Repository 'chira_collapse'
hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/chira_collapse

Changeset 0:872249f5495a (2020-01-19)
Next changeset 1:b3065e4df04c (2020-03-11)
Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
added:
all_fasta.loc.sample
chira_collapse.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
b
diff -r 000000000000 -r 872249f5495a all_fasta.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/all_fasta.loc.sample Sun Jan 19 16:32:04 2020 -0500
b
@@ -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.
+#
b
diff -r 000000000000 -r 872249f5495a chira_collapse.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/chira_collapse.xml Sun Jan 19 16:32:04 2020 -0500
[
@@ -0,0 +1,48 @@
+<tool id="chira_collapse" name="ChiRA collapse" version="@WRAPPER_VERSION@0">
+    <description>deduplicate fastq reads</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />    
+    <command><![CDATA[
+        chira_collapse.py
+        -i '$in'
+        -u '$umi_len'
+        -o '$out'
+    ]]></command>
+
+    <inputs>
+        <param format="fastq" name="in" type="data" label="Input FASTQ file"/>
+        <param name="umi_len" type="integer" value="0"
+               label="Length of the UMI if present at the 5' end of your reads"/>
+    </inputs>
+    <outputs>
+        <data format="fasta" name="out" label="ChiRA collapse FASTQ on ${on_string}"/>
+    </outputs>
+
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="in" value="reads.fastq" />
+            <output name="out" file="reads.fasta" />
+        </test>
+    </tests>
+
+    <help>
+
+.. class:: infomark
+
+**What it does**
+
+This tool deduplicates the reads from the FASTQ file and writes into a fasta each read once with it's read count.
+
+**Inputs**
+
+* Quality and adapter trimmed FASTQ file
+
+**Outputs**
+
+* FASTA file with unique sequences. The headers of the sequence are in the following format: >sequence_id|UMI|read_count
+
+    </help>
+    <expand macro="citations" />
+</tool>
b
diff -r 000000000000 -r 872249f5495a macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Sun Jan 19 16:32:04 2020 -0500
b
@@ -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>
b
diff -r 000000000000 -r 872249f5495a test-data/alignments.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/alignments.bed Sun Jan 19 16:32:04 2020 -0500
b
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b
diff -r 000000000000 -r 872249f5495a test-data/annotation.gtf
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/annotation.gtf Sun Jan 19 16:32:04 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 872249f5495a test-data/chimeras
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/chimeras Sun Jan 19 16:32:04 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 872249f5495a test-data/loci.counts
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/loci.counts Sun Jan 19 16:32:04 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 872249f5495a test-data/merged.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/merged.bed Sun Jan 19 16:32:04 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 872249f5495a test-data/reads.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/reads.fasta Sun Jan 19 16:32:04 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 872249f5495a test-data/reads.fastq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/reads.fastq Sun Jan 19 16:32:04 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 872249f5495a test-data/ref.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ref.fasta Sun Jan 19 16:32:04 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 872249f5495a test-data/ref1.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ref1.fasta Sun Jan 19 16:32:04 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 872249f5495a test-data/ref2.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ref2.fasta Sun Jan 19 16:32:04 2020 -0500
b
@@ -0,0 +1,10 @@
+>ENSMUST00000137264
+CTACTCACATGAAGGGAGGACGATGCGCAACCCTCCACCCACCTGCCTCATCGCCTGTAACCGCGATTCTTACCCTCTCAGAAAGAACCAGAAGCCTTCCCTCTGTGGGCTAATACGTGCCAGCCAAACCTGTGGGCCAGCTGAGCTGAGGGTCAGGGCTGGTTGTTTCTGTAGGCTTTCTCTTCTGAGTGGAGACCAAGAAGACTGAAGAGTTTGGCAGCCTTGTTAGACGCCCATGGACAGGTTTTGGTCTCTGGCACTC
+>ENSMUST00000136025
+GATCTGATTGAGTCACAGCTGAGATGTGGCACCAGGACTCTTGGCTACACTCAGTTCTCTCAGTTTGACTGAGTACTCTGGGATCACAGAAGTGACTACATGATGCAGCCCAGAGGTCTGAACTCAAAGCTTCTGCCTGCCTACCTTATCTCACTGCTGGCAAATGCATCCCCTCTGCTCCACCCATC
+>ENSMUST00000182010
+GCATTTGCCAAGAATGTTTTCATTAATCAAGAACGAAAGTCGGAGTTTCGAAGACGATCAGATACCGTTGTAGTTCCAACCATAAACGATGCCGACTGGC
+>ENSMUST00000160533
+CAAAGGCAGTATCGTGGTGGATTATGATGTCATCCTGAAGGCCAAGTACACCCCAGGATTTGAAAACACATTAGATACCGTCGTCAAAAACCTGGAGACA
+>ENSMUST00000045896
+GAGGCCAATGGTGGCGCCAACCCCTTCGAGGATGATGCCAAGGGAGTTCGTGTACGGGCACTCTATGACTACGACGGTCAGGAGCAGGATGAGCTCAGCT
b
diff -r 000000000000 -r 872249f5495a test-data/segments.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/segments.bed Sun Jan 19 16:32:04 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 872249f5495a test-data/singletons
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/singletons Sun Jan 19 16:32:04 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 872249f5495a 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 16:32:04 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>