| Next changeset 1:ce26b5a859ba (2020-03-02) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2" |
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added:
all_fasta.loc.sample chira_merge.xml macros.xml test-data/alignments.bed test-data/annotation.gtf test-data/chimeras test-data/loci.counts test-data/merged.bed test-data/reads.fasta test-data/reads.fastq test-data/ref.fasta test-data/ref1.fasta test-data/ref2.fasta test-data/segments.bed test-data/singletons tool_data_table_conf.xml.sample |
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| diff -r 000000000000 -r 5db894671434 all_fasta.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/all_fasta.loc.sample Sun Jan 19 16:31:34 2020 -0500 |
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| @@ -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. +# |
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| diff -r 000000000000 -r 5db894671434 chira_merge.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/chira_merge.xml Sun Jan 19 16:31:34 2020 -0500 |
| [ |
| @@ -0,0 +1,97 @@ +<tool id="chira_merge" name="ChiRA merge" version="@WRAPPER_VERSION@0"> + <description>merge aligned positions</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <command><![CDATA[ + chira_merge.py + -b '$alignments' + #if str($annotation.choice) == "yes": + -g '$annotation.gtf' + #end if + -ao '$alignment_overlap' + -so '$segment_overlap' + -o ./ + ]]></command> + + <inputs> + <param format="bed" name="alignments" type="data" label="Input BED file of alignments"/> + <conditional name="annotation"> + <param name="choice" type="select" label="Hybridize interacting loci?" + help="Hybridization is a time consuming process."> + <option value="yes">Yes</option> + <option value="no">No</option> + </param> + <when value="yes"> + <param format="gtf,gff" name="gtf" type="data" label="Annotations in GTF format"/> + </when> + <when value="no"> + <!-- Do nothing --> + </when> + </conditional> + <param name="alignment_overlap" type="float" value="0.7" label="Overlap fraction for merging alignments" min="0" max="1" + help="Minimum fraction of BED entries that must overlap inorder to merge"/> + <param name="segment_overlap" type="float" value="0.7" label="Overlap fraction for merging mapped read positions to segments" min="0" max="1" + help="Matching read positions with greater than this fraction overlap are merged into a segment"/> + </inputs> + <outputs> + <data format="bed" name="segments_bed" from_work_dir="segments.bed" label="ChiRA aligned read segments on ${on_string}"/> + <data format="tabular" name="merged_bed" from_work_dir="merged.bed" label="ChiRA merged alignments on ${on_string}"/> + </outputs> + + <tests> + <!-- Test: Map without annotation --> + <test expect_num_outputs="2"> + <param name="alignments" value="alignments.bed"/> + <param name="choice" value="no" /> + <output name="segments_bed" > + <assert_contents> + <has_text_matching expression="ENSMUST00000160533\t69\t82\t6|1|4,ENSMUST00000160533,69,82,+,42S13M\t0\t+" /> + </assert_contents> + </output> + <output name="merged_bed" > + <assert_contents> + <has_text_matching expression="ENSMUST00000182010\t19\t74\t+\t6|1|1,ENSMUST00000182010,19,68,+,5S49M1S;7|9|1,ENSMUST00000182010,24,74,+,5S50M" /> + </assert_contents> + </output> + </test> + <!