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planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/flaimapper commit 0f4aa594becc89b07073f7fcccd889e38974e10c-dirty |
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README.rst egg/flaimapper-1.1.5-py2.7.egg flaimapper-gtf-from-fasta.xml flaimapper.xml test-data/ncrnadb09.fa test-data/ncrnadb09.fa.fai test-data/ncrnadb09.gtf test-data/snord81.bam test-data/snord81.flaimapper.txt tool_data_table_conf.xml.sample tool_dependencies.xml |
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| @@ -0,0 +1,41 @@ +FlaiMapper wrapper for Galaxy +============================= + +https://github.com/yhoogstrate/flaimapper +http://www.ncbi.nlm.nih.gov/pubmed/25338717 +http://dx.doi.org/10.1093/bioinformatics/btu696 + +Fragment Location Annotation Identification Mapper + +FlaiMapper: computational annotation of small ncRNA-derived fragments using RNA-seq high-throughput data. + +Development +----------- + +* Repository-Maintainer: Youri Hoogstrate +* Repository-Developers: Youri Hoogstrate + +* Repository-Development: https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools + +The tool wrapper has been written by Youri Hoogstrate from the Erasmus +Medical Center (Rotterdam, Netherlands). + +License +------- + +**flaimapper** and **wrapper**: + +GPL (>=3) + +**pysam**: + +The MIT License + +References +---------- +**FlaiMapper: computational annotation of small ncRNA-derived fragments using RNA-seq high-throughput data.** + +*Youri Hoogstrate, Guido Jenster, and Elena S. Martens-Uzunova* - Bioinformatics (2015) 31 (5): 665-673 + +- http://www.ncbi.nlm.nih.gov/pubmed/25338717 +- http://dx.doi.org/10.1093/bioinformatics/btu696 \ No newline at end of file |
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| diff -r 000000000000 -r d6abffbc9ee7 flaimapper-gtf-from-fasta.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/flaimapper-gtf-from-fasta.xml Thu May 21 07:26:46 2015 -0400 |
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| @@ -0,0 +1,114 @@ +<?xml version="1.0" encoding="UTF-8"?> +<tool id="flaimapper-gtf-from-fasta" name="FlaiMapper: extract GTF from FASTA" version="1.1.5.b"> + <description>Extract GTF file from FASTA file (as FlaiMapper reference).</description> + <requirements> + <requirement type="package" version="0.8.2.1">pysam</requirement> + <requirement type="package" version="1.1.5">flaimapper</requirement> + </requirements> + + <stdio> + <regex + match="[fai_load] build FASTA index." + source="stderr" + level="log" + description="The FASTA file is being indexed." /> + </stdio> + + <version_command>flaimapper --version</version_command> + + <command> + gtf-from-fasta + -o $output + $fasta + </command> + + <inputs> + <param name="fasta" type="data" format="fasta" label="Fasta sequence corresponding to reference genome" help="" /> + </inputs> + + <outputs> + <data format="gtf" name="output" label="${tool.name} on ${fasta.name}" /> + </outputs> + + <tests> + <test> + <param name="fasta" value="ncrnadb09.fa" ftype="fasta" /> + + <output name="output" file="ncrnadb09.gtf" /> + </test> + </tests> + + <help> +FlaiMapper wrapper for Galaxy +============================= + +https://github.com/yhoogstrate/flaimapper +http://www.ncbi.nlm.nih.gov/pubmed/25338717 +http://dx.doi.org/10.1093/bioinformatics/btu696 + +Fragment Location Annotation Identification Mapper + +FlaiMapper: computational annotation of small ncRNA-derived fragments using RNA-seq high-throughput data. + +Input formats +------------- +To make FlaiMapper compatible with both an entire reference genome as a +separate ncRNA database, it requires an additional GTF file *(mask file)*. +The major difference between an entire reference and a ncRNA database +is that an entire reference usually contains multiple ncRNAs per sequence +entry (chromosome). While for the ncRNA database, each entry should +represent one single mature ncRNA. + +Therefore the mask file that represents to the FASTA file of a ncRNA +database will only contain the start- and end positions of each entry. +To generate this in an automated fashion, you can make use of this tool +*as long as the FASTA file doesn't contain entire chromosomes* but +mature ncRNA. + +An example input file is **ncRNAdb09**, available at the following URLs: +https://raw.githubusercontent.com/yhoogstrate/flaimapper/master/share/annotations/ncRNA_annotation/ncrnadb09.fa *(reference file)* + +It should generate a GTF/GFF file (mask file) similar to the following URL: +https://raw.githubusercontent.com/yhoogstrate/flaimapper/master/share/annotations/ncRNA_annotation/ncrnadb09.gtf *(mask file)* + +Installation +------------ + +The wrapper makes use of easy_install to install a python egg. Please +ensure you have easy_install installed. + +License +------- + +**flaimapper** and **wrapper**: + +GPL (>=3) + +**pysam**: + +The MIT License + +Contact +------- + +The tool wrapper has been written by Youri Hoogstrate from the Erasmus +Medical Center (Rotterdam, Netherlands). + + +Development +----------- + +* Repository-Maintainer: Youri Hoogstrate +* Repository-Developers: Youri Hoogstrate + +* Repository-Development: https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools + +The tool wrapper has been written by Youri Hoogstrate from the Erasmus +Medical Center (Rotterdam, Netherlands). + + </help> + + <citations> + <citation type="doi">10.1093/bioinformatics/btu696</citation> + </citations> +</tool> |
