum_frags"/> + <param name="max_promiscuity" + type="integer" + value="3" + label="maximum number of partners allowed for a given fusion" + argument="--max_promiscuity"/> + <param name="min_novel_junction_support" + type="integer" + value="3" + label="minimum of 3 junction reads required if breakpoint lacks involvement of only reference junctions" + argument="--min_novel_junction_support"/> + <param name="min_alt_pct_junction" + type="float" + value="10" + label="10% of the dominant isoform junction support" + argument="--min_alt_pct_junction"/> + <param name="aggregate_novel_junction_dist" + type="integer" + value="5" + label="non-ref junctions within 5 are merged into single calls" + argument="--aggregate_novel_junction_dist"/> + <param name="E" + type="float" + value="0.001" + label="E-value threshold for blast searches" + argument="-E"/> + </when> + </conditional> + </inputs> + + <outputs> + <data format="tabular" name="output_final" label="${tool.name} on ${on_string}: fusion_candidates.final" from_work_dir="star-fusion.fusion_candidates.final"/> + </outputs> + + <tests> + <test> + <param name="input_source" value="use_chimeric" /> + <param name="chimeric_junction" ftype="interval" value="test1.tabular" /> + <param name="fasta_type_selector" value="history" /> + <param name="ownFile" ftype="fasta" value="test1.fa" /> + <param name="geneModel" ftype="gtf" value="test1.gtf" /> + <param name="blast_pairs" ftype="tabular" value="test1-test1.blastn.tabular" /> + <param name="settingsType" value="default" /> + + <!-- Last column of the results contains data in a random order so exact matching is not feasible --> + <output name="output_final"> + <assert_contents> + <has_line line="#fusion_name	JunctionReads	SpanningFrags	Splice_type	LeftGene	LeftBreakpoint	RightGene	RightBreakpoint	JunctionReads	SpanningFrags" /> + <has_text text="GENE1--GENE2	24	0	INCL_NON_REF_SPLICE	GENE1^GENE1	chr1:240:+	GENE2^GENE2	chr2:241:+" /> + </assert_contents> + </output> + </test> + <test> + <param name="input_source" value="use_fastq" /> + <param name="left_fq" ftype="fastqsanger" value="test1.fastqsanger"/> + <param name="fasta_type_selector" value="history" /> + <param name="ownFile" ftype="fasta" value="test1.fa" /> + <param name="geneModel" ftype="gtf" value="test1.gtf" /> + <param name="blast_pairs" ftype="tabular" value="test1-test1.blastn.tabular" /> + <param name="settingsType" value="default" /> + + <!-- Last column of the results contains data in a random order so exact matching is not feasible --> + <output name="output_final"> + <assert_contents> + <has_line line="#fusion_name	JunctionReads	SpanningFrags	Splice_type	LeftGene	LeftBreakpoint	RightGene	RightBreakpoint	JunctionReads	SpanningFrags" /> + <has_text text="GENE1--GENE2	24	0	INCL_NON_REF_SPLICE	GENE1^GENE1	chr1:240:+	GENE2^GENE2	chr2:241:+" /> + </assert_contents> + </output> + </test> + </tests> + <help> +**What it does** + +STAR-Fusion is a component of the Trinity Cancer Transcriptome Analysis Toolkit (CTAT). STAR-Fusion uses the STAR aligner to identify candidate fusion transcripts supported by Illumina