# HG changeset patch
# User iuc
# Date 1526670634 14400
# Node ID 75a14cc16d4d8f227afa02fcd6ee1a677424c964

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gtfToBed12 commit adc4f5c431fca0bcdf93188b7065bdc4c9c424c6

diff -r 000000000000 -r 75a14cc16d4d gtfToBed12.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/gtfToBed12.xml	Fri May 18 15:10:34 2018 -0400
@@ -0,0 +1,127 @@
+<tool id="gtftobed12" name="Convert GTF to BED12" version="357">
+    <requirements>
+        <requirement type="package" version="357">ucsc-gtftogenepred</requirement>
+        <requirement type="package" version="357">ucsc-genepredtobed</requirement>
+    </requirements>
+    <command detect_errors="aggressive"><![CDATA[
+        gtfToGenePred
+            #if $advanced_options.advanced_options_selector == "advanced":
+                $advanced_options.ignoreGroupsWithoutExons
+                $advanced_options.simple
+                $advanced_options.allErrors
+                $advanced_options.impliedStopAfterCds
+                $advanced_options.includeVersion
+                #if $advanced_options.infoOut:
+                    -infoOut='${transcript_info_file}'
+                #end if
+                #for $prefix in $advanced_options.sourcePrefixes
+                    -sourcePrefix='${prefix.sourcePrefix}'
+                #end for
+            #end if
+            '${gtf_file}'
+            'temp.genePred' &&
+        genePredToBed 'temp.genePred' '${bed_file}'
+        ]]>
+    </command>
+    <inputs>
+        <param name="gtf_file" type="data" format="gtf" label="GTF File to convert" />
+        <conditional name="advanced_options">
+            <param name="advanced_options_selector" type="select" label="Advanced options"
+                help="Advanced options for gtfToGenePred.">
+                <option value="default" selected="true">Use default options</option>
+                <option value="advanced">Set advanced options</option>
+            </param>
+            <when value="default" />
+            <when value="advanced">
+                <repeat name="sourcePrefixes" title="Source Prefixes"
+                    help="Only process entries where the source name has the specified prefixes">
+                    <param argument="-sourcePrefix" label="Source prefix"
+                        type="text" />
+                </repeat>
+                <param argument="-ignoreGroupsWithoutExons" label="Ignore groups without exons"
+                    help="Ignore groups that do not have exons, otherwise they will cause an error."
+                    type="boolean" truevalue="-ignoreGroupsWithoutExons" falsevalue="" checked="false" />
+                <param argument="-simple" label="Skip hierarchy check"
+                    help="Only check column validity, not heirarchy, may result in invalid output."
+                    type="boolean" truevalue="-simple" falsevalue="" checked="false" />
+                <param argument="-allErrors" label="Skip all errors"
+                    help="Skip groups with errors rather than aborting. Useful for getting information
+                    about as many errors as possible."
+                    type="boolean" truevalue="-allErrors" falsevalue="" checked="false" />
+                <param argument="-impliedStopAfterCds" label="Implied stop codon in after CDS"
+                    help="Assume there is an implied stop codon after CDS."
+                    type="boolean" truevalue="-impliedStopAfterCds" falsevalue="" checked="false" />
+                <param argument="-includeVersion" label="Include gene and transcript version"
+                    help="If gene_version and/or transcript_version attributes exist, include the version
+                    in the corresponding identifiers."
+                    type="boolean" truevalue="-includeVersion" falsevalue="" checked="false" />
+                <param argument="-infoOut" label="Output transcript information file"
+                    help="Outputs a file with information about each transcript."
+                    type="boolean" checked="false" />
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data name="bed_file" format="bed12" metadata_source="gtf_file" />
+        <data name="transcript_info_file" format="tabular" metadata_source="gtf_file">
+            <filter>advanced_options['infoOut']</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <param name="gtf_file" value="gtf2bed_test.gtf"/>
+            <output name="bed_file" file="gtf2bed_test.bed" ftype="bed12"/>
+        </test>
+        <test>
+            <param name="gtf_file" value="gtf2bed_test_missing_exon.gtf"/>
+            <param name="advanced_options_selector" value="advanced" />
+            <param name="ignoreGroupsWithoutExons" value="true" />
+            <output name="bed_file" file="gtf2bed_test_missing_exon.bed" ftype="bed12"/>
+        </test>
+        <test>
+            <param name="gtf_file" value="gtf2bed_test.gtf"/>
+            <param name="advanced_options_selector" value="advanced" />
+            <param name="includeVersion" value="true" />
+            <output name="bed_file" file="gtf2bed_test_include_version.bed" ftype="bed12"/>
+        </test>
+        <test>
+            <param name="gtf_file" value="gtf2bed_test.gtf"/>
+            <param name="advanced_options_selector" value="advanced" />
+            <param name="infoOut" value="true" />
+            <output name="bed_file" file="gtf2bed_test.bed" ftype="bed12"/>
+            <output name="transcript_info_file" file="gtf2bed_test_transcript_info.txt" ftype="tabular"/>
+        </test>
+        <test>
+            <param name="gtf_file" value="gtf2bed_test.gtf"/>
+            <param name="advanced_options_selector" value="advanced" />
+            <repeat name="sourcePrefixes">
+                <param name="sourcePrefix" value="hav" />
+            </repeat>
+            <output name="bed_file" file="gtf2bed_test_havana.bed" ftype="bed12"/>
+        </test>
+        <test>
+            <param name="gtf_file" value="gtf2bed_test.gtf"/>
+            <param name="advanced_options_selector" value="advanced" />
+            <repeat name="sourcePrefixes">
+                <param name="sourcePrefix" value="hav" />
+            </repeat>
+            <repeat name="sourcePrefixes">
+                <param name="sourcePrefix" value="ens" />
+            </repeat>
+            <output name="bed_file" file="gtf2bed_test.bed" ftype="bed12"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+Converts a GTF_ file to a BED12_ formatted file using UCSC tools from Jim Kent.
+
+``gtfToGenePred``, followed by ``genePredToBed``
+
+.. _GTF: https://genome.ucsc.edu/FAQ/FAQformat.html#format4
+.. _BED12: https://genome.ucsc.edu/FAQ/FAQformat.html#format1
+        ]]>
+    </help>
+
+    <citations>
+        <citation type="doi">10.1101/gr.229102</citation>
+    </citations>
+</tool>
diff -r 000000000000 -r 75a14cc16d4d test-data/gtf2bed_test.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gtf2bed_test.bed	Fri May 18 15:10:34 2018 -0400
@@ -0,0 +1,21 @@
+1	11868	14409	ENST00000456328	0	+	14409	14409	0	3	359,109,1189,	0,744,1352,
+1	12009	13670	ENST00000450305	0	+	13670	13670	0	6	48,49,85,78,154,218,	0,169,603,965,1211,1443,
+1	14403	29570	ENST00000488147	0	-	29570	29570	0	11	98,34,152,159,198,136,137,147,99,154,37,	0,601,1392,2203,2454,2829,3202,3511,3864,10334,15130,