-- Test: Map with annotation --> + <test expect_num_outputs="2"> + <param name="alignments" value="alignments.bed" /> + <param name="choice" value="yes" /> + <param name="gtf" value="annotation.gtf" /> + <output name="segments_bed" > + <assert_contents> + <has_text_matching expression="5\t137142331\t137142344\t6|1|4,ENSMUST00000160533,69,82,+,42S13M\t0\t-" /> + </assert_contents> + </output> + <output name="merged_bed" > + <assert_contents> + <has_text_matching expression="17\t39846976\t39847031\t+\t6|1|1,ENSMUST00000182010,19,68,+,5S49M1S;7|9|1,ENSMUST00000182010,24,74,+,5S50M" /> + </assert_contents> + </output> + </test> + </tests> + + <help> + +.. class:: infomark + +**What it does** + +This tool merges the overlapping aligned positions to define the read concentrated loci. If an annotation GTF file produced, the transcriptomic alignment positions are first converted to their corresponding genomic positions. + +**Inputs** + +* Alignments in BED format +* An annotation GTF file contaning reference genomic positions. + +**Output** + +* BED file containing the alignments with reads categorized into segments depending on which part of the read is aligned. +* Tabular file containing merged alignments. 4th column contains all the alignments merged into that location. + + </help> + <expand macro="citations" /> +</tool> |
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| diff -r 000000000000 -r 5db894671434 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Sun Jan 19 16:31:34 2020 -0500 |
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| @@ -0,0 +1,15 @@ +<macros> + <token name="@WRAPPER_VERSION@">@TOOL_VERSION@+galaxy</token> + <token name="@TOOL_VERSION@">1.0.2</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">chira</requirement> + <yield/> + </requirements> + </xml> + <xml name="citations"> + <citations> + <yield /> + </citations> + </xml> +</macros> |
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| diff -r 000000000000 -r 5db894671434 test-data/alignments.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/alignments.bed Sun Jan 19 16:31:34 2020 -0500 |
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| b'@@ -0,0 +1,337 @@\n+mmu-miR-124-3p\t0\t20\t3|2,mmu-miR-124-3p,0,20,+,5S20M30S\t0\t+\n+ENSMUST00000182884\t6023\t6051\t28|3,ENSMUST00000182884,6023,6051,+,27S28M\t0\t+\n+ENSMUST00000182010\t428\t477\t36|10,ENSMUST00000182010,428,477,+,5S49M1S\t0\t+\n+ENSMUST00000113560\t1969\t1992\t38|2,ENSMUST00000113560,1969,1992,+,32S23M\t0\t+\n+mmu-miR-9-5p\t0\t23\t11|1,mmu-miR-9-5p,0,23,+,5S23M27S\t0\t+\n+mmu-miR-9-5p\t0\t23\t38|2,mmu-miR-9-5p,0,23,+,5S23M27S\t0\t+\n+ENSMUST00000138581\t1621\t1644\t38|2,ENSMUST00000138581,1621,1644,+,32S23M\t0\t+\n+ENSMUST00000182010\t419\t468\t34|1,ENSMUST00000182010,419,468,+,5S49M1S\t0\t+\n+ENSMUST00000047061\t2204\t2232\t28|3,ENSMUST00000047061,2204,2232,+,27S28M\t0\t+\n+ENSMUST00000100207\t1580\t1603\t38|2,ENSMUST00000100207,1580,1603,+,32S23M\t0\t+\n+ENSMUST00000172109\t1499\t1514\t11|1,ENSMUST00000172109,1499,1514,+,35S15M5S\t0\t+\n+ENSMUST00000182795\t2429\t2457\t28|3,ENSMUST00000182795,2429,2457,+,27S28M\t0\t+\n+ENSMUST00000075326\t1661\t1684\t38|2,ENSMUST00000075326,1661,1684,+,32S23M\t0\t+\n+ENSMUST00000106215\t953\t1003\t21|3,ENSMUST00000106215,953,1003,+,5S50M\t0\t+\n+ENSMUST00000182439\t2218\t2246\t28|3,ENSMUST00000182439,2218,2246,+,27S28M\t0\t+\n+ENSMUST00000185502\t4240\t4290\t7|1,ENSMUST00000185502,4240,4290,+,5S50M\t0\t+\n+ENSMUST00000166060\t435\t467\t19|2,ENSMUST00000166060,435,467,+,26S12M3D17M\t0\t+\n+ENSMUST00000107857\t399\t431\t19|2,ENSMUST00000107857,399,431,+,26S12M3D17M\t0\t+\n+ENSMUST00000155835\t2617\t2667\t4|2,ENSMUST00000155835,2617,2667,+,5S50M\t0\t+\n+ENSMUST00000071555\t1077\t1127\t21|3,ENSMUST00000071555,1077,1127,+,5S50M\t0\t+\n+ENSMUST00000181221\t1499\t1514\t11|1,ENSMUST00000181221,1499,1514,+,35S15M5S\t0\t+\n+ENSMUST00000182010\t424\t474\t35|9,ENSMUST00000182010,424,474,+,5S50M\t0\t+\n+ENSMUST00000100208\t1748\t1771\t38|2,ENSMUST00000100208,1748,1771,+,32S23M\t0\t+\n+ENSMUST00000113562\t1759\t1782\t38|2,ENSMUST00000113562,1759,1782,+,32S23M\t0\t+\n+ENSMUST00000128302\t226\t257\t6|