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| diff -r 000000000000 -r d6abffbc9ee7 flaimapper.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/flaimapper.xml Thu May 21 07:26:46 2015 -0400 |
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| @@ -0,0 +1,161 @@ +<?xml version="1.0" encoding="UTF-8"?> +<tool id="flaimapper" name="FlaiMapper" version="1.1.5.a"> + <description>Detect small ncRNA derived fragments using Fragment Location Annotation Identification Mapper.</description> + <requirements> + <requirement type="package" version="0.8.2.1">pysam</requirement> + <requirement type="package" version="1.1.5">flaimapper</requirement> + </requirements> + + <stdio> + <regex match="[fai_load] build FASTA index." source="stderr" level="log" /> + </stdio> + + <version_command>flaimapper --version</version_command> + + <command> + flaimapper + -v + -f $output_format + -o $output + -m $mask + -r $fasta + + #for $alignment in $alignments + $alignment + #end for + </command> + + <inputs> + <param name="alignments" type="data" format="bam" label="Alignment file(s)" help="Aligned small RNA-Seq reads which may not be fragmented. In case you add multiple BAM files, FlaiMapper will simply concatenate the data and perform one single analysis on the entire set of alignments." multiple="true" /> + + <param name="mask" type="data" format="gtf,gff,gff3" label="small ncRNA Annotation (gtf)" help="" /> + + <param name="fasta" type="data" format="fasta" label="Fasta sequence corresponding to reference genome" help="" /> + + <param name="output_format" type="select" label="Output format"> + <option value="1">Tabular (1 fragment per column)</option> + <option value="2">Tabular (1 precursor per column)</option> + <option value="3">GenBank</option> + <!-- option value="gtf">GTF/GFF</option --> + </param> + </inputs> + + <outputs> + <data format="tabular" name="output" label="${tool.name} on ${', '.join([ str(a.hid)+': '+a.name for a in $alignments ])}" /> + </outputs> + + <tests> + <test> + <param name="alignments" value="snord81.bam" ftype="bam" /> + <param name="mask" value="ncrnadb09.gtf" ftype="gtf" /> + <param name="fasta" value="ncrnadb09.fa" ftype="fasta" /> + <param name="output_format" value="1" /> + + <output name="output" file="snord81.flaimapper.txt" /> + </test> + </tests> + + <help> +FlaiMapper wrapper for Galaxy +============================= + +https://github.com/yhoogstrate/flaimapper +http://www.ncbi.nlm.nih.gov/pubmed/25338717 +http://dx.doi.org/10.1093/bioinformatics/btu696 + +Fragment Location Annotation Identification Mapper + +FlaiMapper: computational annotation of small ncRNA-derived fragments using RNA-seq high-throughput data. + + +Input +----- + +Alignments +********** + +Aligned reads from small RNA-Seq experiments have to be provided in the BAM format. +In case you add multiple BAM files, FlaiMapper will simply concatenate the data and perform one single analysis on the entire set of alignments. + +Mask File +********* + +There are two strategies to analyze using FlaiMapper: + +- Relative to mature ncRNA sequences +- Relative to chromosomes + +Therefore FlaiMapper requires a list of ncRNA annotations relative to the used reference genome for the alignment files. These ncRNA locations within the sequences provided in the FASTA file (MASK) regions should be provided in the GFF/GTF format: + +- http://genome.ucsc.edu/FAQ/FAQformat.html#format3 +- http://www.ensembl.org/info/website/upload/gff.html + +If you are making use of a ncRNA database that has no GTF file available you can make use of the galaxy tool **flaimapper-gtf-from-fasta** to create one. + + +You can access **ncRNAdb09** GTF file at the following URL: +https://raw.githubusercontent.com/yhoogstrate/flaimapper/master/share/annotations/ncRNA_annotation/ncrnadb09.gtf *(mask file)* + +Fasta sequence +************** + +The reference sequence should be provided in FASTA format. + +You can access **ncRNAdb09** FASTA file at the following URL: +https://raw.githubusercontent.com/yhoogstrate/flaimapper/master/share/annotations/ncRNA_annotation/ncrnadb09.fa *(reference file)* + +Example- and reference data +*************************** + +To align reads to ncRNA you need aligner specific indexed version of the reference. We have made +the following available for ncRNAdb09: + + - **Tophat1**: https://github.com/yhoogstrate/flaimapper/blob/master/share/annotations/ncRNA_annotation/ncrnadb09.bt2.tar.gz + - **Tophat2**: https://github.com/yhoogstrate/flaimapper/blob/master/share/annotations/ncRNA_annotation/ncrnadb09.bt2.tar.gz + +If you want to test FlaiMapper with example data you can obtain several +alignment files from the following directory tree: + +https://github.com/yhoogstrate/flaimapper/tree/master/share/small_RNA-seq_alignments + +Installation +------------ + +The wrapper makes use of easy_install to install a python egg. Please +ensure you have easy_install installed. + +License +------- + +**flaimapper** and **wrapper**: + +GPL (>=3) + +**pysam**: + +The MIT License + +Contact +------- + +The tool wrapper has been written by Youri Hoogstrate from the Erasmus +Medical Center (Rotterdam, Netherlands). + + +Development +----------- + +* Repository-Maintainer: Youri Hoogstrate +* Repository-Developers: Youri Hoogstrate + +* Repository-Development: https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools + +The tool wrapper has been written by Youri Hoogstrate from the Erasmus +Medical Center (Rotterdam, Netherlands). + + </help> + + <citations> + <citation type="doi">10.1093/bioinformatics/btu696</citation> + </citations> +</tool> |
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@@\n+>HGNC=35371&HUGO-Symbol=MIR1306&HUGO-Name=microRNA_1306&LOCI=[chr22:20073571-20073675:strand=+]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_031706&GENOME=hg19\n+GCGCTGCCCCGTGAGCAGTCTCCACCACCTCCCCTGCAAACGTCCAGTGGTGCAGAGGTAATGGACGTTGGCTCTGGTGGTGATGGACAGTCCGAACTCCCTGCT\n+>HGNC=35334&HUGO-Symbol=MIR1266&HUGO-Name=microRNA_1266&LOCI=[chr15:52569304-52569407:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_031670&GENOME=hg19\n+TTGATGCTAGACAGGTAGTGTCCCTCAGGGCTGTAGAACAGGGCTGGGATTACTAAAGCCCTGTTCTATGCCCTGAGGGACACTGAGCATGTCATTTCACTTCT\n+>HGNC=38360&HUGO-Symbol=MIR4290&HUGO-Name=microRNA_4290&LOCI=[chr9:92785713-92785827:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_036253&GENOME=hg19\n+ATGGTGGGCTGCCACCAAGAAGGTGAAGGGAGGGTCAGTCCCAATCTGAATCCCACCAAAATAGGTGGTAGAGGGTTGCCCTCCTTTCTTCCCTCACCTCTGACCCCGCTCTTCG\n+>HGNC=38349&HUGO-Symbol=MIR323B&HUGO-Name=microRNA_323b&LOCI=[chr14:101522546-101522647:strand=+]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_029969&GENOME=hg19\n+TGCCACCTCATGGTACTCGGAGGGAGGTTGTCCGTGGTGAGTTCGCATTATTTAATGATGCCCAATACACGGTCGACCTCTTTTCGGTATCAGATCTCACCA\n+>HGNC=38901&HUGO-Symbol=MIR3927&HUGO-Name=microRNA_3927&LOCI=[chr9:112273745-112273835:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_037493&GENOME=hg19\n+AACCCCAATATGCCAATGCCTATCACATATCTGCCTGTCCTATGACAAACATGGCAGGTAGATATTTGATAGGCATTGGCACACTGGCAAA\n+>HGNC=38982&HUGO-Symbol=MIR3668&HUGO-Name=microRNA_3668&LOCI=[chr6:140526379-140526473:strand=+]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_037441&GENOME=hg19\n+CTGGCCTAAAATATATGAAATGTAGAGATTGATCAAAATAGTTTCTATCAAAATAGTTTTGATCAATCTCTGCAATTTTATATATGAGGAAACTG\n+>HGNC=32900&HUGO-Symbol=MIR644&HUGO-Name=microRNA_644&LOCI=[chr20:33054120-33054233:strand=+]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_030374&GENOME=hg19\n+TTTTTGCTGATTTTTTTTTAGTATTTTTCCATCAGTGTTCATAAGGAATGTTGCTCTGTAGTTTTCTTATAGTGTGGCTTTCTTAGAGCAAAGATGGTTCCCTATTACTTTCTA\n+>HGNC=38257&HUGO-Symbol=MIR4307&HUGO-Name=microRNA_4307&LOCI=[chr14:27377838-27377941:strand=+]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_036193&GENOME=hg19\n+AAATGGGCTTTCAGAAGAAAAAACAGGAGATAAAGTTTGTGATAATGTTTGTCTATATAGTTATGAATGTTTTTTCCTGTTTCCTTCAGGGCCATAATACTCCC\n+>HGNC=33034&HUGO-Symbol=SNORD115-15&HUGO-Name=small_nucleolar_RNA,_C/D_box_115-15&LOCI=[chr15:25442713-25442813:strand=+]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003307.1&GENOME=hg19\n+GTCCTGGGTTGGGTCGATGATGAGAACCTTATATGTTCTGAAGAGAGGTGATGACTTAAAAATCATGCTCAATAGGATTACGCTGAGGCCCAGCCTAGGTG\n+>HGNC=35347&HUGO-Symbol=MIR1276&HUGO-Name=microRNA_1276&LOCI=[chr15:86313717-86313819:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_031682&GENOME=hg19\n+CCATCACTTGCCCCAGCTAGGTAAAGAGCCCTGTGGAGACACCTGGATTCAGAGAACATGTCTCCACTGAGCACTTGGGCCTTGATGGCGGCTCTTGTTCCAA\n+>HGNC=41574&HUGO-Symbol=MIR4673&HUGO-Name=microRNA_4673&LOCI=[chr9:139414010-139414088:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_039820&GENOME=hg19\n+TGTGTCGGGGGTCCAGGCAGGAGCCGGACTGGACCTCAGGGAAGAGGCTGACCCGGCCCCTCTTGCGGCAGGCTTCACC\n+>HGNC=41792&HUGO-Symbol=MIR4482&HUGO-Name=microRNA_4482&LOCI=[chr10:106028084-106028173:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_039702&GENOME=hg19\n+AAAATTGAATAGTGAGCAACCCAGTGGGCTATGGAAATGTGTGGAAGATGGCATTTCTATTTCTCAGTGGGGCTCTTACCTATTACTCAT\n+>HGNC=32981&HUGO-Symbol=SNORD113-2&HUGO-Name=small_nucleolar_RNA,_C/D_box_113-2&LOCI=[chr14:101393669-101393759:strand=+]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003230.1&GENOME=hg19\n+TATGTCAAGTATAGCCAATCATTAGTATTCTGAGCTGTAGGAATCAAAGATTTTGATTAGATTCTGTAACTCAGAGGTTTATTAGAAAAAA\n+>HGNC=31495&HUGO-Symbol=MIR106B&HUGO-Name=microRNA_106b&LOCI=[chr7:99691606-99691707:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_029831&GENOME=hg19\n+CCGCTCCAGCCCTGCCGGGGCTAAAGTGCTGACAGTGCAGATAGTGGTCCTCTCCGTGCTACCGCACTGTGGGTACTTGCTGCTCCAGCAGGGCACGCACAG\n+>HGNC=33053&HUGO-Symbol=SNORD115-34&HUGO-Name=small_nucleolar_RNA,_C/D_box_115-34&LOCI=[chr15:25477524-25477625:strand=+]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003349.1&GENOME=hg19\n+GTCCTAGGTTGGGTCAATGATGAGAACCTTATAATGTTCTGAAGAGAGGTGATGACTTAAAAATCATGCTCAATAGGATTACGCTGAGGCCCAGCCTAGGTG\n+>HGNC=30355&HUGO-Symbol=SNORD38A&HUGO-Name=small_nucleolar_RNA,_C/D_box_38A&LOCI=[chr1:45243504-45243594:strand=+]'..b'ME=TRNAValTAC&LOCI=[chr11:59318460-59318532:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chr11.tRNA16-ValTAC&GENOME=hg19\n+GGTTCCATAGTGTAGCGGTtATCACGTCTGCTTTACACGCAGAAGGtCCTGGGTTCGAGCCCCAGTGGAACCAcca\n+>NAME=TRNAAsnGTT&LOCI=[chr1:149326272-149326345:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chr1.tRNA97-AsnGTT&GENOME=hg19\n+GTCTCTGTGGCGCAATCGGCtAGCGCGTTTGGCTGTTAACTAAAAAGtTGGTGGTTCGAACACACCCAGAGGCGcca\n+>NAME=TRNAAsnGTT&LOCI=[chr1:148760356-148760429:strand=-&chr1:148598314-148598387:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chr1.tRNA107-AsnGTT&GENOME=hg19\n+GTCTCTGTGGCGCAATCGGTtAGCGCATTCGGCTGTTAACCGAAAGGtTGGTGGTTCGAGCCCACCCAGGGACGcca\n+>NAME=TRNAUndet???&LOCI=[chr1:178678038-178678110:strand=+]&SOURCE=UCSC&SOURCE-ACCESSION=chr1.tRNA53-Undet???&GENOME=hg19\n+GGCAGTAAAGTAGGGTGGTtAAGACAAGGGGCTCTGGAGCAAGACTGCCCAAGATCAAATCCTGGTGCTGCCAcca\n+>NAME=TRNATyrGTA&LOCI=[chr2:27273650-27273738:strand=+]&SOURCE=UCSC&SOURCE-ACCESSION=chr2.tRNA2-TyrGTA&GENOME=hg19\n+CCTTCGATAGCTCAGTTGGTAGAGCGGAGGACTGTAGATCCTTAGGtCGCTGGTTCGATTCCGGCTCGAAGGAcca\n+>NAME=TRNAValTAC&LOCI=[chr10:5895674-5895746:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chr10.tRNA6-ValTAC&GENOME=hg19\n+GGTTCCATAGTGTAGTGGTtATCACATCTGCTTTACACGCAGAAGGtCCTGGGTTCAAGCCCCAGTGGAACCAcca\n+>NAME=TRNASerTGA&LOCI=[chr10:69524261-69524342:strand=+]&SOURCE=UCSC&SOURCE-ACCESSION=chr10.tRNA2-SerTGA&GENOME=hg19\n+GCAGCGATGGCCGAGTGGTtAAGGCGTTGGACTTGAAATCCAATGGGGTCTCCCCGCGCAGGTTCGAACCCTGCTCGCTGCGcca\n+>NAME=TRNALysCTT&LOCI=[chr1:55423542-55423614:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chr1.tRNA128-LysCTT&GENOME=hg19\n+GCCCAGCTAGCTCAGTCGGTAGAGCATGAGACTCTTAATCTCAGGGtCATGGGTTTGAGCCCCACGTTTGGTGcca\n+>NAME=TRNAUndet???&LOCI=[chr17:66390957-66391031:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chr17.tRNA22-Undet???&GENOME=hg19\n+GGCAGAATGGTGCAGCGGTtcAGCACCCAGGCTCTGCAGCCAGCTGTTGCCTGGGCTCAAATCCCAGCTCTGCCAcca\n+>HGNC=30357&HUGO-Symbol=SNORD13P1&HUGO-Name=small_nucleolar_RNA,_C/D_box_13_pseudogene 1&LOCI=[chr22:42471953-42472275:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NG_008259&GENOME=hg19\n+ATTGTTGAACTATAGGGTATGAACTATAGGGTGTCCAGTGTACAGCATTTTATGGCTACTTGGTGTCACTCTAGAGCCACATAGCAAGTGGCTTCAAGAGGTAATTCTTGATCCTTTTGTAGTTCATGAGCGTGATGATTGGGTGTTCACATGCATGTGTGAGCTGTGCCACCCTCGAACCTTGTTACCATGTAGGCACATTACCGATCTGACATGAAGAAAAGAAAAGAAAAAAAAAGAAAAAGAGATAATTCTTTAGCTCAAGGGAGGAGTAAGACTTGACAGCTGTTGCGTTTCAGTATGTCTGGGCCTGATTATTTAAA\n+>HGNC=10111&HUGO-Symbol=SNORD13P2&HUGO-Name=small_nucleolar_RNA,_C/D_box_13_pseudogene_2&LOCI=[chr7:4728950-4729374:strand=+]&SOURCE=RefSeq&SOURCE-ACCESSION=NG_008260&GENOME=hg19\n+ATACGTGGCTGGGTTGCCATGCTCCATCTGCTGAGAGGCGTATTGTGAGTGGCAGGTGTTATGGATCACAGCCTCTGCATATGTGCCAGCAGAAAAAGTAATTGTAACCAGCAAAGCATTTTACTACATAAACGTTTTAGCCCCTATAAAAACATCCGGAGATCCTTTTGTTGTTCATGAGCATGACAATTGGGTGTTTTCATGCAGCGAGTGAGATGTGCCACCCTGGAACCTTGTTACGACGTCGCATGTTACCTGTCTGACCTGAAAAATAATTAATAAGTAAAACATACGGAAGCCAGTTTCTCATGGCTATTTCCAACTAGTCACTTGAAGAATATGGAATTAGTTATACAATTAGTTATACGTTGTATAACCATCATAAAATTAGTTACAGATTGATGTGACATTATCTTGAAATTAAT\n+>HGNC=10112&HUGO-Symbol=SNORD13P3&HUGO-Name=small_nucleolar_RNA,_C/D_box_13_pseudogene_3&LOCI=[chr3:47291905-47292226:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NG_008261&GENOME=hg19\n+GAGGGTTCTCAGCTTGAAGTTCCTTGTGCCTCTTTTAGGGAAGACACTCAGATGGTATATCGAGTATAAAATGACTTAGCGATTCTTCTCCTCAAAATGTGTCATTTATGATCCTTTTGTAGTTCATGAGTGTGATGATTGTGTGTTCATACGCTTGTGTGAGATGTGCCACCCTTGAACCTTGTTACGACATTGGCACATTACCCGTCTGATCTGAAAAAAAAAGTATCATTTATTTACTTACCTAAAATCTATGGAGTGCTTACTATGTGCCAAGTGCTTTTTAAAGCACTTGGAATACCTGACTGCATGAACAGAAACA\n+>HGNC=30357&HUGO-Symbol=SNORD73B&HUGO-Name=small_nucleolar_RNA,_C/D_box_U73B_(pseudogene)&LOCI=[chr4:152023199-152023293:strand=+]&SOURCE=UCSC&SOURCE-ACCESSION=U73b&GENOME=hg19\n+TGTATGTGGGAATGAATGATGACAAAATGTTTCAGTCCCAAATGATACATACTGATTATACCATTATATTTATCCTGACATTCCTCTAAGGCTTT\n+>HGNC=23027&HUGO-Symbol=VTRNA3-1P&HUGO-Name=vault_RNA_3-1,_pseudogene&LOCI=[chrX:53489141-53489261:strand=+]&SOURCE=RefSeq&SOURCE-ACCESSION=NG_007501&GENOME=hg19\n+TGCCTCTAGGGGCTGGCTTTAGCTCAGCGGTTACTTCGACAATGCTTTCCATGGTTAGGAAACCAACCTCTCTGGGTGGTTTGAGACCCGTGGGCCCTCTCCAGTCCTTTTGTGGTCGCCA\n' 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| b'@@ -0,0 +1,2269 @@\n+HGNC=35371&HUGO-Symbol=MIR1306&HUGO-Name=microRNA_1306&LOCI=[chr22:20073571-20073675:strand=+]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_031706&GENOME=hg19\t105\t149\t105\t106\n+HGNC=35334&HUGO-Symbol=MIR1266&HUGO-Name=microRNA_1266&LOCI=[chr15:52569304-52569407:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_031670&GENOME=hg19\t104\t404\t104\t105\n+HGNC=38360&HUGO-Symbol=MIR4290&HUGO-Name=microRNA_4290&LOCI=[chr9:92785713-92785827:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_036253&GENOME=hg19\t115\t657\t115\t116\n+HGNC=38349&HUGO-Symbol=MIR323B&HUGO-Name=microRNA_323b&LOCI=[chr14:101522546-101522647:strand=+]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_029969&GENOME=hg19\t102\t924\t102\t103\n+HGNC=38901&HUGO-Symbol=MIR3927&HUGO-Name=microRNA_3927&LOCI=[chr9:112273745-112273835:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_037493&GENOME=hg19\t91\t1177\t91\t92\n+HGNC=38982&HUGO-Symbol=MIR3668&HUGO-Name=microRNA_3668&LOCI=[chr6:140526379-140526473:strand=+]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_037441&GENOME=hg19\t95\t1419\t95\t96\n+HGNC=32900&HUGO-Symbol=MIR644&HUGO-Name=microRNA_644&LOCI=[chr20:33054120-33054233:strand=+]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_030374&GENOME=hg19\t114\t1662\t114\t115\n+HGNC=38257&HUGO-Symbol=MIR4307&HUGO-Name=microRNA_4307&LOCI=[chr14:27377838-27377941:strand=+]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_036193&GENOME=hg19\t104\t1926\t104\t105\n+HGNC=33034&HUGO-Symbol=SNORD115-15&HUGO-Name=small_nucleolar_RNA,_C/D_box_115-15&LOCI=[chr15:25442713-25442813:strand=+]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003307.1&GENOME=hg19\t101\t2208\t101\t102\n+HGNC=35347&HUGO-Symbol=MIR1276&HUGO-Name=microRNA_1276&LOCI=[chr15:86313717-86313819:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_031682&GENOME=hg19\t103\t2459\t103\t104\n+HGNC=41574&HUGO-Symbol=MIR4673&HUGO-Name=microRNA_4673&LOCI=[chr9:139414010-139414088:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_039820&GENOME=hg19\t79\t2713\t79\t80\n+HGNC=41792&HUGO-Symbol=MIR4482&HUGO-Name=microRNA_4482&LOCI=[chr10:106028084-106028173:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_039702&GENOME=hg19\t90\t2944\t90\t91\n+HGNC=32981&HUGO-Symbol=SNORD113-2&HUGO-Name=small_nucleolar_RNA,_C/D_box_113-2&LOCI=[chr14:101393669-101393759:strand=+]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003230.1&GENOME=hg19\t91\t3212\t91\t92\n+HGNC=31495&HUGO-Symbol=MIR106B&HUGO-Name=microRNA_106b&LOCI=[chr7:99691606-99691707:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_029831&GENOME=hg19\t102\t3452\t102\t103\n+HGNC=33053&HUGO-Symbol=SNORD115-34&HUGO-Name=small_nucleolar_RNA,_C/D_box_115-34&LOCI=[chr15:25477524-25477625:strand=+]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003349.1&GENOME=hg19\t102\t3732\t102\t103\n+HGNC=30355&HUGO-Symbol=SNORD38A&HUGO-Name=small_nucleolar_RNA,_C/D_box_38A&LOCI=[chr1:45243504-45243594:strand=+]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_001456&GENOME=hg19\t91\t4003\t91\t92\n+HGNC=35310&HUGO-Symbol=MIR1244-1&HUGO-Name=microRNA_1244-1&LOCI=[chr2:232578014-232578118:strand=+&chr5:118310271-118310375:strand=+&chr12:9392053-9392157:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_036052&GENOME=hg19&MERGED=[HGNC=38321&HGNC=38390]\t105\t4345\t105\t106\n+HGNC=32608&HUGO-Symbol=SNORA18&HUGO-Name=small_nucleolar_RNA,_H/ACA_box_18&LOCI=[chr11:93466622-93466773:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_002959&GENOME=hg19\t152\t4620\t152\t153\n+HGNC=32589&HUGO-Symbol=SNORA5B&HUGO-Name=small_nucleolar_RNA,_H/ACA_box_5B&LOCI=[chr7:45145557-45145708:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_002990&GENOME=hg19\t152\t4941\t152\t153\n+HGNC=38301&HUGO-Symbol=MIR4305&HUGO-Name=microRNA_4305&LOCI=[chr13:40238161-40238282:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_036190&GENOME=hg19\t122\t5243\t122\t123\n+HGNC=38271&HUGO-Symbol=MIR3162&HUGO-Name=microRNA_3162&LOCI=[chr11:59362540-59362641:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_036120&GENOME=hg19\t102\t5515\t102\t103\n+HGNC=33680&HUGO-Symbol=MIR937&HUGO-Name=microRNA_937&LOCI=[chr8:144895117-144895222:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_030633&GENOME=hg19\t106\t5766\t106\t107\n+HGNC=38339&HUGO-Symbol=MIR4273&HUGO-Name=microRNA_4273&LOCI=[chr3:75787421-75787524:strand=+]&SOURCE=Ref'..b'=+]&SOURCE=UCSC&SOURCE-ACCESSION=chr16.tRNA10-LysCTT&GENOME=hg19\t76\t573624\t76\t77\n+NAME=TRNAGlnTTG&LOCI=[chr16:3419813-3419884:strand=+]&SOURCE=UCSC&SOURCE-ACCESSION=chr16.tRNA14-GlnTTG&GENOME=hg19\t75\t573817\t75\t76\n+NAME=TRNAGluCTC&LOCI=[chr1:249168447-249168518:strand=+]&SOURCE=UCSC&SOURCE-ACCESSION=chr1.tRNA59-GluCTC&GENOME=hg19\t75\t574011\t75\t76\n+NAME=TRNAValTAC&LOCI=[chrX:18693029-18693101:strand=-&chr11:59318102-59318174:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chrX.tRNA4-ValTAC&GENOME=hg19\t76\t574235\t76\t77\n+NAME=TRNAGlnCTG&LOCI=[chr1:149079364-149079435:strand=+]&SOURCE=UCSC&SOURCE-ACCESSION=chr1.tRNA27-GlnCTG&GENOME=hg19\t75\t574430\t75\t76\n+NAME=TRNAGluCTC&LOCI=[chr3:103879524-103879595:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chr3.tRNA10-GluCTC&GENOME=hg19\t75\t574624\t75\t76\n+NAME=TRNAValCAC&LOCI=[chr1:149684088-149684161:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chr1.tRNA90-ValCAC&GENOME=hg19\t77\t574818\t77\t78\n+NAME=TRNAGlnCTG&LOCI=[chr10:20036608-20036682:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chr10.tRNA5-GlnCTG&GENOME=hg19\t78\t575013\t78\t79\n+NAME=TRNALysCTT&LOCI=[chr15:76674765-76674838:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chr15.tRNA6-LysCTT&GENOME=hg19\t77\t575209\t77\t78\n+NAME=TRNAGluCTC&LOCI=[chrX:51306112-51306183:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chrX.tRNA3-GluCTC&GENOME=hg19\t75\t575402\t75\t76\n+NAME=TRNAAsnGTT&LOCI=[chr1:145979034-145979107:strand=-&chr1:147