+1	17368	17436	ENST00000619216	0	-	17436	17436	0	1	68,	0,
+1	29553	31097	ENST00000473358	0	+	31097	31097	0	3	486,104,122,	0,1010,1422,
+1	30266	31109	ENST00000469289	0	+	31109	31109	0	2	401,134,	0,709,
+1	30365	30503	ENST00000607096	0	+	30503	30503	0	1	138,	0,
+1	34553	36081	ENST00000417324	0	-	36081	36081	0	3	621,205,361,	0,723,1167,
+1	35244	36073	ENST00000461467	0	-	36073	36073	0	2	237,353,	0,476,
+1	52472	53312	ENST00000606857	0	+	53312	53312	0	1	840,	0,
+1	62947	63887	ENST00000492842	0	+	63887	63887	0	1	940,	0,
+1	69090	70008	ENST00000335137	0	+	69090	70008	0	1	918,	0,
+1	89294	120932	ENST00000466430	0	-	120932	120932	0	4	2335,150,105,158,	0,2796,23405,31480,
+1	92229	129217	ENST00000477740	0	-	129217	129217	0	4	11,105,212,163,	0,20470,28491,36825,
+1	110952	129173	ENST00000471248	0	-	129173	129173	0	3	405,105,119,	0,1747,18102,
+1	120724	133723	ENST00000610542	0	-	133723	133723	0	4	145,59,169,350,	0,149,8330,12649,
+1	129080	133566	ENST00000453576	0	-	133566	133566	0	2	143,193,	0,4293,
+1	89550	91105	ENST00000495576	0	-	91105	91105	0	2	500,819,	0,736,
+1	131024	134836	ENST00000442987	0	+	134836	134836	0	1	3812,	0,
+1	135140	135895	ENST00000494149	0	-	135895	135895	0	1	755,	0,
+1	137681	137965	ENST00000595919	0	-	137965	137965	0	1	284,	0,
diff -r 000000000000 -r 75a14cc16d4d test-data/gtf2bed_test.gtf
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gtf2bed_test.gtf	Fri May 18 15:10:34 2018 -0400
@@ -0,0 +1,100 @@
+#!genome-build GRCh38.p2
+#!genome-version GRCh38
+#!genome-date 2013-12
+#!genome-build-accession NCBI:GCA_000001405.17
+#!genebuild-last-updated 2015-01
+1	havana	gene	11869	14409	.	+	.	gene_id "ENSG00000223972"; gene_version "5"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene";
+1	havana	transcript	11869	14409	.	+	.	gene_id "ENSG00000223972"; gene_version "5"; transcript_id "ENST00000456328"; transcript_version "2"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; transcript_name "DDX11L1-002"; transcript_source "havana"; transcript_biotype "processed_transcript"; tag "basic"; transcript_support_level "1";
+1	havana	exon	11869	12227	.	+	.	gene_id "ENSG00000223972"; gene_version "5"; transcript_id "ENST00000456328"; transcript_version "2"; exon_number "1"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; transcript_name "DDX11L1-002"; transcript_source "havana"; transcript_biotype "processed_transcript"; exon_id "ENSE00002234944"; exon_version "1"; tag "basic"; transcript_support_level "1";
+1	havana	exon	12613	12721	.	+	.	gene_id "ENSG00000223972"; gene_version "5"; transcript_id "ENST00000456328"; transcript_version "2"; exon_number "2"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; transcript_name "DDX11L1-002"; transcript_source "havana"; transcript_biotype "processed_transcript"; exon_id "ENSE00003582793"; exon_version "1"; tag "basic"; transcript_support_level "1";
+1	havana	exon	13221	14409	.	+	.	gene_id "ENSG00000223972"; gene_version "5"; transcript_id "ENST00000456328"; transcript_version "2"; exon_number "3"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; transcript_name "DDX11L1-002"; transcript_source "havana"; transcript_biotype "processed_transcript"; exon_id "ENSE00002312635"; exon_version "1"; tag "basic"; transcript_support_level "1";
+1	havana	transcript	12010	13670	.	+	.	gene_id "ENSG00000223972"; gene_version "5"; transcript_id "ENST00000450305"; transcript_version "2"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; transcript_name "DDX11L1-001"; transcript_source "havana"; transcript_biotype "transcribed_unprocessed_pseudogene"; tag "basic"; transcript_support_level "NA";
+1	havana	exon	12010	12057	.	+	.	gene_id "ENSG00000223972"; gene_version "5"; transcript_id "ENST00000450305"; transcript_version "2"; exon_number "1"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; transcript_name "DDX11L1-001"; transcript_source "havana"; transcript_biotype "transcribed_unprocessed_pseudogene"; exon_id "ENSE00001948541"; exon_version "1"; tag "basic"; transcript_support_level "NA";
+1	havana	exon	12179	12227	.	+	.	gene_id "ENSG00000223972"; gene_version "5"; transcript_id "ENST00000450305"; transcript_version "2"; exon_number "2"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; transcript_name "DDX11L1-001"; transcript_source "havana"; transcript_biotype "transcribed_unprocessed_pseudogene"; exon_id "ENSE00001671638"; exon_version "2"; tag "basic"; transcript_support_level "NA";
+1	havana	exon	12613	12697	.	+	.	gene_id "ENSG00000223972"; gene_version "5"; transcript_id "ENST00000450305"; transcript_version "2"; exon_number "3"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; transcript_name "DDX11L1-001"; transcript_source "havana"; transcript_biotype "transcribed_unprocessed_pseudogene"; exon_id "ENSE00001758273"; exon_version "2"; tag "basic"; transcript_support_level "NA";
+1	havana	exon	12975	13052	.	+	.	gene_id "ENSG00000223972"; gene_version "5"; transcript_id "ENST00000450305"; transcript_version "2"; exon_number "4"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; transcript_name "DDX11L1-001"; transcript_source "havana"; transcript_biotype "transcribed_unprocessed_pseudogene"; exon_id "ENSE00001799933"; exon_version "2"; tag "basic"; transcript_support_level "NA";
+1	havana	exon	13221	13374	.	+	.	gene_id "ENSG00000223972"; gene_version "5"; transcript_id "ENST00000450305"; transcript_version "2"; exon_number "5"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; transcript_name "DDX11L1-001"; transcript_source "havana"; transcript_biotype "transcribed_unprocessed_pseudogene"; exon_id "ENSE00001746346"; exon_version "2"; tag "basic"; transcript_support_level "NA";
+1	havana	exon	13453	13670	.	+	.	gene_id "ENSG00000223972"; gene_version "5"; transcript_id "ENST00000450305"; transcript_version "2"; exon_number "6"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; transcript_name "DDX11L1-001"; transcript_source "havana"; transcript_biotype "transcribed_unprocessed_pseudogene"; exon_id "ENSE00001863096"; exon_version "1"; tag "basic"; transcript_support_level "NA";
+1	havana	gene	14404	29570	.	-	.	gene_id "ENSG00000227232"; gene_version "5"; gene_name "WASH7P"; gene_source "havana"; gene_biotype "unprocessed_pseudogene";
+1	havana	transcript	14404	29570	.	-	.	gene_id "ENSG00000227232"; gene_version "5"; transcript_id "ENST00000488147"; transcript_version "1"; gene_name "WASH7P"; gene_source "havana"; gene_biotype "unprocessed_pseudogene"; transcript_name "WASH7P-001"; transcript_source "havana"; transcript_biotype "unprocessed_pseudogene"; tag "basic"; transcript_support_level "NA";
+1	havana	exon	29534	29570	.	-	.	gene_id "ENSG00000227232"; gene_version "5"; transcript_id "ENST00000488147"; transcript_version "1"; exon_number "1"; gene_name "WASH7P"; gene_source "havana"; gene_biotype "unprocessed_pseudogene"; transcript_name "WASH7P-001"; transcript_source "havana"; transcript_biotype "unprocessed_pseudogene"; exon_id "ENSE00001890219"; exon_version "1"; tag "basic"; transcript_support_level "NA";
+1	havana	exon	24738	24891	.	-	.	gene_id "ENSG00000227232"; gene_version "5"; transcript_id "ENST00000488147"; transcript_version "1"; exon_number "2"; gene_name "WASH7P"; gene_source "havana"; gene_biotype "unprocessed_pseudogene"; transcript_name "WASH7P-001"; transcript_source "havana"; transcript_biotype "unprocessed_pseudogene"; exon_id "ENSE00003507205"; exon_version "1"; tag "basic"; transcript_support_level "NA";