4,ENSMUST00000128302,226,257,+,24S31M\t0\t+\n+ENSMUST00000148758\t777\t805\t27|1,ENSMUST00000148758,777,805,+,27S28M\t0\t+\n+ENSMUST00000111596\t608\t626\t19|2,ENSMUST00000111596,608,626,+,30S18M7S\t0\t+\n+ENSMUST00000106992\t3071\t3121\t16|3,ENSMUST00000106992,3071,3121,+,5S50M\t0\t+\n+mmu-miR-9-5p\t0\t23\t32|1,mmu-miR-9-5p,0,23,+,5S23M27S\t0\t+\n+ENSMUST00000182972\t3233\t3261\t28|3,ENSMUST00000182972,3233,3261,+,27S28M\t0\t+\n+ENSMUST00000064989\t2466\t2516\t29|1,ENSMUST00000064989,2466,2516,+,5S50M\t0\t+\n+ENSMUST00000182029\t3343\t3371\t28|3,ENSMUST00000182029,3343,3371,+,27S28M\t0\t+\n+ENSMUST00000182010\t426\t476\t15|2,ENSMUST00000182010,426,476,+,5S50M\t0\t+\n+ENSMUST00000187980\t1254\t1305\t24|1,ENSMUST00000187980,1254,1305,+,4S51M\t0\t+\n+ENSMUST00000182692\t3374\t3402\t28|3,ENSMUST00000182692,3374,3402,+,27S28M\t0\t+\n+ENSMUST00000167541\t285\t336\t1|3,ENSMUST00000167541,285,336,+,4S51M\t0\t+\n+ENSMUST00000113564\t1723\t1746\t38|2,ENSMUST00000113564,1723,1746,+,32S23M\t0\t+\n+ENSMUST00000128500\t1065\t1088\t38|2,ENSMUST00000128500,1065,1088,+,32S23M\t0\t+\n+ENSMUST00000045218\t5944\t5972\t3|2,ENSMUST00000045218,5944,5972,+,27S28M\t0\t+\n+ENSMUST00000111134\t233\t264\t6|4,ENSMUST00000111134,233,264,+,24S31M\t0\t+\n+ENSMUST00000182010\t9\t59\t8|4,ENSMUST00000182010,9,59,+,5S50M\t0\t+\n+ENSMUST00000167930\t463\t495\t19|2,ENSMUST00000167930,463,495,+,26S12M3D17M\t0\t+\n+ENSMUST00000075012\t856\t906\t14|1,ENSMUST00000075012,856,906,+,5S50M\t0\t+\n+ENSMUST00000041591\t326\t377\t1|3,ENSMUST00000041591,326,377,+,4S51M\t0\t+\n+ENSMUST00000106746\t905\t955\t14|1,ENSMUST00000106746,905,955,+,5S50M\t0\t+\n+ENSMUST00000182437\t2388\t2416\t28|3,ENSMUST00000182437,2388,2416,+,27S28M\t0\t+\n+ENSMUST00000171545\t470\t521\t1|3,ENSMUST00000171545,470,521,+,4S51M\t0\t+\n+ENSMUST00000181455\t1765\t1780\t11|1,ENSMUST00000181455,1765,1780,+,35S15M5S\t0\t+\n+ENSMUST00000032571\t4128\t4178\t20|1,ENSMUST00000032571,4128,4178,+,5S15M1D34M\t0\t+\n+ENSMUST00000092432\t5519\t5547\t28|3,ENSMUST00000092432,5519,5547,+,27S28M\t0\t+\n+ENSMUST00000182010\t0\t47\t31|10,ENSMUST00000182010,0,47,+,8S47M\t0\t+\n+mmu-miR-124-3p\t0\t20\t19|2,mmu-miR-124-3p,0,20,+,6S20M29S\t0\t+\n+ENSMUST00000182010\t0\t44\t5|12,ENSMUST00000182010,0,44,+,9S44M2S\t0\t+\n+ENSMUST00000062147\t344\t394\t21|3,ENSMUST00000062147,344,394,+,5S50M\t0\t+\n+ENSMUST00'..b'128275\t79\t93\t2|1,ENSMUST00000128275,79,93,+,40S14M\t0\t+\n+ENSMUST00000194127\t469\t483\t2|1,ENSMUST00000194127,469,483,+,40S14M\t0\t+\n+ENSMUST00000111813\t56\t73\t10|2,ENSMUST00000111813,56,73,+,38S17M\t0\t+\n+ENSMUST00000151752\t1887\t1902\t26|1,ENSMUST00000151752,1887,1902,+,39S15M1S\t0\t+\n+ENSMUST00000137408\t2183\t2198\t26|1,ENSMUST00000137408,2183,2198,+,39S15M1S\t0\t+\n+ENSMUST00000189036\t14\t25\t20|1,ENSMUST00000189036,14,25,+,41S11M2S\t0\t+\n+ENSMUST00000000254\t463\t474\t20|1,ENSMUST00000000254,463,474,+,41S11M2S\t0\t+\n+ENSMUST00000138762\t6784\t6795\t20|1,ENSMUST00000138762,6784,6795,+,43S11M\t0\t+\n+ENSMUST00000129785\t2240\t2251\t20|1,ENSMUST00000129785,2240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|
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| diff -r 000000000000 -r 5db894671434 test-data/annotation.gtf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/annotation.gtf Sun Jan 19 16:31:34 2020 -0500 |
| b |