520767-147520840:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chr1.tRNA113-AsnGTT&GENOME=hg19\t77\t575631\t77\t78\n+NAME=TRNALysTTT&LOCI=[chr2:224186315-224186387:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chr2.tRNA16-LysTTT&GENOME=hg19\t76\t575827\t76\t77\n+NAME=TRNAGlyCCC&LOCI=[chr17:19764175-19764245:strand=+]&SOURCE=UCSC&SOURCE-ACCESSION=chr17.tRNA13-GlyCCC&GENOME=hg19\t74\t576022\t74\t75\n+NAME=TRNASerAGA&LOCI=[chr6:27509554-27509635:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chr6.tRNA147-SerAGA&GENOME=hg19\t85\t576214\t85\t86\n+NAME=TRNAValTAC&LOCI=[chr11:59318460-59318532:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chr11.tRNA16-ValTAC&GENOME=hg19\t76\t576418\t76\t77\n+NAME=TRNAAsnGTT&LOCI=[chr1:149326272-149326345:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chr1.tRNA97-AsnGTT&GENOME=hg19\t77\t576613\t77\t78\n+NAME=TRNAAsnGTT&LOCI=[chr1:148760356-148760429:strand=-&chr1:148598314-148598387:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chr1.tRNA107-AsnGTT&GENOME=hg19\t77\t576844\t77\t78\n+NAME=TRNAUndet???&LOCI=[chr1:178678038-178678110:strand=+]&SOURCE=UCSC&SOURCE-ACCESSION=chr1.tRNA53-Undet???&GENOME=hg19\t76\t577044\t76\t77\n+NAME=TRNATyrGTA&LOCI=[chr2:27273650-27273738:strand=+]&SOURCE=UCSC&SOURCE-ACCESSION=chr2.tRNA2-TyrGTA&GENOME=hg19\t76\t577236\t76\t77\n+NAME=TRNAValTAC&LOCI=[chr10:5895674-5895746:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chr10.tRNA6-ValTAC&GENOME=hg19\t76\t577428\t76\t77\n+NAME=TRNASerTGA&LOCI=[chr10:69524261-69524342:strand=+]&SOURCE=UCSC&SOURCE-ACCESSION=chr10.tRNA2-SerTGA&GENOME=hg19\t85\t577622\t85\t86\n+NAME=TRNALysCTT&LOCI=[chr1:55423542-55423614:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chr1.tRNA128-LysCTT&GENOME=hg19\t76\t577825\t76\t77\n+NAME=TRNAUndet???&LOCI=[chr17:66390957-66391031:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chr17.tRNA22-Undet???&GENOME=hg19\t78\t578024\t78\t79\n+HGNC=30357&HUGO-Symbol=SNORD13P1&HUGO-Name=small_nucleolar_RNA,_C/D_box_13_pseudogene\t323\t578285\t323\t324\n+HGNC=10111&HUGO-Symbol=SNORD13P2&HUGO-Name=small_nucleolar_RNA,_C/D_box_13_pseudogene_2&LOCI=[chr7:4728950-4729374:strand=+]&SOURCE=RefSeq&SOURCE-ACCESSION=NG_008260&GENOME=hg19\t425\t578788\t425\t426\n+HGNC=10112&HUGO-Symbol=SNORD13P3&HUGO-Name=small_nucleolar_RNA,_C/D_box_13_pseudogene_3&LOCI=[chr3:47291905-47292226:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NG_008261&GENOME=hg19\t322\t579395\t322\t323\n+HGNC=30357&HUGO-Symbol=SNORD73B&HUGO-Name=small_nucleolar_RNA,_C/D_box_U73B_(pseudogene)&LOCI=[chr4:152023199-152023293:strand=+]&SOURCE=UCSC&SOURCE-ACCESSION=U73b&GENOME=hg19\t95\t579895\t95\t96\n+HGNC=23027&HUGO-Symbol=VTRNA3-1P&HUGO-Name=vault_RNA_3-1,_pseudogene&LOCI=[chrX:53489141-53489261:strand=+]&SOURCE=RefSeq&SOURCE-ACCESSION=NG_007501&GENOME=hg19\t121\t580153\t121\t122\n' |
| b |
| diff -r 000000000000 -r d6abffbc9ee7 test-data/ncrnadb09.gtf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ncrnadb09.gtf Thu May 21 07:26:46 2015 -0400 |
| [ |
| b'@@ -0,0 +1,2269 @@\n+HGNC=35371&HUGO-Symbol=MIR1306&HUGO-Name=microRNA_1306&LOCI=[chr22:20073571-20073675:strand=+]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_031706&GENOME=hg19\tflaimapper\tncRNA\t0\t105\t1\t+\t0\n+HGNC=35334&HUGO-Symbol=MIR1266&HUGO-Name=microRNA_1266&LOCI=[chr15:52569304-52569407:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_031670&GENOME=hg19\tflaimapper\tncRNA\t0\t104\t1\t-\t0\n+HGNC=38360&HUGO-Symbol=MIR4290&HUGO-Name=microRNA_4290&LOCI=[chr9:92785713-92785827:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_036253&GENOME=hg19\tflaimapper\tncRNA\t0\t115\t1\t-\t0\n+HGNC=38349&HUGO-Symbol=MIR323B&HUGO-Name=microRNA_323b&LOCI=[chr14:101522546-101522647:strand=+]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_029969&GENOME=hg19\tflaimapper\tncRNA\t0\t102\t1\t+\t0\n+HGNC=38901&HUGO-Symbol=MIR3927&HUGO-Name=microRNA_3927&LOCI=[chr9:112273745-112273835:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_037493&GENOME=hg19\tflaimapper\tncRNA\t0\t91\t1\t-\t0\n+HGNC=38982&HUGO-Symbol=MIR3668&HUGO-Name=microRNA_3668&LOCI=[chr6:140526379-140526473:strand=+]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_037441&GENOME=hg19\tflaimapper\tncRNA\t0\t95\t1\t+\t0\n+HGNC=32900&HUGO-Symbol=MIR644&HUGO-Name=microRNA_644&LOCI=[chr20:33054120-33054233:strand=+]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_030374&GENOME=hg19\tflaimapper\tncRNA\t0\t114\t1\t+\t0\n+HGNC=38257&HUGO-Symbol=MIR4307&HUGO-Name=microRNA_4307&LOCI=[chr14:27377838-27377941:strand=+]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_036193&GENOME=hg19\tflaimapper\tncRNA\t0\t104\t1\t+\t0\n+HGNC=33034&HUGO-Symbol=SNORD115-15&HUGO-Name=small_nucleolar_RNA,_C/D_box_115-15&LOCI=[chr15:25442713-25442813:strand=+]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003307.1&GENOME=hg19\tflaimapper\tncRNA\t0\t101\t1\t+\t0\n+HGNC=35347&HUGO-Symbol=MIR1276&HUGO-Name=microRNA_1276&LOCI=[chr15:86313717-86313819:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_031682&GENOME=hg19\tflaimapper\tncRNA\t0\t103\t1\t-\t0\n+HGNC=