+1	havana	exon	18268	18366	.	-	.	gene_id "ENSG00000227232"; gene_version "5"; transcript_id "ENST00000488147"; transcript_version "1"; exon_number "3"; gene_name "WASH7P"; gene_source "havana"; gene_biotype "unprocessed_pseudogene"; transcript_name "WASH7P-001"; transcript_source "havana"; transcript_biotype "unprocessed_pseudogene"; exon_id "ENSE00003477500"; exon_version "1"; tag "basic"; transcript_support_level "NA";
+1	havana	exon	17915	18061	.	-	.	gene_id "ENSG00000227232"; gene_version "5"; transcript_id "ENST00000488147"; transcript_version "1"; exon_number "4"; gene_name "WASH7P"; gene_source "havana"; gene_biotype "unprocessed_pseudogene"; transcript_name "WASH7P-001"; transcript_source "havana"; transcript_biotype "unprocessed_pseudogene"; exon_id "ENSE00003565697"; exon_version "1"; tag "basic"; transcript_support_level "NA";
+1	havana	exon	17606	17742	.	-	.	gene_id "ENSG00000227232"; gene_version "5"; transcript_id "ENST00000488147"; transcript_version "1"; exon_number "5"; gene_name "WASH7P"; gene_source "havana"; gene_biotype "unprocessed_pseudogene"; transcript_name "WASH7P-001"; transcript_source "havana"; transcript_biotype "unprocessed_pseudogene"; exon_id "ENSE00003475637"; exon_version "1"; tag "basic"; transcript_support_level "NA";
+1	havana	exon	17233	17368	.	-	.	gene_id "ENSG00000227232"; gene_version "5"; transcript_id "ENST00000488147"; transcript_version "1"; exon_number "6"; gene_name "WASH7P"; gene_source "havana"; gene_biotype "unprocessed_pseudogene"; transcript_name "WASH7P-001"; transcript_source "havana"; transcript_biotype "unprocessed_pseudogene"; exon_id "ENSE00003502542"; exon_version "1"; tag "basic"; transcript_support_level "NA";
+1	havana	exon	16858	17055	.	-	.	gene_id "ENSG00000227232"; gene_version "5"; transcript_id "ENST00000488147"; transcript_version "1"; exon_number "7"; gene_name "WASH7P"; gene_source "havana"; gene_biotype "unprocessed_pseudogene"; transcript_name "WASH7P-001"; transcript_source "havana"; transcript_biotype "unprocessed_pseudogene"; exon_id "ENSE00003553898"; exon_version "1"; tag "basic"; transcript_support_level "NA";
+1	havana	exon	16607	16765	.	-	.	gene_id "ENSG00000227232"; gene_version "5"; transcript_id "ENST00000488147"; transcript_version "1"; exon_number "8"; gene_name "WASH7P"; gene_source "havana"; gene_biotype "unprocessed_pseudogene"; transcript_name "WASH7P-001"; transcript_source "havana"; transcript_biotype "unprocessed_pseudogene"; exon_id "ENSE00003621279"; exon_version "1"; tag "basic"; transcript_support_level "NA";
+1	havana	exon	15796	15947	.	-	.	gene_id "ENSG00000227232"; gene_version "5"; transcript_id "ENST00000488147"; transcript_version "1"; exon_number "9"; gene_name "WASH7P"; gene_source "havana"; gene_biotype "unprocessed_pseudogene"; transcript_name "WASH7P-001"; transcript_source "havana"; transcript_biotype "unprocessed_pseudogene"; exon_id "ENSE00002030414"; exon_version "1"; tag "basic"; transcript_support_level "NA";
+1	havana	exon	15005	15038	.	-	.	gene_id "ENSG00000227232"; gene_version "5"; transcript_id "ENST00000488147"; transcript_version "1"; exon_number "10"; gene_name "WASH7P"; gene_source "havana"; gene_biotype "unprocessed_pseudogene"; transcript_name "WASH7P-001"; transcript_source "havana"; transcript_biotype "unprocessed_pseudogene"; exon_id "ENSE00001935574"; exon_version "1"; tag "basic"; transcript_support_level "NA";
+1	havana	exon	14404	14501	.	-	.	gene_id "ENSG00000227232"; gene_version "5"; transcript_id "ENST00000488147"; transcript_version "1"; exon_number "11"; gene_name "WASH7P"; gene_source "havana"; gene_biotype "unprocessed_pseudogene"; transcript_name "WASH7P-001"; transcript_source "havana"; transcript_biotype "unprocessed_pseudogene"; exon_id "ENSE00001843071"; exon_version "1"; tag "basic"; transcript_support_level "NA";
+1	ensembl	gene	17369	17436	.	-	.	gene_id "ENSG00000278267"; gene_version "1"; gene_name "MIR6859-1"; gene_source "ensembl"; gene_biotype "miRNA";
+1	ensembl	transcript	17369	17436	.	-	.	gene_id "ENSG00000278267"; gene_version "1"; transcript_id "ENST00000619216"; transcript_version "1"; gene_name "MIR6859-1"; gene_source "ensembl"; gene_biotype "miRNA"; transcript_name "MIR6859-1-201"; transcript_source "ensembl"; transcript_biotype "miRNA"; tag "basic"; transcript_support_level "NA";
+1	ensembl	exon	17369	17436	.	-	.	gene_id "ENSG00000278267"; gene_version "1"; transcript_id "ENST00000619216"; transcript_version "1"; exon_number "1"; gene_name "MIR6859-1"; gene_source "ensembl"; gene_biotype "miRNA"; transcript_name "MIR6859-1-201"; transcript_source "ensembl"; transcript_biotype "miRNA"; exon_id "ENSE00003746039"; exon_version "1"; tag "basic"; transcript_support_level "NA";
+1	havana	gene	29554	31109	.	+	.	gene_id "ENSG00000243485"; gene_version "3"; gene_name "RP11-34P13.3"; gene_source "havana"; gene_biotype "lincRNA";
+1	havana	transcript	29554	31097	.	+	.	gene_id "ENSG00000243485"; gene_version "3"; transcript_id "ENST00000473358"; transcript_version "1"; gene_name "RP11-34P13.3"; gene_source "havana"; gene_biotype "lincRNA"; transcript_name "RP11-34P13.3-001"; transcript_source "havana"; transcript_biotype "lincRNA"; tag "basic"; transcript_support_level "5";
+1	havana	exon	29554	30039	.	+	.	gene_id "ENSG00000243485"; gene_version "3"; transcript_id "ENST00000473358"; transcript_version "1"; exon_number "1"; gene_name "RP11-34P13.3"; gene_source "havana"; gene_biotype "lincRNA"; transcript_name "RP11-34P13.3-001"; transcript_source "havana"; transcript_biotype "lincRNA"; exon_id "ENSE00001947070"; exon_version "1"; tag "basic"; transcript_support_level "5";
+1	havana	exon	30564	30667	.	+	.	gene_id "ENSG00000243485"; gene_version "3"; transcript_id "ENST00000473358"; transcript_version "1"; exon_number "2"; gene_name "RP11-34P13.3"; gene_source "havana"; gene_biotype "lincRNA"; transcript_name "RP11-34P13.3-001"; transcript_source "havana"; transcript_biotype "lincRNA"; exon_id "ENSE00001922571"; exon_version "1"; tag "basic"; transcript_support_level "5";
+1	havana	exon	30976	31097	.	+	.	gene_id "ENSG00000243485"; gene_version "3"; transcript_id "ENST00000473358"; transcript_version "1"; exon_number "3"; gene_name "RP11-34P13.3"; gene_source "havana"; gene_biotype "lincRNA"; transcript_name "RP11-34P13.3-001"; transcript_source "havana"; transcript_biotype "lincRNA"; exon_id "ENSE00001827679"; exon_version "1"; tag "basic"; transcript_support_level "5";
+1	havana	transcript	30267	31109	.	+	.	gene_id "ENSG00000243485"; gene_version "3"; transcript_id "ENST00000469289"; transcript_version "1"; gene_name "RP11-34P13.3"; gene_source "havana"; gene_biotype "lincRNA"; transcript_name "RP11-34P13.3-002"; transcript_source "havana"; transcript_biotype "lincRNA"; transcript_support_level "5";
+1	havana	exon	30267	30667	.	+	.	gene_id "ENSG00000243485"; gene_version "3"; transcript_id "ENST00000469289"; transcript_version "1"; exon_number "1"; gene_name "RP11-34P13.3"; gene_source "havana"; gene_biotype "lincRNA"; transcript_name "RP11-34P13.3-002"; transcript_source "havana"; transcript_biotype "lincRNA"; exon_id "ENSE00001841699"; exon_version "1"; transcript_support_level "5";