| b'@@ -0,0 +1,58 @@\n+14\t.\tmiRNA\t115044183\t115044205\t.\t+\t.\tID=MIMAT0000529;Alias=MIMAT0000529;Name=mmu-miR-20a-5p;Derives_from=MI0000568\n+16\t.\tmiRNA\t93369775\t93369796\t.\t+\t.\tID=MIMAT0017240;Alias=MIMAT0017240;Name=mmu-miR-802-3p;Derives_from=MI0004249\n+1\t.\tmiRNA\t36348732\t36348753\t.\t-\t.\tID=MIMAT0027696;Alias=MIMAT0027696;Name=mmu-miR-6898-5p;Derives_from=MI0022745\n+18\t.\tmiRNA\t37854605\t37854625\t.\t-\t.\tID=MIMAT0027861;Alias=MIMAT0027861;Name=mmu-miR-6979-3p;Derives_from=MI0022827\n+11\thavana\ttranscript\t116338339\t116347444\t.\t-\t.\tgene_id "ENSMUSG00000052949"; gene_version "10"; transcript_id "ENSMUST00000137264"; transcript_version "1"; gene_name "Rnf157"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Rnf157-011"; transcript_source "havana"; transcript_biotype "processed_transcript"; transcript_support_level "3";\n+11\thavana\texon\t116347342\t116347444\t.\t-\t.\tgene_id "ENSMUSG00000052949"; gene_version "10"; transcript_id "ENSMUST00000137264"; transcript_version "1"; exon_number "1"; gene_name "Rnf157"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Rnf157-011"; transcript_source "havana"; transcript_biotype "processed_transcript"; exon_id "ENSMUSE00000834936"; exon_version "1"; transcript_support_level "3";\n+11\thavana\texon\t116347033\t116347098\t.\t-\t.\tgene_id "ENSMUSG00000052949"; gene_version "10"; transcript_id "ENSMUST00000137264"; transcript_version "1"; exon_number "2"; gene_name "Rnf157"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Rnf157-011"; transcript_source "havana"; transcript_biotype "processed_transcript"; exon_id "ENSMUSE00001212609"; exon_version "1"; transcript_support_level "3";\n+11\thavana\texon\t116345907\t116345955\t.\t-\t.\tgene_id "ENSMUSG00000052949"; gene_version "10"; transcript_id "ENSMUST00000137264"; transcript_version "1"; exon_number "3"; gene_name "Rnf157"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Rnf157-011"; transcript_source "havana"; transcript_biotype "processed_transcript"; exon_id "ENSMUSE00001217820"; exon_version "1"; transcript_support_level "3";\n+11\thavana\texon\t116340338\t116340378\t.\t-\t.\tgene_id "ENSMUSG00000052949"; gene_version "10"; transcript_id "ENSMUST00000137264"; transcript_version "1"; exon_number "4"; gene_name "Rnf157"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Rnf157-011"; transcript_source "havana"; transcript_biotype "processed_transcript"; exon_id "ENSMUSE00001233021"; exon_version "1"; transcript_support_level "3";\n+11\thavana\texon\t116338339\t116338830\t.\t-\t.\tgene_id "ENSMUSG00000052949"; gene_version "10"; transcript_id "ENSMUST00000137264"; transcript_version "1"; exon_number "5"; gene_name "Rnf157"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Rnf157-011"; transcript_source "havana"; transcript_biotype "processed_transcript"; exon_id "ENSMUSE00000796470"; exon_version "1"; transcript_support_level "3";\n+2\thavana\ttranscript\t128237693\t128239643\t.\t-\t.\tgene_id "ENSMUSG00000086879"; gene_version "1"; transcript_id "ENSMUST00000136025"; transcript_version "1"; gene_name "Gm14012"; gene_source "havana"; gene_biotype "lincRNA"; transcript_name "Gm14012-001"; transcript_source "havana"; transcript_biotype "lincRNA"; tag "basic"; transcript_support_level "1";\n+2\thavana\texon\t128239424\t128239643\t.\t-\t.\tgene_id "ENSMUSG00000086879"; gene_version "1"; transcript_id "ENSMUST00000136025"; transcript_version "1"; exon_number "1"; gene_name "Gm14012"; gene_source "havana"; gene_biotype "lincRNA"; transcript_name "Gm14012-001"; transcript_source "havana"; transcript_biotype "lincRNA"; exon_id "ENSMUSE00000756585"; exon_version "1"; tag "basic"; transcript_support_level "1";\n+2\thavana\texon\t128238858\t128239058\t.\t-\t.\tgene_id "ENSMUSG00000086879"; gene_version "1"; transcript_id "ENSMUST00000136025"; transcript_version "1"; exon_number "2"; gene_name "Gm14012"; gene_source "havana"; gene_biotype "lincRNA"; transcript_nam'..b'_version "3"; tag "basic"; transcript_support_level "1 (assigned to previous version 4)";\n+17\tensembl_havana\texon\t27707880\t27708067\t.\t+\t.