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Changeset 4:3de621c44cf9 (2017-09-14)

Previous changeset 3:5348cfd3ba5c (2017-08-10) Next changeset 5:76a3992021c1 (2017-09-14)

Commit message:
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/dr-disco commit 272a4e52b9b11adee8d681a2e84802e945d1112a

modified:
macros.xml
test-data/fix_test-01.fixed.bam
test-data/integrate_test_terg_s041.out.no-gtf.txt
test-data/integrate_test_terg_s041.out.txt
test-data/integrate_tmprss-erg.hg38.gtf

diff -r 5348cfd3ba5c -r 3de621c44cf9 macros.xml
--- a/macros.xml Thu Aug 10 05:38:27 2017 -0400
+++ b/macros.xml Thu Sep 14 04:30:12 2017 -0400

@@ -1,12 +1,12 @@
<macros>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="0.9.0">dr-disco</requirement>
+            <requirement type="package" version="0.10.0">dr-disco</requirement>
             <yield/>
         </requirements>
     </xml>

-    <token name="@TOOL_VERSION@">0.9.0</token>
+    <token name="@TOOL_VERSION@">0.10.0</token>

     <xml name="version_command">
         <version_command>dr-disco --version | head -n 1</version_command>
@@ -14,7 +14,6 @@

     <xml name="citations">
         <citations>
-            
             <citation type="bibtex">
                @unpublished{dr_disco,
                   author = {Youri Hoogstrate},

diff -r 5348cfd3ba5c -r 3de621c44cf9 test-data/fix_test-01.fixed.bam

Binary file test-data/fix_test-01.fixed.bam has changed

diff -r 5348cfd3ba5c -r 3de621c44cf9 test-data/integrate_test_terg_s041.out.no-gtf.txt
--- a/test-data/integrate_test_terg_s041.out.no-gtf.txt Thu Aug 10 05:38:27 2017 -0400
+++ b/test-data/integrate_test_terg_s041.out.no-gtf.txt Thu Sep 14 04:30:12 2017 -0400