+1	havana	exon	30976	31109	.	+	.	gene_id "ENSG00000243485"; gene_version "3"; transcript_id "ENST00000469289"; transcript_version "1"; exon_number "2"; gene_name "RP11-34P13.3"; gene_source "havana"; gene_biotype "lincRNA"; transcript_name "RP11-34P13.3-002"; transcript_source "havana"; transcript_biotype "lincRNA"; exon_id "ENSE00001890064"; exon_version "1"; transcript_support_level "5";
+1	ensembl	gene	30366	30503	.	+	.	gene_id "ENSG00000274890"; gene_version "1"; gene_name "MIR1302-2"; gene_source "ensembl"; gene_biotype "miRNA";
+1	ensembl	transcript	30366	30503	.	+	.	gene_id "ENSG00000274890"; gene_version "1"; transcript_id "ENST00000607096"; transcript_version "1"; gene_name "MIR1302-2"; gene_source "ensembl"; gene_biotype "miRNA"; transcript_name "MIR1302-2-201"; transcript_source "ensembl"; transcript_biotype "miRNA"; tag "basic"; transcript_support_level "NA";
+1	ensembl	exon	30366	30503	.	+	.	gene_id "ENSG00000274890"; gene_version "1"; transcript_id "ENST00000607096"; transcript_version "1"; exon_number "1"; gene_name "MIR1302-2"; gene_source "ensembl"; gene_biotype "miRNA"; transcript_name "MIR1302-2-201"; transcript_source "ensembl"; transcript_biotype "miRNA"; exon_id "ENSE00003695741"; exon_version "1"; tag "basic"; transcript_support_level "NA";
+1	havana	gene	34554	36081	.	-	.	gene_id "ENSG00000237613"; gene_version "2"; gene_name "FAM138A"; gene_source "havana"; gene_biotype "lincRNA";
+1	havana	transcript	34554	36081	.	-	.	gene_id "ENSG00000237613"; gene_version "2"; transcript_id "ENST00000417324"; transcript_version "1"; gene_name "FAM138A"; gene_source "havana"; gene_biotype "lincRNA"; transcript_name "FAM138A-001"; transcript_source "havana"; transcript_biotype "lincRNA"; tag "basic"; transcript_support_level "1";
+1	havana	exon	35721	36081	.	-	.	gene_id "ENSG00000237613"; gene_version "2"; transcript_id "ENST00000417324"; transcript_version "1"; exon_number "1"; gene_name "FAM138A"; gene_source "havana"; gene_biotype "lincRNA"; transcript_name "FAM138A-001"; transcript_source "havana"; transcript_biotype "lincRNA"; exon_id "ENSE00001656588"; exon_version "1"; tag "basic"; transcript_support_level "1";
+1	havana	exon	35277	35481	.	-	.	gene_id "ENSG00000237613"; gene_version "2"; transcript_id "ENST00000417324"; transcript_version "1"; exon_number "2"; gene_name "FAM138A"; gene_source "havana"; gene_biotype "lincRNA"; transcript_name "FAM138A-001"; transcript_source "havana"; transcript_biotype "lincRNA"; exon_id "ENSE00001669267"; exon_version "1"; tag "basic"; transcript_support_level "1";
+1	havana	exon	34554	35174	.	-	.	gene_id "ENSG00000237613"; gene_version "2"; transcript_id "ENST00000417324"; transcript_version "1"; exon_number "3"; gene_name "FAM138A"; gene_source "havana"; gene_biotype "lincRNA"; transcript_name "FAM138A-001"; transcript_source "havana"; transcript_biotype "lincRNA"; exon_id "ENSE00001727627"; exon_version "1"; tag "basic"; transcript_support_level "1";
+1	havana	transcript	35245	36073	.	-	.	gene_id "ENSG00000237613"; gene_version "2"; transcript_id "ENST00000461467"; transcript_version "1"; gene_name "FAM138A"; gene_source "havana"; gene_biotype "lincRNA"; transcript_name "FAM138A-002"; transcript_source "havana"; transcript_biotype "lincRNA"; transcript_support_level "3";
+1	havana	exon	35721	36073	.	-	.	gene_id "ENSG00000237613"; gene_version "2"; transcript_id "ENST00000461467"; transcript_version "1"; exon_number "1"; gene_name "FAM138A"; gene_source "havana"; gene_biotype "lincRNA"; transcript_name "FAM138A-002"; transcript_source "havana"; transcript_biotype "lincRNA"; exon_id "ENSE00001618781"; exon_version "2"; transcript_support_level "3";
+1	havana	exon	35245	35481	.	-	.	gene_id "ENSG00000237613"; gene_version "2"; transcript_id "ENST00000461467"; transcript_version "1"; exon_number "2"; gene_name "FAM138A"; gene_source "havana"; gene_biotype "lincRNA"; transcript_name "FAM138A-002"; transcript_source "havana"; transcript_biotype "lincRNA"; exon_id "ENSE00001874421"; exon_version "1"; transcript_support_level "3";
+1	havana	gene	52473	53312	.	+	.	gene_id "ENSG00000268020"; gene_version "3"; gene_name "OR4G4P"; gene_source "havana"; gene_biotype "unprocessed_pseudogene";
+1	havana	transcript	52473	53312	.	+	.	gene_id "ENSG00000268020"; gene_version "3"; transcript_id "ENST00000606857"; transcript_version "1"; gene_name "OR4G4P"; gene_source "havana"; gene_biotype "unprocessed_pseudogene"; transcript_name "OR4G4P-001"; transcript_source "havana"; transcript_biotype "unprocessed_pseudogene"; tag "basic"; transcript_support_level "NA";
+1	havana	exon	52473	53312	.	+	.	gene_id "ENSG00000268020"; gene_version "3"; transcript_id "ENST00000606857"; transcript_version "1"; exon_number "1"; gene_name "OR4G4P"; gene_source "havana"; gene_biotype "unprocessed_pseudogene"; transcript_name "OR4G4P-001"; transcript_source "havana"; transcript_biotype "unprocessed_pseudogene"; exon_id "ENSE00003698237"; exon_version "1"; tag "basic"; transcript_support_level "NA";
+1	havana	gene	62948	63887	.	+	.	gene_id "ENSG00000240361"; gene_version "1"; gene_name "OR4G11P"; gene_source "havana"; gene_biotype "unprocessed_pseudogene";
+1	havana	transcript	62948	63887	.	+	.	gene_id "ENSG00000240361"; gene_version "1"; transcript_id "ENST00000492842"; transcript_version "1"; gene_name "OR4G11P"; gene_source "havana"; gene_biotype "unprocessed_pseudogene"; transcript_name "OR4G11P-001"; transcript_source "havana"; transcript_biotype "unprocessed_pseudogene"; tag "basic"; transcript_support_level "NA";
+1	havana	exon	62948	63887	.	+	.	gene_id "ENSG00000240361"; gene_version "1"; transcript_id "ENST00000492842"; transcript_version "1"; exon_number "1"; gene_name "OR4G11P"; gene_source "havana"; gene_biotype "unprocessed_pseudogene"; transcript_name "OR4G11P-001"; transcript_source "havana"; transcript_biotype "unprocessed_pseudogene"; exon_id "ENSE00001830178"; exon_version "1"; tag "basic"; transcript_support_level "NA";
+1	ensembl_havana	gene	69091	70008	.	+	.	gene_id "ENSG00000186092"; gene_version "4"; gene_name "OR4F5"; gene_source "ensembl_havana"; gene_biotype "protein_coding";
+1	ensembl_havana	transcript	69091	70008	.	+	.	gene_id "ENSG00000186092"; gene_version "4"; transcript_id "ENST00000335137"; transcript_version "3"; gene_name "OR4F5"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "OR4F5-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS30547"; tag "basic"; transcript_support_level "NA";
+1	ensembl_havana	exon	69091	70008	.	+	.	gene_id "ENSG00000186092"; gene_version "4"; transcript_id "ENST00000335137"; transcript_version "3"; exon_number "1"; gene_name "OR4F5"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "OR4F5-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS30547"; exon_id "ENSE00002319515"; exon_version "1"; tag "basic"; transcript_support_level "NA";
+1	ensembl_havana	CDS	69091	70005	.	+	0	gene_id "ENSG00000186092"; gene_version "4"; transcript_id "ENST00000335137"; transcript_version "3"; exon_number "1"; gene_name "OR4F5"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "OR4F5-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS30547"; protein_id "ENSP00000334393"; protein_version "3"; tag "basic"; transcript_support_level "NA";
+1	ensembl_havana	start_codon	69091	69093	.	+	0	gene_id "ENSG00000186092"; gene_version "4"; transcript_id "ENST00000335137"; transcript_version "3"; exon_number "1"; gene_name "OR4F5"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "OR4F5-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS30547"; tag "basic"; transcript_support_level "NA";