reads. STAR-Fusion further processes the output generated by the STAR aligner to map junction reads and spanning reads to a reference annotation set. + +**Input: files required to run STAR-Fusion** + - A genome reference sequence (FASTA-format) + - A corresponding protein-coding gene annotation set (GTF/GFF Format) + - A last-matching gene pairs file - in Galaxy you can create such files with the *ncbi_blast_plus* tool suite containing *blastn*: https://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus + - A STAR chimeric/junction output file - this is optional as STAR Fusion can control running STAR as well. + +The authors of STAR Fusion have made some of these files avaialble at: https://data.broadinstitute.org/Trinity/CTAT_RESOURCE_LIB/. The gene annotations in each case are restricted to the protein-coding and lincRNA transcripts. +More info: https://github.com/STAR-Fusion/STAR-Fusion/wiki + + </help> + + <citations> + <citation type="bibtex"> + @unpublished{star_fusion, + author = {Brian Haas and Nicolas Stransky and Daniel Nicorici}, + title = {STAR-Fusion}, + url = {https://github.com/STAR-Fusion/STAR-Fusion} + } + </citation> + </citations> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test1-test1.blastn.tabular Tue Sep 06 04:55:21 2016 -0400 @@ -0,0 +1,2 @@ +chr1 chr1 100.00 480 0 0 1 480 1 480 0.0 866 +chr2 chr2 100.00 480 0 0 1 480 1 480 0.0 866
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test1.fa Tue Sep 06 04:55:21 2016 -0400 @@ -0,0 +1,18 @@ +>chr1 +GACGGACGTATTCCTCTGGCCTCAACGGTTCCTGCTTTCGCTGGGATCCAAGATTGGCAG +CTGAAACCGCCTTTCCAAAGTGAGTCCTTCGTCTGTGACTAACTGTGCCAAATCGTCTTG +CAAACTCCTGATCCAGTTTAACTCACCAAATTATAGCCATACAGACCCAAATTTTAAATC +ATATCACGCGACTAGCCTCTGCTTAATTTCTGTGCTCAAGGGTTTTGGTCCGCCCGAGCG +GTGCAGCCGATTAGGACCATCTAATGCACTTGTTACAAGACTTCTTTTAAATACTTTCTT +CCTGCCCAGTAGCGGATGATAATGGTTGTTGCCAGCCGGTGTGGAAGGTAACAGCACCGG +TGCGAGCCTAATGTGCCGTCTCCACCAACACAAGGCTATCCGGTCGTATAATAGGATTCC +GCAATGGGGTTAGCAAATGGCAGCCTAAACGATATCGGGGACTTGCGATGTACATGCTTT +>chr2 +TCAACAATAAGCGCTTTTTGTAGGCAGGGGCACCCCCTATCAGTGGCTGCGCCAAAACAT +CTTCGGATCCCCTTGTCCAATCAAATTGATCGAATTCTTTCATTTAAGACCCTAATATGA +CATCATTAGTGATTAAATGCCACTCCCAAAATTCTGCCTAGAAATGTTTAAGTTCGCTCC +ACTAAAGTTGTTTAAAACGACTACTAAATCCGCGTGATAGGGGATTTCATATTTAATCTT +TTATCGTAAGGAACAGCCGATCTTAATGGATGGCCGCAGGTGGTATGGAAGCTATAAGCG +CGGGTGAGAGGGTAATTAGGCGTGTTCACCTACACTACGCTAACGGGCGATTCTATAAGA +TTGCACATTGCGTCTACTTATAAGATGTCTCAACGGCATGCGCAACTTGTGAAGTGCCTA +CTATCCTTAAACGCATATCTCGCACAGTAACTCCCCAATATGTGAGCATCTGATGTTGCC
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test1.fastqsanger Tue Sep 06 04:55:21 2016 -0400 @@ -0,0 +1,332 @@ +@test_chimeric_mRNA_0 +CAAACTCCTGATCCAGTTTAACTCACCAAATTATAGCCATACAGACCCAAATTTTAAATCATATCACGCGACTAG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_chimeric_mRNA_2 +AACTCCTGATCCAGTTTAACTCACCAAATTATAGCCATACAGACCCAAATTTTAAATCATATCACGCGACTAGCC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_chimeric_mRNA_4 +CTCCTGATCCAGTTTAACTCACCAAATTATAGCCATACAGACCCAAATTTTAAATCATATCACGCGACTAGCCTC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_chimeric_mRNA_6 +CCTGATCCAGTTTAACTCACCAAATTATAGCCATACAGACCCAAATTTTAAATCATATCACGCGACTAGCCTCTG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_chimeric_mRNA_8 +TGATCCAGTTTAACTCACCAAATTATAGCCATACAGACCCAAATTTTAAATCATATCACGCGACTAGCCTCTGCT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_chimeric_mRNA_10 +ATCCAGTTTAACTCACCAAATTATAGCCATACAGACCCAAATTTTAAATCATATCACGCGACTAGCCTCTGCTTA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_chimeric_mRNA_12 +CCAGTTTAACTCACCAAATTATAGCCATACAGACCCAAATTTTAAATCATATCACGCGACTAGCCTCTGCTTAAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_chimeric_mRNA_14 +AGTTTAACTCACCAAATTATAGCCATACAGACCCAAATTTTAAATCATATCACGCGACTAGCCTCTGCTTAATTT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_chimeric_mRNA_16 +TTTAACTCACCAAATTATAGCCATACAGACCCAAATTTTAAATCATATCACGCGACTAGCCTCTGCTTAATTTCT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_chimeric_mRNA_18 +TAACTCACCAAATTATAGCCATACAGACCCAAATTTTAAATCATATCACGCGACTAGCCTCTGCTTAATTTCTGT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_chimeric_mRNA_20 +ACTCACCAAATTATAGCCATACAGACCCAAATTTTAAATCATATCACGCGACTAGCCTCTGCTTAATTTCTGTGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_chimeric_mRNA_22 +TCACCAAATTATAGCCATACAGACCCAAATTTTAAATCATATCACGCGACTAGCCTCTGCTTAATTTCTGTGCTC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_chimeric_mRNA_24 +ACCAAATTATAGCCATACAGACCCAAATTTTAAATCATATCACGCGACTAGCCTCTGCTTAATTTCTGTGCTCAA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_chimeric_mRNA_26 +CAAATTATAGCCATACAGACCCAAATTTTAAATCATATCACGCGACTAGCCTCTGCTTAATTTCTGTGCTCAAGG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_chimeric_mRNA_28 +AATTATAGCCATACAGACCCAAATTTTAAATCATATCACGCGACTAGCCTCTGCTTAATTTCTGTGCTCAAGGGT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_chimeric_mRNA_30 +TTATAGCCATACAGACCCAAATTTTAAATCATATCACGCGACTAGCCTCTGCTTAATTTCTGTGCTCAAGGGTTT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_chimeric_mRNA_32 +ATAGCCATACAGACCCAAATTTTAAATCATATCACGCGACTAGCCTCTGCTTAATTTCTGTGCTCAAGGGTTTTG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_chimeric_mRNA_34 +AGCCATACAGACCCAAATTTTAAATCATATCACGCGACTAGCCTCTGCTTAATTTCTGTGCTCAAGGGTTTTGGT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_chimeric_mRNA_36 +CCATACAGACCCAAATTTTAAATCATATCACGCGACTAGCCTCTGCTTAATTTCTGTGCTCAAGGGTTTTGGTCC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_chimeric_mRNA_38 +ATACAGACCCAAATTTTAAATCATATCACGCGACTAGCCTCTGCTTAATTTCTGTGCTCAAGGGTTTTGGTCCGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_chimeric_mRNA_40 +ACAGACCCAAATTTTAAATCATATCACGCGACTAGCCTCTGCTTAATTTCTGTGCTCAAGGGTTTTGGTCCGCCC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_chimeric_mRNA_42 +AGACCCAAATTTTAAATCATATCACGCGACTAGCCTCTGCTTAATTTCTGTGCTCAAGGGTTTTGGTCCGCCCGA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_chimeric_mRNA_44 +ACCCAAATTTTAAATCATATCACGCGACTAGCCTCTGCTTAATTTCTGTGCTCAAGGGTTTTGGTCCGCCCGAGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_chimeric_mRNA_46 +CCAAATTTTAAATCATATCACGCGACTAGCCTCTGCTTAATTTCTGTGCTCAAGGGTTTTGGTCCGCCCGAGCGT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_chimeric_mRNA_48 +AAATTTTAAATCATATCACGCGACTAGCCTCTGCTTAATTTCTGTGCTCAAGGGTTTTGGTCCGCCCGAGCGTTA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_chimeric_mRNA_50 +ATTTTAAATCATATCACGCGACTAGCCTCTGCTTAATTTCTGTGCTCAAGGGTTTTGGTCCGCCCGAGCGTTATC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_chimeric_mRNA_52 +TTTAAATCATATCACGCGACTAGCCTCTGCTTAATTTCTGTGCTCAAGGGTTTTGGTCCGCCCGAGCGTTATCGT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_chimeric_mRNA_54 +TAAATCATATCACGCGACTAGCCTCTGCTTAATTTCTGTGCTCAAGGGTTTTGGTCCGCCCGAGCGTTATCGTAA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_chimeric_mRNA_56 +AATCATATCACGCGACTAGCCTCTGCTTAATTTCTGTGCTCAAGGGTTTTGGTCCGCCCGAGCGTTATCGTAAGG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_chimeric_mRNA_58 +TCATATCACGCGACTAGCCTCTGCTTAATTTCTGTGCTCAAGGGTTTTGGTCCGCCCGAGCGTTATCGTAAGGAA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_chimeric_mRNA_60 +ATATCACGCGACTAGCCTCTGCTTAATTTCTGTGCTCAAGGGTTTTGGTCCGCCCGAGCGTTATCGTAAGGAACA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_chimeric_mRNA_62 +ATCACGCGACTAGCCTCTGCTTAATTTCTGTGCTCAAGGGTTTTGGTCCGCCCGAGCGTTATCGTAAGGAACAGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_chimeric_mRNA_64 +CACGCGACTAGCCTCTGCTTAATTTCTGTGCTCAAGGGTTTTGGTCCGCCCGAGCGTTATCGTAAGGAACAGCCG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_chimeric_mRNA_66 +CGCGACTAGCCTCTGCTTAATTTCTGTGCTCAAGGGTTTTGGTCCGCCCGAGCGTTATCGTAAGGAACAGCCGAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_chimeric_mRNA_68 +CGACTAGCCTCTGCTTAATTTCTGTGCTCAAGGGTTTTGGTCCGCCCGAGCGTTATCGTAAGGAACAGCCGATCT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_chimeric_mRNA_70 +ACTAGCCTCTGCTTAATTTCTGTGCTCAAGGGTTTTGGTCCGCCCGAGCGTTATCGTAAGGAACAGCCGATCTTA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_chimeric_mRNA_72 +TAGCCTCTGCTTAATTTCTGTGCTCAAGGGTTTTGGTCCGCCCGAGCGTTATCGTAAGGAACAGCCGATCTTAAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_chimeric_mRNA_74 +GCCTCTGCTTAATTTCTGTGCTCAAGGGTTTTGGTCCGCCCGAGCGTTATCGTAAGGAACAGCCGATCTTAATGG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_chimeric_mRNA_76 +CTCTGCTTAATTTCTGTGCTCAAGGGTTTTGGTCCGCCCGAGCGTTATCGTAAGGAACAGCCGATCTTAATGGAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_chimeric_mRNA_78 +CTGCTTAATTTCTGTGCTCAAGGGTTTTGGTCCGCCCGAGCGTTATCGTAAGGAACAGCCGATCTTAATGGATGG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_chimeric_mRNA_80 +GCTTAATTTCTGTGCTCAAGGGTTTTGGTCCGCCCGAGCGTTATCGTAAGGAACAGCCGATCTTAATGGATGGCC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_chimeric_mRNA_82 +TTAATTTCTGTGCTCAAGGGTTTTGGTCCGCCCGAGCGTTATCGTAAGGAACAGCCGATCTTAATGGATGGCCGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_chimeric_mRNA_84 +AATTTCTGTGCTCAAGGGTTTTGGTCCGCCCGAGCGTTATCGTAAGGAACAGCCGATCTTAATGGATGGCCGCAG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_chimeric_mRNA_86 +TTTCTGTGCTCAAGGGTTTTGGTCCGCCCGAGCGTTATCGTAAGGAACAGCCGATCTTAATGGATGGCCGCAGGT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_chimeric_mRNA_88 +TCTGTGCTCAAGGGTTTTGGTCCGCCCGAGCGTTATCGTAAGGAACAGCCGATCTTAATGGATGGCCGCAGGTGG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_chimeric_mRNA_90 +TGTGCTCAAGGGTTTTGGTCCGCCCGAGCGTTATCGTAAGGAACAGCCGATCTTAATGGATGGCCGCAGGTGGTA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_chimeric_mRNA_92 +TGCTCAAGGGTTTTGGTCCGCCCGAGCGTTATCGTAAGGAACAGCCGATCTTAATGGATGGCCGCAGGTGGTATG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_chimeric_mRNA_94 +CTCAAGGGTTTTGGTCCGCCCGAGCGTTATCGTAAGGAACAGCCGATCTTAATGGATGGCCGCAGGTGGTATGGA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_chimeric_mRNA_96 +CAAGGGTTTTGGTCCGCCCGAGCGTTATCGTAAGGAACAGCCGATCTTAATGGATGGCCGCAGGTGGTATGGAAG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_chimeric_mRNA_98 +AGGGTTTTGGTCCGCCCGAGCGTTATCGTAAGGAACAGCCGATCTTAATGGATGGCCGCAGGTGGTATGGAAGCT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_chimeric_mRNA_100 +GGTTTTGGTCCGCCCGAGCGTTATCGTAAGGAACAGCCGATCTTAATGGATGGCCGCAGGTGGTATGGAAGCTAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_chimeric_mRNA_102 +TTTTGGTCCGCCCGAGCGTTATCGTAAGGAACAGCCGATCTTAATGGATGGCCGCAGGTGGTATGGAAGCTATAA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_chimeric_mRNA_104 +TTGGTCCGCCCGAGCGTTATCGTAAGGAACAGCCGATCTTAATGGATGGCCGCAGGTGGTATGGAAGCTATAAGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_chimeric_mRNA_106 +GGTCCGCCCGAGCGTTATCGTAAGGAACAGCCGATCTTAATGGATGGCCGCAGGTGGTATGGAAGCTATAAGCGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_chimeric_mRNA_108 +TCCGCCCGAGCGTTATCGTAAGGAACAGCCGATCTTAATGGATGGCCGCAGGTGGTATGGAAGCTATAAGCGCGG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_chimeric_mRNA_110 +CGCCCGAGCGTTATCGTAAGGAACAGCCGATCTTAATGGATGGCCGCAGGTGGTATGGAAGCTATAAGCGCGGGT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_chimeric_mRNA_112 +CCCGAGCGTTATCGTAAGGAACAGCCGATCTTAATGGATGGCCGCAGGTGGTATGGAAGCTATAAGCGCGGGTGA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_chimeric_mRNA_114 +CGAGCGTTATCGTAAGGAACAGCCGATCTTAATGGATGGCCGCAGGTGGTATGGAAGCTATAAGCGCGGGTGAGA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_chimeric_mRNA_116 +AGCGTTATCGTAAGGAACAGCCGATCTTAATGGATGGCCGCAGGTGGTATGGAAGCTATAAGCGCGGGTGAGAGG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_chimeric_mRNA_118 +CGTTATCGTAAGGAACAGCCGATCTTAATGGATGGCCGCAGGTGGTATGGAAGCTATAAGCGCGGGTGAGAGGGT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_chimeric_mRNA_120 +TTATCGTAAGGAACAGCCGATCTTAATGGATGGCCGCAGGTGGTATGGAAGCTATAAGCGCGGGTGAGAGGGTAA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_chimeric_mRNA_122 +ATCGTAAGGAACAGCCGATCTTAATGGATGGCCGCAGGTGGTATGGAAGCTATAAGCGCGGGTGAGAGGGTAATT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_chimeric_mRNA_124 +CGTAAGGAACAGCCGATCTTAATGGATGGCCGCAGGTGGTATGGAAGCTATAAGCGCGGGTGAGAGGGTAATTAG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_chimeric_mRNA_126 +TAAGGAACAGCCGATCTTAATGGATGGCCGCAGGTGGTATGGAAGCTATAAGCGCGGGTGAGAGGGTAATTAGGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_chimeric_mRNA_128 +AGGAACAGCCGATCTTAATGGATGGCCGCAGGTGGTATGGAAGCTATAAGCGCGGGTGAGAGGGTAATTAGGCGT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_chimeric_mRNA_130 +GAACAGCCGATCTTAATGGATGGCCGCAGGTGGTATGGAAGCTATAAGCGCGGGTGAGAGGGTAATTAGGCGTGT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_chimeric_mRNA_132 +ACAGCCGATCTTAATGGATGGCCGCAGGTGGTATGGAAGCTATAAGCGCGGGTGAGAGGGTAATTAGGCGTGTTC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_chimeric_mRNA_134 +AGCCGATCTTAATGGATGGCCGCAGGTGGTATGGAAGCTATAAGCGCGGGTGAGAGGGTAATTAGGCGTGTTCAC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_chimeric_mRNA_136 +CCGATCTTAATGGATGGCCGCAGGTGGTATGGAAGCTATAAGCGCGGGTGAGAGGGTAATTAGGCGTGTTCACCT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_chimeric_mRNA_138 +GATCTTAATGGATGGCCGCAGGTGGTATGGAAGCTATAAGCGCGGGTGAGAGGGTAATTAGGCGTGTTCACCTAC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_chimeric_mRNA_140 +TCTTAATGGATGGCCGCAGGTGGTATGGAAGCTATAAGCGCGGGTGAGAGGGTAATTAGGCGTGTTCACCTACAC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_chimeric_mRNA_142 +TTAATGGATGGCCGCAGGTGGTATGGAAGCTATAAGCGCGGGTGAGAGGGTAATTAGGCGTGTTCACCTACACTA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_chimeric_mRNA_144 +AATGGATGGCCGCAGGTGGTATGGAAGCTATAAGCGCGGGTGAGAGGGTAATTAGGCGTGTTCACCTACACTACG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_chimeric_mRNA_146 +TGGATGGCCGCAGGTGGTATGGAAGCTATAAGCGCGGGTGAGAGGGTAATTAGGCGTGTTCACCTACACTACGCT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_chimeric_mRNA_148 +GATGGCCGCAGGTGGTATGGAAGCTATAAGCGCGGGTGAGAGGGTAATTAGGCGTGTTCACCTACACTACGCTAA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_chimeric_mRNA_150 +TGGCCGCAGGTGGTATGGAAGCTATAAGCGCGGGTGAGAGGGTAATTAGGCGTGTTCACCTACACTACGCTAACG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_chimeric_mRNA_152 +GCCGCAGGTGGTATGGAAGCTATAAGCGCGGGTGAGAGGGTAATTAGGCGTGTTCACCTACACTACGCTAACGGG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_chimeric_mRNA_154 +CGCAGGTGGTATGGAAGCTATAAGCGCGGGTGAGAGGGTAATTAGGCGTGTTCACCTACACTACGCTAACGGGCG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_chimeric_mRNA_156 +CAGGTGGTATGGAAGCTATAAGCGCGGGTGAGAGGGTAATTAGGCGTGTTCACCTACACTACGCTAACGGGCGAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_chimeric_mRNA_158 +GGTGGTATGGAAGCTATAAGCGCGGGTGAGAGGGTAATTAGGCGTGTTCACCTACACTACGCTAACGGGCGATTC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_chimeric_mRNA_160 +TGGTATGGAAGCTATAAGCGCGGGTGAGAGGGTAATTAGGCGTGTTCACCTACACTACGCTAACGGGCGATTCTA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_chimeric_mRNA_162 +GTATGGAAGCTATAAGCGCGGGTGAGAGGGTAATTAGGCGTGTTCACCTACACTACGCTAACGGGCGATTCTATA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@test_chimeric_mRNA_164 +ATGGAAGCTATAAGCGCGGGTGAGAGGGTAATTAGGCGTGTTCACCTACACTACGCTAACGGGCGATTCTATAAG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test1.gtf Tue Sep 06 04:55:21 2016 -0400 @@ -0,0 +1,8 @@ +chr1 test gene 140 363 . + . gene_id "GENE1"; gene_name "GENE1"; transcript_id "GENE1_t1"; +chr1 test transcript 150 353 . + . gene_id "GENE1"; gene_name "GENE1"; transcript_id "GENE1_t1"; +chr1 test exon 150 353 . + . gene_id "GENE1"; transcript_id "GENE1_t1"; exon_number "1"; gene_name "GENE1"; +chr1 test CDS 153 350 . + . gene_id "GENE1"; transcript_id "GENE1_t1"; exon_number "1"; gene_name "GENE1"; +chr2 test gene 140 363 . + . gene_id "GENE2"; gene_name "GENE2"; transcript_id "GENE2_t1"; +chr2 test transcript 150 353 . + . gene_id "GENE2"; gene_name "GENE2"; transcript_id "GENE2_t1"; +chr2 test exon 150 353 . + . gene_id "GENE2"; transcript_id "GENE2_t1"; exon_number "1"; gene_name "GENE2"; +chr2 test CDS 153 350 . + . gene_id "GENE2"; transcript_id "GENE2_t1"; exon_number "1"; gene_name "GENE2";