\tgene_id "ENSMUSG00000040276"; gene_version "10"; transcript_id "ENSMUST00000045896"; transcript_version "5"; exon_number "9"; gene_name "Pacsin1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Pacsin1-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS28567"; exon_id "ENSMUSE00000459997"; exon_version "1"; tag "basic"; transcript_support_level "1 (assigned to previous version 4)";\n+17\tensembl_havana\tCDS\t27707880\t27708067\t.\t+\t1\tgene_id "ENSMUSG00000040276"; gene_version "10"; transcript_id "ENSMUST00000045896"; transcript_version "5"; exon_number "9"; gene_name "Pacsin1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Pacsin1-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS28567"; protein_id "ENSMUSP00000044168"; protein_version "3"; tag "basic"; transcript_support_level "1 (assigned to previous version 4)";\n+17\tensembl_havana\texon\t27708426\t27711106\t.\t+\t.\tgene_id "ENSMUSG00000040276"; gene_version "10"; transcript_id "ENSMUST00000045896"; transcript_version "5"; exon_number "10"; gene_name "Pacsin1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Pacsin1-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS28567"; exon_id "ENSMUSE00000348638"; exon_version "2"; tag "basic"; transcript_support_level "1 (assigned to previous version 4)";\n+17\tensembl_havana\tCDS\t27708426\t27708532\t.\t+\t2\tgene_id "ENSMUSG00000040276"; gene_version "10"; transcript_id "ENSMUST00000045896"; transcript_version "5"; exon_number "10"; gene_name "Pacsin1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Pacsin1-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS28567"; protein_id "ENSMUSP00000044168"; protein_version "3"; tag "basic"; transcript_support_level "1 (assigned to previous version 4)";\n+17\tensembl_havana\tstop_codon\t27708533\t27708535\t.\t+\t0\tgene_id "ENSMUSG00000040276"; gene_version "10"; transcript_id "ENSMUST00000045896"; transcript_version "5"; exon_number "10"; gene_name "Pacsin1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Pacsin1-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS28567"; tag "basic"; transcript_support_level "1 (assigned to previous version 4)";\n+17\tensembl_havana\tUTR\t27655588\t27655759\t.\t+\t.\tgene_id "ENSMUSG00000040276"; gene_version "10"; transcript_id "ENSMUST00000045896"; transcript_version "5"; gene_name "Pacsin1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Pacsin1-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS28567"; tag "basic"; transcript_support_level "1 (assigned to previous version 4)";\n+17\tensembl_havana\tUTR\t27701767\t27701887\t.\t+\t.\tgene_id "ENSMUSG00000040276"; gene_version "10"; transcript_id "ENSMUST00000045896"; transcript_version "5"; gene_name "Pacsin1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Pacsin1-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS28567"; tag "basic"; transcript_support_level "1 (assigned to previous version 4)";\n+17\tensembl_havana\tUTR\t27708536\t27711106\t.\t+\t.\tgene_id "ENSMUSG00000040276"; gene_version "10"; transcript_id "ENSMUST00000045896"; transcript_version "5"; gene_name "Pacsin1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Pacsin1-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS28567"; tag "basic"; transcript_support_level "1 (assigned to previous version 4)";\n' |
| b |
| diff -r 000000000000 -r 5db894671434 test-data/chimeras --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/chimeras Sun Jan 19 16:31:34 2020 -0500 |
| b |