+1	ensembl_havana	stop_codon	70006	70008	.	+	0	gene_id "ENSG00000186092"; gene_version "4"; transcript_id "ENST00000335137"; transcript_version "3"; exon_number "1"; gene_name "OR4F5"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "OR4F5-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS30547"; tag "basic"; transcript_support_level "NA";
+1	ensembl_havana	gene	89295	133723	.	-	.	gene_id "ENSG00000238009"; gene_version "5"; gene_name "RP11-34P13.7"; gene_source "ensembl_havana"; gene_biotype "lincRNA";
+1	havana	transcript	89295	120932	.	-	.	gene_id "ENSG00000238009"; gene_version "5"; transcript_id "ENST00000466430"; transcript_version "4"; gene_name "RP11-34P13.7"; gene_source "ensembl_havana"; gene_biotype "lincRNA"; transcript_name "RP11-34P13.7-001"; transcript_source "havana"; transcript_biotype "lincRNA"; tag "basic"; transcript_support_level "5 (assigned to previous version 3)";
+1	havana	exon	120775	120932	.	-	.	gene_id "ENSG00000238009"; gene_version "5"; transcript_id "ENST00000466430"; transcript_version "4"; exon_number "1"; gene_name "RP11-34P13.7"; gene_source "ensembl_havana"; gene_biotype "lincRNA"; transcript_name "RP11-34P13.7-001"; transcript_source "havana"; transcript_biotype "lincRNA"; exon_id "ENSE00001606755"; exon_version "2"; tag "basic"; transcript_support_level "5 (assigned to previous version 3)";
+1	havana	exon	112700	112804	.	-	.	gene_id "ENSG00000238009"; gene_version "5"; transcript_id "ENST00000466430"; transcript_version "4"; exon_number "2"; gene_name "RP11-34P13.7"; gene_source "ensembl_havana"; gene_biotype "lincRNA"; transcript_name "RP11-34P13.7-001"; transcript_source "havana"; transcript_biotype "lincRNA"; exon_id "ENSE00001957285"; exon_version "1"; tag "basic"; transcript_support_level "5 (assigned to previous version 3)";
+1	havana	exon	92091	92240	.	-	.	gene_id "ENSG00000238009"; gene_version "5"; transcript_id "ENST00000466430"; transcript_version "4"; exon_number "3"; gene_name "RP11-34P13.7"; gene_source "ensembl_havana"; gene_biotype "lincRNA"; transcript_name "RP11-34P13.7-001"; transcript_source "havana"; transcript_biotype "lincRNA"; exon_id "ENSE00001944529"; exon_version "1"; tag "basic"; transcript_support_level "5 (assigned to previous version 3)";
+1	havana	exon	89295	91629	.	-	.	gene_id "ENSG00000238009"; gene_version "5"; transcript_id "ENST00000466430"; transcript_version "4"; exon_number "4"; gene_name "RP11-34P13.7"; gene_source "ensembl_havana"; gene_biotype "lincRNA"; transcript_name "RP11-34P13.7-001"; transcript_source "havana"; transcript_biotype "lincRNA"; exon_id "ENSE00001846804"; exon_version "1"; tag "basic"; transcript_support_level "5 (assigned to previous version 3)";
+1	havana	transcript	92230	129217	.	-	.	gene_id "ENSG00000238009"; gene_version "5"; transcript_id "ENST00000477740"; transcript_version "4"; gene_name "RP11-34P13.7"; gene_source "ensembl_havana"; gene_biotype "lincRNA"; transcript_name "RP11-34P13.7-003"; transcript_source "havana"; transcript_biotype "lincRNA"; transcript_support_level "5 (assigned to previous version 3)";
+1	havana	exon	129055	129217	.	-	.	gene_id "ENSG00000238009"; gene_version "5"; transcript_id "ENST00000477740"; transcript_version "4"; exon_number "1"; gene_name "RP11-34P13.7"; gene_source "ensembl_havana"; gene_biotype "lincRNA"; transcript_name "RP11-34P13.7-003"; transcript_source "havana"; transcript_biotype "lincRNA"; exon_id "ENSE00001919246"; exon_version "1"; transcript_support_level "5 (assigned to previous version 3)";
+1	havana	exon	120721	120932	.	-	.	gene_id "ENSG00000238009"; gene_version "5"; transcript_id "ENST00000477740"; transcript_version "4"; exon_number "2"; gene_name "RP11-34P13.7"; gene_source "ensembl_havana"; gene_biotype "lincRNA"; transcript_name "RP11-34P13.7-003"; transcript_source "havana"; transcript_biotype "lincRNA"; exon_id "ENSE00001171005"; exon_version "3"; transcript_support_level "5 (assigned to previous version 3)";
+1	havana	exon	112700	112804	.	-	.	gene_id "ENSG00000238009"; gene_version "5"; transcript_id "ENST00000477740"; transcript_version "4"; exon_number "3"; gene_name "RP11-34P13.7"; gene_source "ensembl_havana"; gene_biotype "lincRNA"; transcript_name "RP11-34P13.7-003"; transcript_source "havana"; transcript_biotype "lincRNA"; exon_id "ENSE00001957285"; exon_version "1"; transcript_support_level "5 (assigned to previous version 3)";
+1	havana	exon	92230	92240	.	-	.	gene_id "ENSG00000238009"; gene_version "5"; transcript_id "ENST00000477740"; transcript_version "4"; exon_number "4"; gene_name "RP11-34P13.7"; gene_source "ensembl_havana"; gene_biotype "lincRNA"; transcript_name "RP11-34P13.7-003"; transcript_source "havana"; transcript_biotype "lincRNA"; exon_id "ENSE00001896976"; exon_version "1"; transcript_support_level "5 (assigned to previous version 3)";
+1	havana	transcript	110953	129173	.	-	.	gene_id "ENSG00000238009"; gene_version "5"; transcript_id "ENST00000471248"; transcript_version "1"; gene_name "RP11-34P13.7"; gene_source "ensembl_havana"; gene_biotype "lincRNA"; transcript_name "RP11-34P13.7-002"; transcript_source "havana"; transcript_biotype "lincRNA"; transcript_support_level "5";
+1	havana	exon	129055	129173	.	-	.	gene_id "ENSG00000238009"; gene_version "5"; transcript_id "ENST00000471248"; transcript_version "1"; exon_number "1"; gene_name "RP11-34P13.7"; gene_source "ensembl_havana"; gene_biotype "lincRNA"; transcript_name "RP11-34P13.7-002"; transcript_source "havana"; transcript_biotype "lincRNA"; exon_id "ENSE00001934975"; exon_version "1"; transcript_support_level "5";
+1	havana	exon	112700	112804	.	-	.	gene_id "ENSG00000238009"; gene_version "5"; transcript_id "ENST00000471248"; transcript_version "1"; exon_number "2"; gene_name "RP11-34P13.7"; gene_source "ensembl_havana"; gene_biotype "lincRNA"; transcript_name "RP11-34P13.7-002"; transcript_source "havana"; transcript_biotype "lincRNA"; exon_id "ENSE00001957285"; exon_version "1"; transcript_support_level "5";
+1	havana	exon	110953	111357	.	-	.	gene_id "ENSG00000238009"; gene_version "5"; transcript_id "ENST00000471248"; transcript_version "1"; exon_number "3"; gene_name "RP11-34P13.7"; gene_source "ensembl_havana"; gene_biotype "lincRNA"; transcript_name "RP11-34P13.7-002"; transcript_source "havana"; transcript_biotype "lincRNA"; exon_id "ENSE00001879696"; exon_version "1"; transcript_support_level "5";
+1	ensembl	transcript	120725	133723	.	-	.	gene_id "ENSG00000238009"; gene_version "5"; transcript_id "ENST00000610542"; transcript_version "1"; gene_name "RP11-34P13.7"; gene_source "ensembl_havana"; gene_biotype "lincRNA"; transcript_name "RP11-34P13.7-201"; transcript_source "ensembl"; transcript_biotype "lincRNA"; transcript_support_level "5";
+1	ensembl	exon	133374	133723	.	-	.	gene_id "ENSG00000238009"; gene_version "5"; transcript_id "ENST00000610542"; transcript_version "1"; exon_number "1"; gene_name "RP11-34P13.7"; gene_source "ensembl_havana"; gene_biotype "lincRNA"; transcript_name "RP11-34P13.7-201"; transcript_source "ensembl"; transcript_biotype "lincRNA"; exon_id "ENSE00003748456"; exon_version "1"; transcript_support_level "5";
+1	ensembl	exon	129055	129223	.	-	.	gene_id "ENSG00000238009"; gene_version "5"; transcript_id "ENST00000610542"; transcript_version "1"; exon_number "2"; gene_name "RP11-34P13.7"; gene_source "ensembl_havana"; gene_biotype "lincRNA"; transcript_name "RP11-34P13.7-201"; transcript_source "ensembl"; transcript_biotype "lincRNA"; exon_id "ENSE00003734824"; exon_version "1"; transcript_support_level "5";