41574&HUGO-Symbol=MIR4673&HUGO-Name=microRNA_4673&LOCI=[chr9:139414010-139414088:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_039820&GENOME=hg19\tflaimapper\tncRNA\t0\t79\t1\t-\t0\n+HGNC=41792&HUGO-Symbol=MIR4482&HUGO-Name=microRNA_4482&LOCI=[chr10:106028084-106028173:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_039702&GENOME=hg19\tflaimapper\tncRNA\t0\t90\t1\t-\t0\n+HGNC=32981&HUGO-Symbol=SNORD113-2&HUGO-Name=small_nucleolar_RNA,_C/D_box_113-2&LOCI=[chr14:101393669-101393759:strand=+]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003230.1&GENOME=hg19\tflaimapper\tncRNA\t0\t91\t1\t+\t0\n+HGNC=31495&HUGO-Symbol=MIR106B&HUGO-Name=microRNA_106b&LOCI=[chr7:99691606-99691707:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_029831&GENOME=hg19\tflaimapper\tncRNA\t0\t102\t1\t-\t0\n+HGNC=33053&HUGO-Symbol=SNORD115-34&HUGO-Name=small_nucleolar_RNA,_C/D_box_115-34&LOCI=[chr15:25477524-25477625:strand=+]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003349.1&GENOME=hg19\tflaimapper\tncRNA\t0\t102\t1\t+\t0\n+HGNC=30355&HUGO-Symbol=SNORD38A&HUGO-Name=small_nucleolar_RNA,_C/D_box_38A&LOCI=[chr1:45243504-45243594:strand=+]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_001456&GENOME=hg19\tflaimapper\tncRNA\t0\t91\t1\t+\t0\n+HGNC=35310&HUGO-Symbol=MIR1244-1&HUGO-Name=microRNA_1244-1&LOCI=[chr2:232578014-232578118:strand=+&chr5:118310271-118310375:strand=+&chr12:9392053-9392157:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_036052&GENOME=hg19&MERGED=[HGNC=38321&HGNC=38390]\tflaimapper\tncRNA\t0\t105\t1\t-\t0\n+HGNC=32608&HUGO-Symbol=SNORA18&HUGO-Name=small_nucleolar_RNA,_H/ACA_box_18&LOCI=[chr11:93466622-93466773:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_002959&GENOME=hg19\tflaimapper\tncRNA\t0\t152\t1\t-\t0\n+HGNC=32589&HUGO-Symbol=SNORA5B&HUGO-Name=small_nucleolar_RNA,_H/ACA_box_5B&LOCI=[chr7:45145557-45145708:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_002990&GENOME=hg19\tflaimapper\tncRNA\t0\t152\t1\t-\t0\n+HGNC=38301&HUGO-Symbol=MIR4305&HUGO-Name=microRNA_4305&LOCI=[chr13:40238161-40238282:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_036190&GENOME=hg19\tflaimapper\tncRNA\t0\t122\t1\t-\t0\n+HGNC=38271&HUGO-Symbol=MIR3162&HUGO-Name=microRNA_3162&LOCI=[chr11:59362540-59362641:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_036120&GENOME=hg19\tflaimapper\tncRNA\t0\t102\t1\t-\t0\n+H'..b'.tRNA59-GluCTC&GENOME=hg19\tflaimapper\tncRNA\t0\t75\t1\t+\t0\n+NAME=TRNAValTAC&LOCI=[chrX:18693029-18693101:strand=-&chr11:59318102-59318174:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chrX.tRNA4-ValTAC&GENOME=hg19\tflaimapper\tncRNA\t0\t76\t1\t-\t0\n+NAME=TRNAGlnCTG&LOCI=[chr1:149079364-149079435:strand=+]&SOURCE=UCSC&SOURCE-ACCESSION=chr1.tRNA27-GlnCTG&GENOME=hg19\tflaimapper\tncRNA\t0\t75\t1\t+\t0\n+NAME=TRNAGluCTC&LOCI=[chr3:103879524-103879595:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chr3.tRNA10-GluCTC&GENOME=hg19\tflaimapper\tncRNA\t0\t75\t1\t-\t0\n+NAME=TRNAValCAC&LOCI=[chr1:149684088-149684161:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chr1.tRNA90-ValCAC&GENOME=hg19\tflaimapper\tncRNA\t0\t77\t1\t-\t0\n+NAME=TRNAGlnCTG&LOCI=[chr10:20036608-20036682:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chr10.tRNA5-GlnCTG&GENOME=hg19\tflaimapper\tncRNA\t0\t78\t1\t-\t0\n+NAME=TRNALysCTT&LOCI=[chr15:76674765-76674838:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chr15.tRNA6-LysCTT&GENOME=hg19\tflaimapper\tncRNA\t0\t77\t1\t-\t0\n+NAME=TRNAGluCTC&LOCI=[chrX:51306112-51306183:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chrX.tRNA3-GluCTC&GENOME=hg19\tflaimapper\tncRNA\t0\t75\t1\t-\t0\n+NAME=TRNAAsnGTT&LOCI=[chr1:145979034-145979107:strand=-&chr1:147520767-147520840:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chr1.tRNA113-AsnGTT&GENOME=hg19\tflaimapper\tncRNA\t0\t77\t1\t-\t0\n+NAME=TRNALysTTT&LOCI=[chr2:224186315-224186387:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chr2.tRNA16-LysTTT&GENOME=hg19\tflaimapper\tncRNA\t0\t76\t1\t-\t0\n+NAME=TRNAGlyCCC&LOCI=[chr17:19764175-19764245:strand=+]&SOURCE=UCSC&SOURCE-ACCESSION=chr17.tRNA13-GlyCCC&GENOME=hg19\tflaimapper\tncRNA\t0\t74\t1\t+\t0\n+NAME=TRNASerAGA&LOCI=[chr6:27509554-27509635:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chr6.tRNA147-SerAGA&GENOME=hg19\tflaimapper\tncRNA\t0\t85\t1\t-\t0\n+NAME=TRNAValTAC&LOCI=[chr11:59318460-59318532:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chr11.tRNA16-ValTAC&GENOME=hg19\tflaimapper\tncRNA\t0\t76\t1\t-\t0\n+NAME=TRNAAsnGTT&LOCI=[chr1:149326272-149326345:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chr1.tRNA97-AsnGTT&GENOME=hg19\tflaimapper\tncRNA\t0\t77\t1\t-\t0\n+NAME=TRNAAsnGTT&LOCI=[chr1:148760356-148760429:strand=-&chr1:148598314-148598387:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chr1.tRNA107-AsnGTT&GENOME=hg19\tflaimapper\tncRNA\t0\t77\t1\t-\t0\n+NAME=TRNAUndet???&LOCI=[chr1:178678038-178678110:strand=+]&SOURCE=UCSC&SOURCE-ACCESSION=chr1.tRNA53-Undet???