| @@ -0,0 +1,3 @@ +tagid txid1 txid2 geneid1 geneid2 symbol1 symbol2 region1 region2 tx_pos_start1 tx_pos_end1 tx_pos_strand1 length1 tx_pos_start2 tx_pos_end2 tx_pos_strand2 length2 read_info genomic_pos1 genomic_pos2 locus1 locus2 groupid1 groupid2 tpm1 tpm2 score1 score2 score sequences hybrid hybrid_pos mfe +4|1 ENSMUST00000136025 mmu-miR-6979-3p NA NA NA NA NA NA 32 46 + NA 2 12 + NA 2,15,30,39,54 ENSMUST00000136025:32:46:+ mmu-miR-6979-3p:2:12:+ ENSMUST00000136025:32:46:+ mmu-miR-6979-3p:2:12:+ 1 7 121100.0 165100.0 1.0 1.0 2.0 CAGGACUCUUGGCU&GUGUCUGUCU NA NA NA +3|2 mmu-miR-20a-5p ENSMUST00000136025 NA NA NA NA NA NA 0 23 + NA 132 142 + NA 6,28,35,44,55 mmu-miR-20a-5p:0:23:+ ENSMUST00000136025:132:142:+ mmu-miR-20a-5p:0:23:+ ENSMUST00000136025:132:142:+ 5 2 75660.0 165100.0 1.0 1.0 2.0 UAAAGUGCUUAUAGUGCAGGUAG&CUGCCUGCCU ((.((((((((&)))))))))) 13&1 -10.88 |
| b |
| diff -r 000000000000 -r 5db894671434 test-data/loci.counts --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/loci.counts Sun Jan 19 16:31:34 2020 -0500 |
| b |
| @@ -0,0 +1,9 @@ +6|1|1 ENSMUST00000182010 4 0 19 68 + 5S49M1S ENSMUST00000182010:19:68:+ ENSMUST00000182010:19:74:+ 1 1 6.485e+04 +7|9|1 ENSMUST00000182010 4 0 24 74 + 5S50M ENSMUST00000182010:24:74:+ ENSMUST00000182010:19:74:+ 1 1 6.485e+04 +4|1|2 ENSMUST00000136025 0 1 32 46 + 1S14M39S ENSMUST00000136025:32:46:+ ENSMUST00000136025:32:46:+ 1 1 1.211e+05 +3|2|2 ENSMUST00000136025 1 2 132 142 + 34S10M11S ENSMUST00000136025:132:142:+ ENSMUST00000136025:132:142:+ 1 1 1.651e+05 +2|2|2 ENSMUST00000137264 2 3 12 27 + 4S15M30S ENSMUST00000137264:12:27:+ ENSMUST00000137264:12:27:+ 1 1 1.135e+05 +6|1|4 ENSMUST00000160533 3 4 69 82 + 42S13M ENSMUST00000160533:69:82:+ ENSMUST00000160533:69:82:+ 1 1 1.297e+05 +3|2|1 mmu-miR-20a-5p 5 5 0 23 + 5S23M27S mmu-miR-20a-5p:0:23:+ mmu-miR-20a-5p:0:23:+ 1 1 7.566e+04 +2|2|1 mmu-miR-6898-5p 6 6 11 21 + 10M39S mmu-miR-6898-5p:11:21:+ mmu-miR-6898-5p:11:21:+ 1 1 1.651e+05 +4|1|1 mmu-miR-6979-3p 7 7 2 12 + 29S10M15S mmu-miR-6979-3p:2:12:+ mmu-miR-6979-3p:2:12:+ 1 1 1.651e+05 |
| b |
| diff -r 000000000000 -r 5db894671434 test-data/merged.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/merged.bed Sun Jan 19 16:31:34 2020 -0500 |
| b |
| @@ -0,0 +1,8 @@ +ENSMUST00000136025 32 46 + 4|1|2,ENSMUST00000136025,32,46,+,1S14M39S +ENSMUST00000136025 132 142 + 3|2|2,ENSMUST00000136025,132,142,+,34S10M11S +ENSMUST00000137264 12 27 + 2|2|2,ENSMUST00000137264,12,27,+,4S15M30S +ENSMUST00000160533 69 82 + 6|1|4,ENSMUST00000160533,69,82,+,42S13M +ENSMUST00000182010 19 74 + 6|1|1,ENSMUST00000182010,19,68,+,5S49M1S;7|9|1,ENSMUST00000182010,24,74,+,5S50M +mmu-miR-20a-5p 0 23 + 3|2|1,mmu-miR-20a-5p,0,23,+,5S23M27S +mmu-miR-6898-5p 11 21 + 2|2|1,mmu-miR-6898-5p,11,21,+,10M39S +mmu-miR-6979-3p 2 12 + 4|1|1,mmu-miR-6979-3p,2,12,+,29S10M15S |
| b |
| diff -r 000000000000 -r 5db894671434 test-data/reads.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/reads.fasta Sun Jan 19 16:31:34 2020 -0500 |
| b |
| @@ -0,0 +1,14 @@ +>1|1 +AAAAGACTCTGTAGACATGGCTGGTCTTGAACTCACAGAGATTTGTCTGCCTTTC +>2|2 +ATGCAGGGAGGACGATGCGAATGGGGAATCAGGCTAAACAGTTTGAATA +>3|2 +CGCGGTAAAGTGCTTATAGTGCAGGTAGACAGTACTGCCTGCCTTAATGAATGAA +>4|1 +TCAGGACTCTTGGCTGTATCCTTTCCTAAGTGTCTGTCTTCCTTACCACTAACA +>5|8 +TGTAGACACAAGGTACACCAATGCCTCTCTGACCACCCATGAGTCTTTGACCTA +>6|1 +TGTGGTCATTAATCAAGAACGAAAGTCGGAGGTTCGAAGACGATTAGATACCGTC +>7|9 +TGTTGAATCAAGAACGAAAGTCGGAGGTTCGAAGACGATCAGATACCGTCGTAGT |
| b |
| diff -r 000000000000 -r 5db894671434 test-data/reads.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/reads.fastq Sun Jan 19 16:31:34 2020 -0500 |
| b |