+1	ensembl	exon	120874	120932	.	-	.	gene_id "ENSG00000238009"; gene_version "5"; transcript_id "ENST00000610542"; transcript_version "1"; exon_number "3"; gene_name "RP11-34P13.7"; gene_source "ensembl_havana"; gene_biotype "lincRNA"; transcript_name "RP11-34P13.7-201"; transcript_source "ensembl"; transcript_biotype "lincRNA"; exon_id "ENSE00003740919"; exon_version "1"; transcript_support_level "5";
+1	ensembl	exon	120725	120869	.	-	.	gene_id "ENSG00000238009"; gene_version "5"; transcript_id "ENST00000610542"; transcript_version "1"; exon_number "4"; gene_name "RP11-34P13.7"; gene_source "ensembl_havana"; gene_biotype "lincRNA"; transcript_name "RP11-34P13.7-201"; transcript_source "ensembl"; transcript_biotype "lincRNA"; exon_id "ENSE00003749543"; exon_version "1"; transcript_support_level "5";
+1	havana	transcript	129081	133566	.	-	.	gene_id "ENSG00000238009"; gene_version "5"; transcript_id "ENST00000453576"; transcript_version "2"; gene_name "RP11-34P13.7"; gene_source "ensembl_havana"; gene_biotype "lincRNA"; transcript_name "RP11-34P13.7-004"; transcript_source "havana"; transcript_biotype "lincRNA"; transcript_support_level "2";
+1	havana	exon	133374	133566	.	-	.	gene_id "ENSG00000238009"; gene_version "5"; transcript_id "ENST00000453576"; transcript_version "2"; exon_number "1"; gene_name "RP11-34P13.7"; gene_source "ensembl_havana"; gene_biotype "lincRNA"; transcript_name "RP11-34P13.7-004"; transcript_source "havana"; transcript_biotype "lincRNA"; exon_id "ENSE00001737600"; exon_version "2"; transcript_support_level "2";
+1	havana	exon	129081	129223	.	-	.	gene_id "ENSG00000238009"; gene_version "5"; transcript_id "ENST00000453576"; transcript_version "2"; exon_number "2"; gene_name "RP11-34P13.7"; gene_source "ensembl_havana"; gene_biotype "lincRNA"; transcript_name "RP11-34P13.7-004"; transcript_source "havana"; transcript_biotype "lincRNA"; exon_id "ENSE00001827073"; exon_version "1"; transcript_support_level "2";
+1	havana	gene	89551	91105	.	-	.	gene_id "ENSG00000239945"; gene_version "1"; gene_name "RP11-34P13.8"; gene_source "havana"; gene_biotype "lincRNA";
+1	havana	transcript	89551	91105	.	-	.	gene_id "ENSG00000239945"; gene_version "1"; transcript_id "ENST00000495576"; transcript_version "1"; gene_name "RP11-34P13.8"; gene_source "havana"; gene_biotype "lincRNA"; transcript_name "RP11-34P13.8-001"; transcript_source "havana"; transcript_biotype "lincRNA"; tag "basic"; transcript_support_level "5";
+1	havana	exon	90287	91105	.	-	.	gene_id "ENSG00000239945"; gene_version "1"; transcript_id "ENST00000495576"; transcript_version "1"; exon_number "1"; gene_name "RP11-34P13.8"; gene_source "havana"; gene_biotype "lincRNA"; transcript_name "RP11-34P13.8-001"; transcript_source "havana"; transcript_biotype "lincRNA"; exon_id "ENSE00001907785"; exon_version "1"; tag "basic"; transcript_support_level "5";
+1	havana	exon	89551	90050	.	-	.	gene_id "ENSG00000239945"; gene_version "1"; transcript_id "ENST00000495576"; transcript_version "1"; exon_number "2"; gene_name "RP11-34P13.8"; gene_source "havana"; gene_biotype "lincRNA"; transcript_name "RP11-34P13.8-001"; transcript_source "havana"; transcript_biotype "lincRNA"; exon_id "ENSE00001927725"; exon_version "1"; tag "basic"; transcript_support_level "5";
+1	havana	gene	131025	134836	.	+	.	gene_id "ENSG00000233750"; gene_version "3"; gene_name "CICP27"; gene_source "havana"; gene_biotype "processed_pseudogene";
+1	havana	transcript	131025	134836	.	+	.	gene_id "ENSG00000233750"; gene_version "3"; transcript_id "ENST00000442987"; transcript_version "3"; gene_name "CICP27"; gene_source "havana"; gene_biotype "processed_pseudogene"; transcript_name "CICP27-001"; transcript_source "havana"; transcript_biotype "processed_pseudogene"; tag "basic"; transcript_support_level "NA";
+1	havana	exon	131025	134836	.	+	.	gene_id "ENSG00000233750"; gene_version "3"; transcript_id "ENST00000442987"; transcript_version "3"; exon_number "1"; gene_name "CICP27"; gene_source "havana"; gene_biotype "processed_pseudogene"; transcript_name "CICP27-001"; transcript_source "havana"; transcript_biotype "processed_pseudogene"; exon_id "ENSE00001625118"; exon_version "3"; tag "basic"; transcript_support_level "NA";
+1	havana	gene	135141	135895	.	-	.	gene_id "ENSG00000268903"; gene_version "1"; gene_name "RP11-34P13.15"; gene_source "havana"; gene_biotype "processed_pseudogene";
+1	havana	transcript	135141	135895	.	-	.	gene_id "ENSG00000268903"; gene_version "1"; transcript_id "ENST00000494149"; transcript_version "2"; gene_name "RP11-34P13.15"; gene_source "havana"; gene_biotype "processed_pseudogene"; transcript_name "RP11-34P13.15-001"; transcript_source "havana"; transcript_biotype "processed_pseudogene"; tag "basic"; transcript_support_level "NA";
+1	havana	exon	135141	135895	.	-	.	gene_id "ENSG00000268903"; gene_version "1"; transcript_id "ENST00000494149"; transcript_version "2"; exon_number "1"; gene_name "RP11-34P13.15"; gene_source "havana"; gene_biotype "processed_pseudogene"; transcript_name "RP11-34P13.15-001"; transcript_source "havana"; transcript_biotype "processed_pseudogene"; exon_id "ENSE00001879101"; exon_version "2"; tag "basic"; transcript_support_level "NA";
+1	havana	gene	137682	137965	.	-	.	gene_id "ENSG00000269981"; gene_version "1"; gene_name "RP11-34P13.16"; gene_source "havana"; gene_biotype "processed_pseudogene";
+1	havana	transcript	137682	137965	.	-	.	gene_id "ENSG00000269981"; gene_version "1"; transcript_id "ENST00000595919"; transcript_version "1"; gene_name "RP11-34P13.16"; gene_source "havana"; gene_biotype "processed_pseudogene"; transcript_name "RP11-34P13.16-001"; transcript_source "havana"; transcript_biotype "processed_pseudogene"; tag "basic"; transcript_support_level "NA";
+1	havana	exon	137682	137965	.	-	.	gene_id "ENSG00000269981"; gene_version "1"; transcript_id "ENST00000595919"; transcript_version "1"; exon_number "1"; gene_name "RP11-34P13.16"; gene_source "havana"; gene_biotype "processed_pseudogene"; transcript_name "RP11-34P13.16-001"; transcript_source "havana"; transcript_biotype "processed_pseudogene"; exon_id "ENSE00001936432"; exon_version "2"; tag "basic"; transcript_support_level "NA";
diff -r 000000000000 -r 75a14cc16d4d test-data/gtf2bed_test_havana.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gtf2bed_test_havana.bed	Fri May 18 15:10:34 2018 -0400
@@ -0,0 +1,17 @@
+1	11868	14409	ENST00000456328	0	+	14409	14409	0	3	359,109,1189,	0,744,1352,
+1	12009	13670	ENST00000450305	0	+	13670	13670	0	6	48,49,85,78,154,218,	0,169,603,965,1211,1443,
+1	14403	29570	ENST00000488147	0	-	29570	29570	0	11	98,34,152,159,198,136,137,147,99,154,37,	0,601,1392,2203,2454,2829,3202,3511,3864,10334,15130,
+1	29553	31097	ENST00000473358	0	+	31097	31097	0	3	486,104,122,	0,1010,1422,
+1	30266	31109	ENST00000469289	0	+	31109	31109	0	2	401,134,	0,709,
+1	34553	36081	ENST00000417324	0	-	36081	36081	0	3	621,205,361,	0,723,1167,
+1	35244	36073	ENST00000461467	0	-	36073	36073	0	2	237,353,	0,476,
+1	52472	53312	ENST00000606857	0	+	53312	53312	0	1	840,	0,
+1	62947	63887	ENST00000492842	0	+	63887	63887	0	1	940,	0,
+1	89294	120932	ENST00000466430	0	-	120932	120932	0	4	2335,150,105,158,	0,2796,23405,31480,
+1	92229	129217	ENST00000477740	0	-	129217	129217	0	4	11,105,212,163,	0,20470,28491,36825,