&GENOME=hg19\tflaimapper\tncRNA\t0\t76\t1\t+\t0\n+NAME=TRNATyrGTA&LOCI=[chr2:27273650-27273738:strand=+]&SOURCE=UCSC&SOURCE-ACCESSION=chr2.tRNA2-TyrGTA&GENOME=hg19\tflaimapper\tncRNA\t0\t76\t1\t+\t0\n+NAME=TRNAValTAC&LOCI=[chr10:5895674-5895746:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chr10.tRNA6-ValTAC&GENOME=hg19\tflaimapper\tncRNA\t0\t76\t1\t-\t0\n+NAME=TRNASerTGA&LOCI=[chr10:69524261-69524342:strand=+]&SOURCE=UCSC&SOURCE-ACCESSION=chr10.tRNA2-SerTGA&GENOME=hg19\tflaimapper\tncRNA\t0\t85\t1\t+\t0\n+NAME=TRNALysCTT&LOCI=[chr1:55423542-55423614:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chr1.tRNA128-LysCTT&GENOME=hg19\tflaimapper\tncRNA\t0\t76\t1\t-\t0\n+NAME=TRNAUndet???&LOCI=[chr17:66390957-66391031:strand=-]&SOURCE=UCSC&SOURCE-ACCESSION=chr17.tRNA22-Undet???&GENOME=hg19\tflaimapper\tncRNA\t0\t78\t1\t-\t0\n+HGNC=30357&HUGO-Symbol=SNORD13P1&HUGO-Name=small_nucleolar_RNA,_C/D_box_13_pseudogene\tflaimapper\tncRNA\t0\t323\t1\t-\t0\n+HGNC=10111&HUGO-Symbol=SNORD13P2&HUGO-Name=small_nucleolar_RNA,_C/D_box_13_pseudogene_2&LOCI=[chr7:4728950-4729374:strand=+]&SOURCE=RefSeq&SOURCE-ACCESSION=NG_008260&GENOME=hg19\tflaimapper\tncRNA\t0\t425\t1\t+\t0\n+HGNC=10112&HUGO-Symbol=SNORD13P3&HUGO-Name=small_nucleolar_RNA,_C/D_box_13_pseudogene_3&LOCI=[chr3:47291905-47292226:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NG_008261&GENOME=hg19\tflaimapper\tncRNA\t0\t322\t1\t-\t0\n+HGNC=30357&HUGO-Symbol=SNORD73B&HUGO-Name=small_nucleolar_RNA,_C/D_box_U73B_(pseudogene)&LOCI=[chr4:152023199-152023293:strand=+]&SOURCE=UCSC&SOURCE-ACCESSION=U73b&GENOME=hg19\tflaimapper\tncRNA\t0\t95\t1\t+\t0\n+HGNC=23027&HUGO-Symbol=VTRNA3-1P&HUGO-Name=vault_RNA_3-1,_pseudogene&LOCI=[chrX:53489141-53489261:strand=+]&SOURCE=RefSeq&SOURCE-ACCESSION=NG_007501&GENOME=hg19\tflaimapper\tncRNA\t0\t121\t1\t+\t0\n' |
| b |
| diff -r 000000000000 -r d6abffbc9ee7 test-data/snord81.bam |
| b |
| Binary file test-data/snord81.bam has changed |
| b |
| diff -r 000000000000 -r d6abffbc9ee7 test-data/snord81.flaimapper.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/snord81.flaimapper.txt Thu May 21 07:26:46 2015 -0400 |
| [ |
| @@ -0,0 +1,4 @@ +Fragment Precursor 5' 3' Sequence Corresponding-reads +HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19_Fragment_1 HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19 14 37 ATACATGATGATCTCAATCCAAC 99 +HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19_Fragment_2 HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19 46 68 CTCACTGATTACTTGATGACAA 171 +HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19_Fragment_3 HGNC=10101&HUGO-Symbol=SNORD81&HUGO-Name=small_nucleolar_RNA,_C/D_box_81&LOCI=[chr1:173833274-173833370:strand=-]&SOURCE=RefSeq&SOURCE-ACCESSION=NR_003938&GENOME=hg19 54 80 TTACTTGATGACAATAAAATATCTGA 82 |
| b |
| diff -r 000000000000 -r d6abffbc9ee7 tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Thu May 21 07:26:46 2015 -0400 |
| b |
| @@ -0,0 +1,8 @@ +<!-- Use the file tool_data_table_conf.xml.oldlocstyle if you don't want to update your loc files as changed in revision 4550:535d276c92bc--> +<tables> +<!-- Location of all GFF/GTF files --> +<table name="gene_sets" comment_char="#"> +<columns>name, dbkey, value, provider, reference</columns> +<file path="tool-data/gene_sets.loc" /> +</table> +</tables> \ No newline at end of file |
| b |
| diff -r 000000000000 -r d6abffbc9ee7 tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Thu May 21 07:26:46 2015 -0400 |
| b |
| @@ -0,0 +1,39 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="pysam" version="0.8.2.1"> + <repository changeset_revision="b8d22acd3017" name="package_pysam_0_8_2" owner="yhoogstrate" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + + <package name="flaimapper" version="1.1.5"> + <install version="1.0"> + <actions> + + <action type="set_environment_for_install"> + <repository changeset_revision="b8d22acd3017" name="package_pysam_0_8_2" owner="yhoogstrate" toolshed="https://toolshed.g2.bx.psu.edu"> + <package name="pysam" version="0.8.2.1" /> + </repository> + </action> + + <action type="make_directory">$INSTALL_DIR</action> + <action type="make_directory">$INSTALL_DIR/bin</action> + + <action type="shell_command">export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR:$INSTALL_DIR"/lib/python":$INSTALL_DIR"/lib64/python":$PYSAM_PATH:$PYSAM_PATH"/lib/python":$PYSAM_PATH"/lib64/python" ; easy_install --prefix=$INSTALL_DIR --install-dir=$INSTALL_DIR --script-dir=$INSTALL_DIR/bin $REPOSITORY_INSTALL_DIR"/egg/flaimapper-1.1.5-py2.7.egg"</action> + + <action type="set_environment"> + <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR:$INSTALL_DIR/lib/python:$INSTALL_DIR/lib64/python</environment_variable> + <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> + </action> + </actions> + </install> + + <readme> + Because I accidentally included too much large files within the + GitHub repository of FlaiMapper it is not convenient to use git + to pull the latest code from. Downloading simply takes way to + long and the package size is unnecessairy large. + + Instead, I have created an egg that can be installed using + easy_install. + </readme> + </package> +</tool_dependency> |