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test1.tabular Tue Sep 06 04:55:21 2016 -0400 @@ -0,0 +1,24 @@ +chr1 241 + chr2 240 + 0 0 0 test_chimeric_mRNA_60 181 60M15S 241 60S15M +chr1 241 + chr2 240 + 0 0 0 test_chimeric_mRNA_62 183 58M17S 241 58S17M +chr1 241 + chr2 240 + 0 0 0 test_chimeric_mRNA_64 185 56M19S 241 56S19M +chr1 241 + chr2 240 + 0 0 0 test_chimeric_mRNA_66 187 54M21S 241 54S21M +chr1 241 + chr2 240 + 0 0 0 test_chimeric_mRNA_68 189 52M23S 241 52S23M +chr1 241 + chr2 240 + 0 0 0 test_chimeric_mRNA_70 191 50M25S 241 50S25M +chr1 241 + chr2 240 + 0 0 0 test_chimeric_mRNA_72 193 48M27S 241 48S27M +chr1 241 + chr2 240 + 0 0 0 test_chimeric_mRNA_74 195 46M29S 241 46S29M +chr1 241 + chr2 240 + 0 0 0 test_chimeric_mRNA_76 197 44M31S 241 44S31M +chr1 241 + chr2 240 + 0 0 0 test_chimeric_mRNA_78 199 42M33S 241 42S33M +chr1 241 + chr2 240 + 0 0 0 test_chimeric_mRNA_80 201 40M35S 241 40S35M +chr1 241 + chr2 240 + 0 0 0 test_chimeric_mRNA_82 203 38M37S 241 38S37M +chr1 241 + chr2 240 + 0 0 0 test_chimeric_mRNA_84 205 36M39S 241 36S39M +chr1 241 + chr2 240 + 0 0 0 test_chimeric_mRNA_86 207 34M41S 241 34S41M +chr1 241 + chr2 240 + 0 0 0 test_chimeric_mRNA_88 209 32M43S 241 32S43M +chr1 241 + chr2 240 + 0 0 0 test_chimeric_mRNA_90 211 30M45S 241 30S45M +chr1 241 + chr2 240 + 0 0 0 test_chimeric_mRNA_92 213 28M47S 241 28S47M +chr1 241 + chr2 240 + 0 0 0 test_chimeric_mRNA_94 215 26M49S 241 26S49M +chr1 241 + chr2 240 + 0 0 0 test_chimeric_mRNA_96 217 24M51S 241 24S51M +chr1 241 + chr2 240 + 0 0 0 test_chimeric_mRNA_98 219 22M53S 241 22S53M +chr1 241 + chr2 240 + 0 0 0 test_chimeric_mRNA_100 221 20M55S 241 20S55M +chr1 241 + chr2 240 + 0 0 0 test_chimeric_mRNA_102 223 18M57S 241 18S57M +chr1 241 + chr2 240 + 0 0 0 test_chimeric_mRNA_104 225 16M59S 241 16S59M +chr1 241 + chr2 240 + 0 0 0 test_chimeric_mRNA_106 227 14M61S 241 14S61M
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/all_fasta.loc.sample Tue Sep 06 04:55:21 2016 -0400 @@ -0,0 +1,18 @@ +#This file lists the locations and dbkeys of all the fasta files +#under the "genome" directory (a directory that contains a directory +#for each build). The script extract_fasta.py will generate the file +#all_fasta.loc. This file has the format (white space characters are +#TAB characters): +# +#<unique_build_id> <dbkey> <display_name> <file_path> +# +#So, all_fasta.loc could look something like this: +# +#apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa +#hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa +# +#Your all_fasta.loc file should contain an entry for each individual +#fasta file. So there will be multiple fasta files for each build, +#such as with hg19 above. +#
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Tue Sep 06 04:55:21 2016 -0400 @@ -0,0 +1,7 @@ +<tables> + <!-- Locations of all fasta files under genome directory --> + <table name="all_fasta" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/all_fasta.loc" /> + </table> +</tables>