+1	110952	129173	ENST00000471248	0	-	129173	129173	0	3	405,105,119,	0,1747,18102,
+1	129080	133566	ENST00000453576	0	-	133566	133566	0	2	143,193,	0,4293,
+1	89550	91105	ENST00000495576	0	-	91105	91105	0	2	500,819,	0,736,
+1	131024	134836	ENST00000442987	0	+	134836	134836	0	1	3812,	0,
+1	135140	135895	ENST00000494149	0	-	135895	135895	0	1	755,	0,
+1	137681	137965	ENST00000595919	0	-	137965	137965	0	1	284,	0,
diff -r 000000000000 -r 75a14cc16d4d test-data/gtf2bed_test_include_version.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gtf2bed_test_include_version.bed	Fri May 18 15:10:34 2018 -0400
@@ -0,0 +1,21 @@
+1	11868	14409	ENST00000456328.2	0	+	14409	14409	0	3	359,109,1189,	0,744,1352,
+1	12009	13670	ENST00000450305.2	0	+	13670	13670	0	6	48,49,85,78,154,218,	0,169,603,965,1211,1443,
+1	14403	29570	ENST00000488147.1	0	-	29570	29570	0	11	98,34,152,159,198,136,137,147,99,154,37,	0,601,1392,2203,2454,2829,3202,3511,3864,10334,15130,
+1	17368	17436	ENST00000619216.1	0	-	17436	17436	0	1	68,	0,
+1	29553	31097	ENST00000473358.1	0	+	31097	31097	0	3	486,104,122,	0,1010,1422,
+1	30266	31109	ENST00000469289.1	0	+	31109	31109	0	2	401,134,	0,709,
+1	30365	30503	ENST00000607096.1	0	+	30503	30503	0	1	138,	0,
+1	34553	36081	ENST00000417324.1	0	-	36081	36081	0	3	621,205,361,	0,723,1167,
+1	35244	36073	ENST00000461467.1	0	-	36073	36073	0	2	237,353,	0,476,
+1	52472	53312	ENST00000606857.1	0	+	53312	53312	0	1	840,	0,
+1	62947	63887	ENST00000492842.1	0	+	63887	63887	0	1	940,	0,
+1	69090	70008	ENST00000335137.3	0	+	69090	70008	0	1	918,	0,
+1	89294	120932	ENST00000466430.4	0	-	120932	120932	0	4	2335,150,105,158,	0,2796,23405,31480,
+1	92229	129217	ENST00000477740.4	0	-	129217	129217	0	4	11,105,212,163,	0,20470,28491,36825,
+1	110952	129173	ENST00000471248.1	0	-	129173	129173	0	3	405,105,119,	0,1747,18102,
+1	120724	133723	ENST00000610542.1	0	-	133723	133723	0	4	145,59,169,350,	0,149,8330,12649,
+1	129080	133566	ENST00000453576.2	0	-	133566	133566	0	2	143,193,	0,4293,
+1	89550	91105	ENST00000495576.1	0	-	91105	91105	0	2	500,819,	0,736,
+1	131024	134836	ENST00000442987.3	0	+	134836	134836	0	1	3812,	0,
+1	135140	135895	ENST00000494149.2	0	-	135895	135895	0	1	755,	0,
+1	137681	137965	ENST00000595919.1	0	-	137965	137965	0	1	284,	0,
diff -r 000000000000 -r 75a14cc16d4d test-data/gtf2bed_test_missing_exon.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gtf2bed_test_missing_exon.bed	Fri May 18 15:10:34 2018 -0400
@@ -0,0 +1,20 @@
+1	12009	13670	ENST00000450305	0	+	13670	13670	0	6	48,49,85,78,154,218,	0,169,603,965,1211,1443,
+1	14403	29570	ENST00000488147	0	-	29570	29570	0	11	98,34,152,159,198,136,137,147,99,154,37,	0,601,1392,2203,2454,2829,3202,3511,3864,10334,15130,
+1	17368	17436	ENST00000619216	0	-	17436	17436	0	1	68,	0,
+1	29553	31097	ENST00000473358	0	+	31097	31097	0	3	486,104,122,	0,1010,1422,
+1	30266	31109	ENST00000469289	0	+	31109	31109	0	2	401,134,	0,709,
+1	30365	30503	ENST00000607096	0	+	30503	30503	0	1	138,	0,
+1	34553	36081	ENST00000417324	0	-	36081	36081	0	3	621,205,361,	0,723,1167,
+1	35244	36073	ENST00000461467	0	-	36073	36073	0	2	237,353,	0,476,
+1	52472	53312	ENST00000606857	0	+	53312	53312	0	1	840,	0,
+1	62947	63887	ENST00000492842	0	+	63887	63887	0	1	940,	0,
+1	69090	70008	ENST00000335137	0	+	69090	70008	0	1	918,	0,
+1	89294	120932	ENST00000466430	0	-	120932	120932	0	4	2335,150,105,158,	0,2796,23405,31480,
+1	92229	129217	ENST00000477740	0	-	129217	129217	0	4	11,105,212,163,	0,20470,28491,36825,
+1	110952	129173	ENST00000471248	0	-	129173	129173	0	3	405,105,119,	0,1747,18102,
+1	120724	133723	ENST00000610542	0	-	133723	133723	0	4	145,59,169,350,	0,149,8330,12649,
+1	129080	133566	ENST00000453576	0	-	133566	133566	0	2	143,193,	0,4293,
+1	89550	91105	ENST00000495576	0	-	91105	91105	0	2	500,819,	0,736,
+1	131024	134836	ENST00000442987	0	+	134836	134836	0	1	3812,	0,
+1	135140	135895	ENST00000494149	0	-	135895	135895	0	1	755,	0,
+1	137681	137965	ENST00000595919	0	-	137965	137965	0	1	284,	0,
diff -r 000000000000 -r 75a14cc16d4d test-data/gtf2bed_test_missing_exon.gtf
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gtf2bed_test_missing_exon.gtf	Fri May 18 15:10:34 2018 -0400
@@ -0,0 +1,97 @@
+#!genome-build GRCh38.p2
+#!genome-version GRCh38
+#!genome-date 2013-12
+#!genome-build-accession NCBI:GCA_000001405.17
+#!genebuild-last-updated 2015-01
+1	havana	gene	11869	14409	.	+	.	gene_id "ENSG00000223972"; gene_version "5"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene";
+1	havana	transcript	11869	14409	.	+	.	gene_id "ENSG00000223972"; gene_version "5"; transcript_id "ENST00000456328"; transcript_version "2"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; transcript_name "DDX11L1-002"; transcript_source "havana"; transcript_biotype "processed_transcript"; tag "basic"; transcript_support_level "1";
+1	havana	transcript	12010	13670	.	+	.	gene_id "ENSG00000223972"; gene_version "5"; transcript_id "ENST00000450305"; transcript_version "2"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; transcript_name "DDX11L1-001"; transcript_source "havana"; transcript_biotype "transcribed_unprocessed_pseudogene"; tag "basic"; transcript_support_level "NA";
+1	havana	exon	12010	12057	.	+	.	gene_id "ENSG00000223972"; gene_version "5"; transcript_id "ENST00000450305"; transcript_version "2"; exon_number "1"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; transcript_name "DDX11L1-001"; transcript_source "havana"; transcript_biotype "transcribed_unprocessed_pseudogene"; exon_id "ENSE00001948541"; exon_version "1"; tag "basic"; transcript_support_level "NA";
+1	havana	exon	12179	12227	.	+	.	gene_id "ENSG00000223972"; gene_version "5"; transcript_id "ENST00000450305"; transcript_version "2"; exon_number "2"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; transcript_name "DDX11L1-001"; transcript_source "havana"; transcript_biotype "transcribed_unprocessed_pseudogene"; exon_id "ENSE00001671638"; exon_version "2"; tag "basic"; transcript_support_level "NA";
+1	havana	exon	12613	12697	.	+	.	gene_id "ENSG00000223972"; gene_version "5"; transcript_id "ENST00000450305"; transcript_version "2"; exon_number "3"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; transcript_name "DDX11L1-001"; transcript_source "havana"; transcript_biotype "transcribed_unprocessed_pseudogene"; exon_id "ENSE00001758273"; exon_version "2"; tag "basic"; transcript_support_level "NA";
+1	havana	exon	12975	13052	.	+	.	gene_id "ENSG00000223972"; gene_version "5"; transcript_id "ENST00000450305"; transcript_version "2"; exon_number "4"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; transcript_name "DDX11L1-001"; transcript_source "havana"; transcript_biotype "transcribed_unprocessed_pseudogene"; exon_id "ENSE00001799933"; exon_version "2"; tag "basic"; transcript_support_level "NA";
+1	havana	exon	13221	13374	.	+	.	gene_id "ENSG00000223972"; gene_version "5"; transcript_id "ENST00000450305"; transcript_version "2"; exon_number "5"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; transcript_name "DDX11L1-001"; transcript_source "havana"; transcript_biotype "transcribed_unprocessed_pseudogene"; exon_id "ENSE00001746346"; exon_version "2"; tag "basic"; transcript_support_level "NA";
+1	havana	exon	13453	13670	.	+	.	gene_id "ENSG00000223972"; gene_version "5"; transcript_id "ENST00000450305"; transcript_version "2"; exon_number "6"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; transcript_name "DDX11L1-001"; transcript_source "havana"; transcript_biotype "transcribed_unprocessed_pseudogene"; exon_id "ENSE00001863096"; exon_version "1"; tag "basic"; transcript_support_level "NA";