| @@ -0,0 +1,96 @@ +@183438/1 +TGTTGAATCAAGAACGAAAGTCGGAGGTTCGAAGACGATCAGATACCGTCGTAGT ++ +GGGGHHHHHHHHHHHGGGGGHHGGGGGGHHGHHGGHGGGHGHHHHHHGGGGGHGG +@397634/1 +TGTTGAATCAAGAACGAAAGTCGGAGGTTCGAAGACGATCAGATACCGTCGTAGT ++ +GGGGHHGHHHHHHHHGGGGGHHGGGGGGHHGHHGGHGGGHGHHHHHHGGGGGHGG +@701890/1 +TGTTGAATCAAGAACGAAAGTCGGAGGTTCGAAGACGATCAGATACCGTCGTAGT ++ +EEGGHGHHHHHHHHHGGGGGGHGGCGGFGHGHHGGHGGGHGHHHHHHGGGGGGFG +@745414/1 +TGTTGAATCAAGAACGAAAGTCGGAGGTTCGAAGACGATCAGATACCGTCGTAGT ++ +GGGGHHHHHHHHHHHGGGGGHHGGGGGGHHGHHGGHGGGHGHHHHHHGGGGGHGF +@753363/1 +TGTTGAATCAAGAACGAAAGTCGGAGGTTCGAAGACGATCAGATACCGTCGTAGT ++ +EEEGHHHFHHHHHHHGGFEEFGGGGGGGHHGHHGGHGGFHGHHHHHHGFGGGGGG +@881071/1 +TGTTGAATCAAGAACGAAAGTCGGAGGTTCGAAGACGATCAGATACCGTCGTAGT ++ +GGGGHHHHHHHHHHHGGGGGHHGGFGGGHHGHHGGHGGGHGHHHHHHGFGGFHGG +@1059959/1 +TGTTGAATCAAGAACGAAAGTCGGAGGTTCGAAGACGATCAGATACCGTCGTAGT ++ +GGGGHHHHHHHHHHHGGGGGHHGGGGGEHHGHHGGHGGGHGHHHHHHGGGGGHGG +@1157152/1 +TGTTGAATCAAGAACGAAAGTCGGAGGTTCGAAGACGATCAGATACCGTCGTAGT ++ +GGGGHHHHHHHHHHHGGGGGHHGGGGGEHHGHHGGHGGGHGHHHHHHGGGGGHGG +@1295751/1 +TGTTGAATCAAGAACGAAAGTCGGAGGTTCGAAGACGATCAGATACCGTCGTAGT ++ +GGGGHHHHHHHHHHHGGGGGHHGGGGGGHHGHHGGHGGGHGHHHHHHGGGGGHGG +@585749/1 +TGTGGTCATTAATCAAGAACGAAAGTCGGAGGTTCGAAGACGATTAGATACCGTC ++ +GGEGGHHHHHHHHHHHFHHHG?FGEHHGGGFEEHHGHHGGFF?FHGHHHHHGEGG +@1209323/1 +ATGCAGGGAGGACGATGCGAATGGGGAATCAGGCTAAACAGTTTGAATA ++ +3AAABFFBBBBBGGEFGGG2AAGHHGGAGHHHHHHHHCHGHHHHHH5GF +@1248864/1 +ATGCAGGGAGGACGATGCGAATGGGGAATCAGGCTAAACAGTTTGAATA ++ +ABBBAF4DAB?BGGEFEFG2AAF3CEGGHHGGFCG33FHFHFHHHHHHH +@475998/1 +CGCGGTAAAGTGCTTATAGTGCAGGTAGACAGTACTGCCTGCCTTAATGAATGAA ++ +GGEEGB1FFFDGGGFHHHDDFGGHFHEFHHHHFDGGGE?GHFHHHHFHHHDEDHD +@478112/1 +CGCGGTAAAGTGCTTATAGTGCAGGTAGACAGTACTGCCTGCCTTAATGAATGAA ++ +EEFGGFGEHHFGHBBFHHHFGHHHHAGHHHFHFFGEF@BFGGAEHFFHHHGHGHF +@74093/1 +TGTAGACACAAGGTACACCAATGCCTCTCTGACCACCCATGAGTCTTTGACCTA ++ +G?FHHFFHFEFHH3FBAGGC2AAFEEGHFGFDEGGGFEAGFGE5AFF5@@BE5G +@448633/1 +TGTAGACACAAGGTACACCAATGCCTCTCTGACCACCCATGAGTCTTTGACCTA ++ +EFGGFHH5BAFA23AAFFHHDGGHHFGHHHEGHCFGFAFGH3FGGBBG@E@FGF +@849624/1 +TGTAGACACAAGGTACACCAATGCCTCTCTGACCACCCATGAGTCTTTGACCTA ++ +AABFBFFFF2CGDBADEFB2FAFFFHBGHFHDFGHAEGCFFEFDD5GGG@BBFE +@1076923/1 +TGTAGACACAAGGTACACCAATGCCTCTCTGACCACCCATGAGTCTTTGACCTA ++ +GCEFGHHHFEFH23DB553A2BGFFDBBA35FGFFGGGEECGH5DD@@@EBEGF +@1278542/1 +TGTAGACACAAGGTACACCAATGCCTCTCTGACCACCCATGAGTCTTTGACCTA ++ +EGGFHGHHHHGHGEGFHHHHHHFHHHFHGFGHHHHHGGEE3GHGGHGFDBGHHE +@1290525/1 +TGTAGACACAAGGTACACCAATGCCTCTCTGACCACCCATGAGTCTTTGACCTA ++ +CEFFDHH5B2AE2F555532AGF3EGH3AFAEHHFHGD133335DFGH5D@3FF +@1379287/1 +TGTAGACACAAGGTACACCAATGCCTCTCTGACCACCCATGAGTCTTTGACCTA ++ +AEEF1FGHHHGHHFGHHHGG/E1EHHHHGHHFDGGEG?CFGBGEGHHGHHHHHH +@1490590/1 +TGTAGACACAAGGTACACCAATGCCTCTCTGACCACCCATGAGTCTTTGACCTA ++ +GEA3BD5DF2EGCGEDF5EGH3AGHHHFHGFBFHBGGGGH33BFFD555D53FG +@854752/1 +AAAAGACTCTGTAGACATGGCTGGTCTTGAACTCACAGAGATTTGTCTGCCTTTC ++ +G?EFFAF5335DD5B5553222B1A55AFAGHHE33BAF325555A5DF5B3F3B +@1180232/1 +TCAGGACTCTTGGCTGTATCCTTTCCTAAGTGTCTGTCTTCCTTACCACTAACA ++ +EGE0F10B01DDBGC/0BFFGGHHHFE21BA2D221DGHH2DBAGHBDFBG1GF |
| b |
| diff -r 000000000000 -r 5db894671434 test-data/ref.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ref.fasta Sun Jan 19 16:31:34 2020 -0500 |
| b |
| @@ -0,0 +1,18 @@ +>mmu-miR-20a-5p +TAAAGTGCTTATAGTGCAGGTAG +>mmu-miR-802-3p +ACGGAGAGTCTTTGTCACTCAG +>mmu-miR-6898-5p +TGTAAGGGGAGATGCAGGGAGC +>mmu-miR-6979-3p +TTGTGTCTGTCTGGCTCCCAG +>ENSMUST00000137264 +CTACTCACATGAAGGGAGGACGATGCGCAACCCTCCACCCACCTGCCTCATCGCCTGTAACCGCGATTCTTACCCTCTCAGAAAGAACCAGAAGCCTTCCCTCTGTGGGCTAATACGTGCCAGCCAAACCTGTGGGCCAGCTGAGCTGAGGGTCAGGGCTGGTTGTTTCTGTAGGCTTTCTCTTCTGAGTGGAGACCAAGAAGACTGAAGAGTTTGGCAGCCTTGTTAGACGCCCATGGACAGGTTTTGGTCTCTGGCACTC +>ENSMUST00000136025 +GATCTGATTGAGTCACAGCTGAGATGTGGCACCAGGACTCTTGGCTACACTCAGTTCTCTCAGTTTGACTGAGTACTCTGGGATCACAGAAGTGACTACATGATGCAGCCCAGAGGTCTGAACTCAAAGCTTCTGCCTGCCTACCTTATCTCACTGCTGGCAAATGCATCCCCTCTGCTCCACCCATC +>ENSMUST00000182010 +GCATTTGCCAAGAATGTTTTCATTAATCAAGAACGAAAGTCGGAGTTTCGAAGACGATCAGATACCGTTGTAGTTCCAACCATAAACGATGCCGACTGGC +>ENSMUST00000160533 +CAAAGGCAGTATCGTGGTGGATTATGATGTCATCCTGAAGGCCAAGTACACCCCAGGATTTGAAAACACATTAGATACCGTCGTCAAAAACCTGGAGACA +>ENSMUST00000045896 +GAGGCCAATGGTGGCGCCAACCCCTTCGAGGATGATGCCAAGGGAGTTCGTGTACGGGCACTCTATGACTACGACGGTCAGGAGCAGGATGAGCTCAGCT |