b'@@ -1,6 +1,6 @@\n-shared-id\tfusion\tchr-A\tpos-A\tdirection-A\tpos-A-acceptor\tpos-A-donor\tchr-B\tpos-B\tdirection-B\tpos-A-acceptor\tpos-A-donor\tgenomic-distance\tfilter-status\tcircRNA\tintronic/exonic\tscore\tsoft+hardclips\tn-split-reads\tn-discordant-reads\tn-edges\tn-nodes-A\tn-nodes-B\tn-splice-junc-A\tn-splice-junc-B\tentropy-bp-edge\tentropy-all-edges\tbp-pos-stddev\tentropy-disco-bps\tlr-A-slope\tlr-A-intercept\tlr-A-rvalue\tlr-A-pvalue\tlr-A-stderr\tlr-B-slope\tlr-B-intercept\tlr-B-rvalue\tlr-B-pvalue\tlr-B-stderr\tdisco/split\tclips/score\tnodes/edge\tframeshift=0\tframeshift=+1\tframeshift=+2\tdata-structure\n-1\tTMPRSS2->ERG\tchr21\t38487350\t-\t200\t0\tchr21\t41479719\t+\t0\t200\t2992369\tvalid\tlinear\tintronic\t151\t96\t48\t7\t1\t1\t1\t0\t0\t0.869\t0.869\t0.2887\t0.8124\t2.1465\t5.6435\t0.9817\t0\t0.0571\t1.9162\t26.2818\t0.99\t0\t0.0376\t0.1458\t0.3179\t2\t\t\t\tchr21:38487350/38487351(-)->chr21:41479719/41479720(+):(discordant_mates:14,spanning_paired_1:41,spanning_paired_1_t:7,spanning_paired_2:41,spanning_paired_2_t:7)\n-1\tTMPRSS2->ERG\tchr21\t38445621\t-\t200\t0\tchr21\t41498118\t+\t0\t200\t3052497\tvalid\tlinear\texonic\t588\t378\t189\t21\t14\t7\t9\t2\t4\t0.7421\t0.8197\t0\t0.7162\t0.7344\t19.9882\t0.9657\t0\t0.0178\t0.7194\t21.976\t0.9648\t0\t0.0177\t0.1111\t0.3214\t1.1429\tTMPRSS2(ENST00000332149.9)-ensembl_havana->ERG(ENST00000288319.11)-ensembl_havana,TMPRSS2(ENST00000332149.9)-ensembl_havana->ERG(ENST00000398905.5)-havana,TMPRSS2(ENST00000332149.9)-ensembl_havana->ERG(ENST00000398907.5)-havana,TMPRSS2(ENST00000332149.9)-ensembl_havana->ERG(ENST00000398910.5)-havana,TMPRSS2(ENST00000332149.9)-ensembl_havana->ERG(ENST00000398911.5)-havana,TMPRSS2(ENST00000332149.9)-ensembl_havana->ERG(ENST00000398919.6)-ensembl_havana,TMPRSS2(ENST00000332149.9)-ensembl_havana->ERG(ENST00000417133.6)-ensembl_havana,TMPRSS2(ENST00000332149.9)-ensembl_havana->ERG(ENST00000442448.5)-ensembl,TMPRSS2(ENST00000398585.7)-ensembl->ERG(ENST00000288319.11)-ensembl_havana,TMPRSS2(ENST00000398585.7)-ensembl->ERG(ENST00000398905.5)-havana,TMPRSS2(ENST00000398585.7)-ensembl->ERG(ENST00000398907.5)-havana,TMPRSS2(ENST00000398585.7)-ensembl->ERG(ENST00000398910.5)-havana,TMPRSS2(ENST00000398585.7)-ensembl->ERG(ENST00000398911.5)-havana,TMPRSS2(ENST00000398585.7)-ensembl->ERG(ENST00000398919.6)-ensembl_havana,TMPRSS2(ENST00000398585.7)-ensembl->ERG(ENST00000417133.6)-ensembl_havana,TMPRSS2(ENST00000398585.7)-ensembl->ERG(ENST00000442448.5)-ensembl,TMPRSS2(ENST00000424093.5)-havana->ERG(ENST00000288319.11)-ensembl_havana,TMPRSS2(ENST00000424093.5)-havana->ERG(ENST00000398905.5)-havana,TMPRSS2(ENST00000424093.5)-havana->ERG(ENST00000398907.5)-havana,TMPRSS2(ENST00000424093.5)-havana->ERG(ENST00000398910.5)-havana,TMPRSS2(ENST00000424093.5)-havana->ERG(ENST00000398911.5)-havana,TMPRSS2(ENST00000424093.5)-havana->ERG(ENST00000398919.6)-ensembl_havana,TMPRSS2(ENST00000424093.5)-havana->ERG(ENST00000417133.6)-ensembl_havana,TMPRSS2(ENST00000424093.5)-havana->ERG(ENST00000442448.5)-ensembl,TMPRSS2(ENST00000454499.5)-havana->ERG(ENST00000288319.11)-ensembl_havana,TMPRSS2(ENST00000454499.5)-havana->ERG(ENST00000398905.5)-havana,TMPRSS2(ENST00000454499.5)-havana->ERG(ENST00000398907.5)-havana,TMPRSS2(ENST00000454499.5)-havana->ERG(ENST00000398910.5)-havana,TMPRSS2(ENST00000454499.5)-havana->ERG(ENST00000398911.5)-havana,TMPRSS2(ENST00000454499.5)-havana->ERG(ENST00000398919.6)-ensembl_havana,TMPRSS2(ENST00000454499.5)-havana->ERG(ENST00000417133.6)-ensembl_havana,TMPRSS2(ENST00000454499.5)-havana->ERG(ENST00000442448.5)-ensembl,TMPRSS2(ENST00000455813.1)-havana->ERG(ENST00000288319.11)-ensembl_havana,TMPRSS2(ENST00000455813.1)-havana->ERG(ENST00000398905.5)-havana,TMPRSS2(ENST00000455813.1)-havana->ERG(ENST00000398907.5)-havana,TMPRSS2(ENST00000455813.1)-havana->ERG(ENST00000398910.5)-havana,TMPRSS2(ENST00000455813.1)-havana->ERG(ENST00000398911.5)-havana,TMPRSS2(ENST00000455813.1)-havana->ERG(ENST00000398919.6)-ensembl_havana,TMPRSS2(ENST00000455813.1)-havana->ERG(ENST00000417133.6)-ensembl_havana,TMPRSS2(ENST00000455813.1)-havana->ERG(ENST00000442448.5)-ensembl,TMPRSS2(E'..b'1.5)-havana(+0),TMPRSS2(ENST00000454499.5)-havana(+2)->ERG(ENST00000398919.6)-ensembl_havana(+0),TMPRSS2(ENST00000454499.5)-havana(+2)->ERG(ENST00000417133.6)-ensembl_havana(+0),TMPRSS2(ENST00000454499.5)-havana(+2)->ERG(ENST00000442448.5)-ensembl(+0),TMPRSS2(ENST00000458356.5)-havana(+2)->ERG(ENST00000288319.11)-ensembl_havana(+0),TMPRSS2(ENST00000458356.5)-havana(+2)->ERG(ENST00000398905.5)-havana(+0),TMPRSS2(ENST00000458356.5)-havana(+2)->ERG(ENST00000398907.5)-havana(+0),TMPRSS2(ENST00000458356.5)-havana(+2)->ERG(ENST00000398910.5)-havana(+0),TMPRSS2(ENST00000458356.5)-havana(+2)->ERG(ENST00000398911.5)-havana(+0),TMPRSS2(ENST00000458356.5)-havana(+2)->ERG(ENST00000398919.6)-ensembl_havana(+0),TMPRSS2(ENST00000458356.5)-havana(+2)->ERG(ENST00000417133.6)-ensembl_havana(+0),TMPRSS2(ENST00000458356.5)-havana(+2)->ERG(ENST00000442448.5)-ensembl(+0)\tchr21:38445621/38445622(-)->chr21:41498118/41498119(+):(discordant_mates:14,spanning_paired_1:114,spanning_paired_1_t:4,spanning_paired_2:114,spanning_paired_2_t:4)&chr21:38445621/38445622(-)->chr21:41508080/41508081(+):(spanning_paired_1:33,spanning_paired_2:33)&chr21:38445621/38445622(-)->chr21:41507949/41507950(+):(discordant_mates:8,spanning_paired_1:15,spanning_paired_2:15)&chr21:38474121/38474122(-)->chr21:41498118/41498119(+):(spanning_paired_1:14,spanning_paired_2:14)&chr21:38445621/38445622(-)->chr21:41480475/41480476(+):(discordant_mates:6,spanning_paired_1:2,spanning_paired_2:2)&chr21:38423561/38423562(-)->chr21:41498118/41498119(+):(spanning_paired_1:2,spanning_paired_2:2)&chr21:38445621/38445622(-)->chr21:41506444/41506445(+):(discordant_mates:6,spanning_paired_1_t:1,spanning_paired_2_t:1)&chr21:38445621/38445622(-)->chr21:41504366/41504367(+):(spanning_paired_1:1,spanning_paired_2:1)&chr21:38446208/38446209(-)->chr21:41498118/41498119(+):(spanning_paired_1:1,spanning_paired_2:1)&chr21:38474121/38474122(-)->chr21:41480475/41480476(+):(spanning_paired_1:1,spanning_paired_2:1)&chr21:38474121/38474122(-)->chr21:41508080/41508081(+):(spanning_paired_1:1,spanning_paired_2:1)&chr21:38423567/38423568(-)->chr21:41485824/41485825(+):(discordant_mates:4)&chr21:38445482/38445483(-)->chr21:41500346/41500347(+):(discordant_mates:2)&chr21:38474093/38474094(-)->chr21:41507966/41507967(+):(discordant_mates:2)\n+2\tchr21:36338771->chr21:36344707\tchr21\t36338771\t+\t0\t10\tchr21\t36344707\t-\t10\t0\t5936\tvalid\tcircular\texonic\t117\t58\t38\t3\t2\t2\t2\t0\t0\t0.8536\t0.8591\t2.436\t0.871\t2.1714\t19.1829\t0.9605\t0\t0.1021\t2.0941\t32.6902\t0.9725\t0\t0.0814\t0.0789\t0.2479\t2\t\t\t\t\tchr21:36338771/36338772(+)->chr21:36344707/36344708(-):(discordant_mates:6,spanning_paired_1:14,spanning_paired_1_t:23,spanning_paired_2:14,spanning_paired_2_t:23)&chr21:36338841/36338842(+)->chr21:36341534/36341535(-):(spanning_paired_1:1,spanning_paired_2:1)\n+3\tchr21:29329693->chr21:29321220\tchr21\t29321220\t+\t10\t0\tchr21\t29329693\t-\t0\t10\t8473\tvalid\tcircular\texonic\t49\t35\t15\t4\t4\t4\t3\t0\t0\t0.8605\t0.8018\t0\t0.6667\t8.3531\t34.3077\t0.9863\t0\t0.4412\t9.4685\t14.5897\t0.9701\t0\t0.749\t0.2667\t0.3571\t1.75\t\t\t\t\tchr21:29321220/29321221(+)->chr21:29329693/29329694(-):(discordant_mates:4,spanning_paired_1:9,spanning_paired_1_t:1,spanning_paired_2:9,spanning_paired_2_t:1)&chr21:29326058/29326059(+)->chr21:29329693/29329694(-):(spanning_paired_1:4,spanning_paired_2:4)&chr21:29327324/29327325(+)->chr21:29329704/29329705(-):(spanning_paired_1_t:1,spanning_paired_2_t:1)&chr21:29321216/29321217(+)->chr21:29329647/29329648(-):(discordant_mates:4)\n+4\tchr21:33432871<->chr21:33414887\tchr21\t33414887\t+\t5\t5\tchr21\t33432871\t-\t5\t5\t17984\tvalid\tcircular\texonic\t20\t12\t6\t2\t3\t3\t2\t1\t0\t0.8277\t0.9167\t0\t0.75\t12.6\t50.8\t0.7995\t0.1045\t5.4663\t12.8\t24.2\t0.8072\t0.0987\t5.4049\t0.3333\t0.3\t1.6667\t\t\t\t\tchr21:33414887/33414888(+)->chr21:33432871/33432872(-):(spanning_paired_1:2,spanning_paired_1_t:3,spanning_paired_2:2,spanning_paired_2_t:3)&chr21:33426883/33426884(+)->chr21:33432871/33432872(-):(spanning_paired_1:1,spanning_paired_2:1)&chr21:33414915/33414916(+)->chr21:33421509/33421510(-):(discordant_mates:4)\n'