| b |
| diff -r 000000000000 -r 5db894671434 test-data/ref1.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ref1.fasta Sun Jan 19 16:31:34 2020 -0500 |
| b |
| @@ -0,0 +1,8 @@ +>mmu-miR-20a-5p +TAAAGTGCTTATAGTGCAGGTAG +>mmu-miR-802-3p +ACGGAGAGTCTTTGTCACTCAG +>mmu-miR-6898-5p +TGTAAGGGGAGATGCAGGGAGC +>mmu-miR-6979-3p +TTGTGTCTGTCTGGCTCCCAG |
| b |
| diff -r 000000000000 -r 5db894671434 test-data/ref2.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ref2.fasta Sun Jan 19 16:31:34 2020 -0500 |
| b |
| @@ -0,0 +1,10 @@ +>ENSMUST00000137264 +CTACTCACATGAAGGGAGGACGATGCGCAACCCTCCACCCACCTGCCTCATCGCCTGTAACCGCGATTCTTACCCTCTCAGAAAGAACCAGAAGCCTTCCCTCTGTGGGCTAATACGTGCCAGCCAAACCTGTGGGCCAGCTGAGCTGAGGGTCAGGGCTGGTTGTTTCTGTAGGCTTTCTCTTCTGAGTGGAGACCAAGAAGACTGAAGAGTTTGGCAGCCTTGTTAGACGCCCATGGACAGGTTTTGGTCTCTGGCACTC +>ENSMUST00000136025 +GATCTGATTGAGTCACAGCTGAGATGTGGCACCAGGACTCTTGGCTACACTCAGTTCTCTCAGTTTGACTGAGTACTCTGGGATCACAGAAGTGACTACATGATGCAGCCCAGAGGTCTGAACTCAAAGCTTCTGCCTGCCTACCTTATCTCACTGCTGGCAAATGCATCCCCTCTGCTCCACCCATC +>ENSMUST00000182010 +GCATTTGCCAAGAATGTTTTCATTAATCAAGAACGAAAGTCGGAGTTTCGAAGACGATCAGATACCGTTGTAGTTCCAACCATAAACGATGCCGACTGGC +>ENSMUST00000160533 +CAAAGGCAGTATCGTGGTGGATTATGATGTCATCCTGAAGGCCAAGTACACCCCAGGATTTGAAAACACATTAGATACCGTCGTCAAAAACCTGGAGACA +>ENSMUST00000045896 +GAGGCCAATGGTGGCGCCAACCCCTTCGAGGATGATGCCAAGGGAGTTCGTGTACGGGCACTCTATGACTACGACGGTCAGGAGCAGGATGAGCTCAGCT |
| b |
| diff -r 000000000000 -r 5db894671434 test-data/segments.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/segments.bed Sun Jan 19 16:31:34 2020 -0500 |
| b |
| @@ -0,0 +1,13 @@ +ENSMUST00000182010 19 68 6|1|1,ENSMUST00000182010,19,68,+,5S49M1S 0 + +ENSMUST00000182010 24 74 7|9|1,ENSMUST00000182010,24,74,+,5S50M 0 + +mmu-miR-20a-5p 0 23 3|2|1,mmu-miR-20a-5p,0,23,+,5S23M27S 0 + +mmu-miR-6898-5p 11 21 2|2|1,mmu-miR-6898-5p,11,21,+,10M39S 0 + +mmu-miR-6979-3p 2 12 4|1|1,mmu-miR-6979-3p,2,12,+,29S10M15S 0 + +ENSMUST00000137264 12 27 2|2|2,ENSMUST00000137264,12,27,+,4S15M30S 0 + +ENSMUST00000136025 32 46 4|1|2,ENSMUST00000136025,32,46,+,1S14M39S 0 + +ENSMUST00000136025 132 142 3|2|2,ENSMUST00000136025,132,142,+,34S10M11S 0 + +ENSMUST00000182010 19 45 6|1|2,ENSMUST00000182010,19,45,+,5S26M24S 0 + +ENSMUST00000182010 24 45 7|9|2,ENSMUST00000182010,24,45,+,5S21M29S 0 + +ENSMUST00000182010 46 58 6|1|3,ENSMUST00000182010,46,58,+,32S12M11S 0 + +ENSMUST00000182010 46 68 7|9|3,ENSMUST00000182010,46,68,+,27S22M6S 0 + +ENSMUST00000160533 69 82 6|1|4,ENSMUST00000160533,69,82,+,42S13M 0 + |
| b |
| diff -r 000000000000 -r 5db894671434 test-data/singletons --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/singletons Sun Jan 19 16:31:34 2020 -0500 |
| b |
| @@ -0,0 +1,4 @@ +tagid txid geneid symbol region tx_pos_start tx_pos_end tx_pos_strand length read_info genomic_pos locus groupid tpm score score sequences +6|1 ENSMUST00000182010 NA NA NA 19 68 + NA 6,54,55 ENSMUST00000182010:19:68:+ ENSMUST00000182010:19:74:+ 0 64850.0 1.0 1.0 UCAUUAAUCAAGAACGAAAGUCGGAGUUUCGAAGACGAUCAGAUACCGUUGUAGU +7|9 ENSMUST00000182010 NA NA NA 24 74 + NA 6,55,55 ENSMUST00000182010:24:74:+ ENSMUST00000182010:19:74:+ 0 64850.0 1.0 1.0 UCAUUAAUCAAGAACGAAAGUCGGAGUUUCGAAGACGAUCAGAUACCGUUGUAGU +2|2 ENSMUST00000137264 NA NA NA 12 27 + NA 5,19,49 ENSMUST00000137264:12:27:+ ENSMUST00000137264:12:27:+ 3 113500.0 1.0 1.0 AGGGAGGACGAUGCG |
| b |
| diff -r 000000000000 -r 5db894671434 tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Sun Jan 19 16:31:34 2020 -0500 |
| b |
| @@ -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="all_fasta.loc" /> + </table> +</tables> |