diff -r 5348cfd3ba5c -r 3de621c44cf9 test-data/integrate_test_terg_s041.out.txt
--- a/test-data/integrate_test_terg_s041.out.txt Thu Aug 10 05:38:27 2017 -0400
+++ b/test-data/integrate_test_terg_s041.out.txt Thu Sep 14 04:30:12 2017 -0400

diff -r 5348cfd3ba5c -r 3de621c44cf9 test-data/integrate_tmprss-erg.hg38.gtf
--- a/test-data/integrate_tmprss-erg.hg38.gtf Thu Aug 10 05:38:27 2017 -0400
+++ b/test-data/integrate_tmprss-erg.hg38.gtf Thu Sep 14 04:30:12 2017 -0400

b'@@ -1,159 +1,490 @@\n chr21\tensembl_havana\tgene\t38380027\t38661780\t.\t-\t.\tgene_id "ENSG00000157554"; gene_version "18"; gene_name "ERG"; gene_source "ensembl_havana"; gene_biotype "protein_coding";\n+chr21\thavana\ttranscript\t38380027\t38498442\t.\t-\t.\tgene_id "ENSG00000157554"; gene_version "18"; transcript_id "ENST00000398905"; transcript_version "5"; gene_name "ERG"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "ERG-203"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS82674"; tag "basic"; transcript_support_level "1";\n+chr21\thavana\texon\t38498363\t38498442\t.\t-\t.\tgene_id "ENSG00000157554"; gene_version "18"; transcript_id "ENST00000398905"; transcript_version "5"; exon_number "1"; gene_name "ERG"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "ERG-203"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS82674"; exon_id "ENSE00001535525"; exon_version "1"; tag "basic"; transcript_support_level "1";\n chr21\thavana\tCDS\t38498363\t38498380\t.\t-\t0\tgene_id "ENSG00000157554"; gene_version "18"; transcript_id "ENST00000398905"; transcript_version "5"; exon_number "1"; gene_name "ERG"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "ERG-203"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS82674"; protein_id "ENSP00000381877"; protein_version "1"; tag "basic"; transcript_support_level "1";\n+chr21\thavana\tstart_codon\t38498378\t38498380\t.\t-\t0\tgene_id "ENSG00000157554"; gene_version "18"; transcript_id "ENST00000398905"; transcript_version "5"; exon_number "1"; gene_name "ERG"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "ERG-203"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS82674"; tag "basic"; transcript_support_level "1";\n+chr21\thavana\texon\t38445404\t38445621\t.\t-\t.\tgene_id "ENSG00000157554"; gene_version "18"; transcript_id "ENST00000398905"; transcript_version "5"; exon_number "2"; gene_name "ERG"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "ERG-203"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS82674"; exon_id "ENSE00003712731"; exon_version "1"; tag "basic"; transcript_support_level "1";\n chr21\thavana\tCDS\t38445404\t38445621\t.\t-\t0\tgene_id "ENSG00000157554"; gene_version "18"; transcript_id "ENST00000398905"; transcript_version "5"; exon_number "2"; gene_name "ERG"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "ERG-203"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS82674"; protein_id "ENSP00000381877"; protein_version "1"; tag "basic"; transcript_support_level "1";\n+chr21\thavana\texon\t38423410\t38423561\t.\t-\t.\tgene_id "ENSG00000157554"; gene_version "18"; transcript_id "ENST00000398905"; transcript_version "5"; exon_number "3"; gene_name "ERG"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "ERG-203"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS82674"; exon_id "ENSE00003508916"; exon_version "1"; tag "basic"; transcript_support_level "1";\n chr21\thavana\tCDS\t38423410\t38423561\t.\t-\t1\tgene_id "ENSG00000157554"; gene_version "18"; transcript_id "ENST00000398905"; transcript_version "5"; exon_number "3"; gene_name "ERG"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "ERG-203"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS82674"; protein_id "ENSP00000381877"; protein_version "1"; tag "basic"; transcript_support_level "1";\n+chr21\thavana\texon\t38403506\t38403709\t.\t-\t.\tgene_id "ENSG00000157554"; gene_version "18"; transcript_id "ENST00000398905"; transcript_version "5"; exon_number "4"; gene_name "ERG"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript'..b'e "havana"; transcript_biotype "protein_coding"; exon_id "ENSE00003502036"; exon_version "1"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "2";\n chr21\thavana\tCDS\t41498119\t41498133\t.\t-\t0\tgene_id "ENSG00000184012"; gene_version "11"; transcript_id "ENST00000455813"; transcript_version "1"; exon_number "2"; gene_name "TMPRSS2"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "TMPRSS2-205"; transcript_source "havana"; transcript_biotype "protein_coding"; protein_id "ENSP00000391784"; protein_version "1"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "2";\n+chr21\thavana\tstart_codon\t41498131\t41498133\t.\t-\t0\tgene_id "ENSG00000184012"; gene_version "11"; transcript_id "ENST00000455813"; transcript_version "1"; exon_number "2"; gene_name "TMPRSS2"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "TMPRSS2-205"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "2";\n+chr21\thavana\texon\t41494356\t41494578\t.\t-\t.\tgene_id "ENSG00000184012"; gene_version "11"; transcript_id "ENST00000455813"; transcript_version "1"; exon_number "3"; gene_name "TMPRSS2"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "TMPRSS2-205"; transcript_source "havana"; transcript_biotype "protein_coding"; exon_id "ENSE00003788834"; exon_version "1"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "2";\n chr21\thavana\tCDS\t41494356\t41494578\t.\t-\t0\tgene_id "ENSG00000184012"; gene_version "11"; transcript_id "ENST00000455813"; transcript_version "1"; exon_number "3"; gene_name "TMPRSS2"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "TMPRSS2-205"; transcript_source "havana"; transcript_biotype "protein_coding"; protein_id "ENSP00000391784"; protein_version "1"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "2";\n+chr21\thavana\tfive_prime_utr\t41506445\t41506604\t.\t-\t.\tgene_id "ENSG00000184012"; gene_version "11"; transcript_id "ENST00000455813"; transcript_version "1"; gene_name "TMPRSS2"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "TMPRSS2-205"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "2";\n+chr21\thavana\tfive_prime_utr\t41498134\t41498189\t.\t-\t.\tgene_id "ENSG00000184012"; gene_version "11"; transcript_id "ENST00000455813"; transcript_version "1"; gene_name "TMPRSS2"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "TMPRSS2-205"; transcript_source "havana"; transcript_biotype "protein_coding"; tag "cds_end_NF"; tag "mRNA_end_NF"; transcript_support_level "2";\n+chr21\thavana\ttranscript\t41529789\t41531098\t.\t-\t.\tgene_id "ENSG00000184012"; gene_version "11"; transcript_id "ENST00000489201"; transcript_version "1"; gene_name "TMPRSS2"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "TMPRSS2-210"; transcript_source "havana"; transcript_biotype "retained_intron"; tag "mRNA_end_NF"; transcript_support_level "3";\n+chr21\thavana\texon\t41530985\t41531098\t.\t-\t.\tgene_id "ENSG00000184012"; gene_version "11"; transcript_id "ENST00000489201"; transcript_version "1"; exon_number "1"; gene_name "TMPRSS2"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "TMPRSS2-210"; transcript_source "havana"; transcript_biotype "retained_intron"; exon_id "ENSE00001838338"; exon_version "1"; tag "mRNA_end_NF"; transcript_support_level "3";\n+chr21\thavana\texon\t41529789\t41530218\t.\t-\t.\tgene_id "ENSG00000184012"; gene_version "11"; transcript_id "ENST00000489201"; transcript_version "1"; exon_number "2"; gene_name "TMPRSS2"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "TMPRSS2-210"; transcript_source "havana"; transcript_biotype "retained_intron"; exon_id "ENSE00001948395"; exon_version "1"; tag "mRNA_end_NF"; transcript_support_level "3";\n'