+1	havana	gene	14404	29570	.	-	.	gene_id "ENSG00000227232"; gene_version "5"; gene_name "WASH7P"; gene_source "havana"; gene_biotype "unprocessed_pseudogene";
+1	havana	transcript	14404	29570	.	-	.	gene_id "ENSG00000227232"; gene_version "5"; transcript_id "ENST00000488147"; transcript_version "1"; gene_name "WASH7P"; gene_source "havana"; gene_biotype "unprocessed_pseudogene"; transcript_name "WASH7P-001"; transcript_source "havana"; transcript_biotype "unprocessed_pseudogene"; tag "basic"; transcript_support_level "NA";
+1	havana	exon	29534	29570	.	-	.	gene_id "ENSG00000227232"; gene_version "5"; transcript_id "ENST00000488147"; transcript_version "1"; exon_number "1"; gene_name "WASH7P"; gene_source "havana"; gene_biotype "unprocessed_pseudogene"; transcript_name "WASH7P-001"; transcript_source "havana"; transcript_biotype "unprocessed_pseudogene"; exon_id "ENSE00001890219"; exon_version "1"; tag "basic"; transcript_support_level "NA";
+1	havana	exon	24738	24891	.	-	.	gene_id "ENSG00000227232"; gene_version "5"; transcript_id "ENST00000488147"; transcript_version "1"; exon_number "2"; gene_name "WASH7P"; gene_source "havana"; gene_biotype "unprocessed_pseudogene"; transcript_name "WASH7P-001"; transcript_source "havana"; transcript_biotype "unprocessed_pseudogene"; exon_id "ENSE00003507205"; exon_version "1"; tag "basic"; transcript_support_level "NA";
+1	havana	exon	18268	18366	.	-	.	gene_id "ENSG00000227232"; gene_version "5"; transcript_id "ENST00000488147"; transcript_version "1"; exon_number "3"; gene_name "WASH7P"; gene_source "havana"; gene_biotype "unprocessed_pseudogene"; transcript_name "WASH7P-001"; transcript_source "havana"; transcript_biotype "unprocessed_pseudogene"; exon_id "ENSE00003477500"; exon_version "1"; tag "basic"; transcript_support_level "NA";
+1	havana	exon	17915	18061	.	-	.	gene_id "ENSG00000227232"; gene_version "5"; transcript_id "ENST00000488147"; transcript_version "1"; exon_number "4"; gene_name "WASH7P"; gene_source "havana"; gene_biotype "unprocessed_pseudogene"; transcript_name "WASH7P-001"; transcript_source "havana"; transcript_biotype "unprocessed_pseudogene"; exon_id "ENSE00003565697"; exon_version "1"; tag "basic"; transcript_support_level "NA";
+1	havana	exon	17606	17742	.	-	.	gene_id "ENSG00000227232"; gene_version "5"; transcript_id "ENST00000488147"; transcript_version "1"; exon_number "5"; gene_name "WASH7P"; gene_source "havana"; gene_biotype "unprocessed_pseudogene"; transcript_name "WASH7P-001"; transcript_source "havana"; transcript_biotype "unprocessed_pseudogene"; exon_id "ENSE00003475637"; exon_version "1"; tag "basic"; transcript_support_level "NA";
+1	havana	exon	17233	17368	.	-	.	gene_id "ENSG00000227232"; gene_version "5"; transcript_id "ENST00000488147"; transcript_version "1"; exon_number "6"; gene_name "WASH7P"; gene_source "havana"; gene_biotype "unprocessed_pseudogene"; transcript_name "WASH7P-001"; transcript_source "havana"; transcript_biotype "unprocessed_pseudogene"; exon_id "ENSE00003502542"; exon_version "1"; tag "basic"; transcript_support_level "NA";
+1	havana	exon	16858	17055	.	-	.	gene_id "ENSG00000227232"; gene_version "5"; transcript_id "ENST00000488147"; transcript_version "1"; exon_number "7"; gene_name "WASH7P"; gene_source "havana"; gene_biotype "unprocessed_pseudogene"; transcript_name "WASH7P-001"; transcript_source "havana"; transcript_biotype "unprocessed_pseudogene"; exon_id "ENSE00003553898"; exon_version "1"; tag "basic"; transcript_support_level "NA";
+1	havana	exon	16607	16765	.	-	.	gene_id "ENSG00000227232"; gene_version "5"; transcript_id "ENST00000488147"; transcript_version "1"; exon_number "8"; gene_name "WASH7P"; gene_source "havana"; gene_biotype "unprocessed_pseudogene"; transcript_name "WASH7P-001"; transcript_source "havana"; transcript_biotype "unprocessed_pseudogene"; exon_id "ENSE00003621279"; exon_version "1"; tag "basic"; transcript_support_level "NA";
+1	havana	exon	15796	15947	.	-	.	gene_id "ENSG00000227232"; gene_version "5"; transcript_id "ENST00000488147"; transcript_version "1"; exon_number "9"; gene_name "WASH7P"; gene_source "havana"; gene_biotype "unprocessed_pseudogene"; transcript_name "WASH7P-001"; transcript_source "havana"; transcript_biotype "unprocessed_pseudogene"; exon_id "ENSE00002030414"; exon_version "1"; tag "basic"; transcript_support_level "NA";
+1	havana	exon	15005	15038	.	-	.	gene_id "ENSG00000227232"; gene_version "5"; transcript_id "ENST00000488147"; transcript_version "1"; exon_number "10"; gene_name "WASH7P"; gene_source "havana"; gene_biotype "unprocessed_pseudogene"; transcript_name "WASH7P-001"; transcript_source "havana"; transcript_biotype "unprocessed_pseudogene"; exon_id "ENSE00001935574"; exon_version "1"; tag "basic"; transcript_support_level "NA";
+1	havana	exon	14404	14501	.	-	.	gene_id "ENSG00000227232"; gene_version "5"; transcript_id "ENST00000488147"; transcript_version "1"; exon_number "11"; gene_name "WASH7P"; gene_source "havana"; gene_biotype "unprocessed_pseudogene"; transcript_name "WASH7P-001"; transcript_source "havana"; transcript_biotype "unprocessed_pseudogene"; exon_id "ENSE00001843071"; exon_version "1"; tag "basic"; transcript_support_level "NA";
+1	ensembl	gene	17369	17436	.	-	.	gene_id "ENSG00000278267"; gene_version "1"; gene_name "MIR6859-1"; gene_source "ensembl"; gene_biotype "miRNA";
+1	ensembl	transcript	17369	17436	.	-	.	gene_id "ENSG00000278267"; gene_version "1"; transcript_id "ENST00000619216"; transcript_version "1"; gene_name "MIR6859-1"; gene_source "ensembl"; gene_biotype "miRNA"; transcript_name "MIR6859-1-201"; transcript_source "ensembl"; transcript_biotype "miRNA"; tag "basic"; transcript_support_level "NA";
+1	ensembl	exon	17369	17436	.	-	.	gene_id "ENSG00000278267"; gene_version "1"; transcript_id "ENST00000619216"; transcript_version "1"; exon_number "1"; gene_name "MIR6859-1"; gene_source "ensembl"; gene_biotype "miRNA"; transcript_name "MIR6859-1-201"; transcript_source "ensembl"; transcript_biotype "miRNA"; exon_id "ENSE00003746039"; exon_version "1"; tag "basic"; transcript_support_level "NA";
+1	havana	gene	29554	31109	.	+	.	gene_id "ENSG00000243485"; gene_version "3"; gene_name "RP11-34P13.3"; gene_source "havana"; gene_biotype "lincRNA";
+1	havana	transcript	29554	31097	.	+	.	gene_id "ENSG00000243485"; gene_version "3"; transcript_id "ENST00000473358"; transcript_version "1"; gene_name "RP11-34P13.3"; gene_source "havana"; gene_biotype "lincRNA"; transcript_name "RP11-34P13.3-001"; transcript_source "havana"; transcript_biotype "lincRNA"; tag "basic"; transcript_support_level "5";
+1	havana	exon	29554	30039	.	+	.	gene_id "ENSG00000243485"; gene_version "3"; transcript_id "ENST00000473358"; transcript_version "1"; exon_number "1"; gene_name "RP11-34P13.3"; gene_source "havana"; gene_biotype "lincRNA"; transcript_name "RP11-34P13.3-001"; transcript_source "havana"; transcript_biotype "lincRNA"; exon_id "ENSE00001947070"; exon_version "1"; tag "basic"; transcript_support_level "5";
+1	havana	exon	30564	30667	.	+	.	gene_id "ENSG00000243485"; gene_version "3"; transcript_id "ENST00000473358"; transcript_version "1"; exon_number "2"; gene_name "RP11-34P13.3"; gene_source "havana"; gene_biotype "lincRNA"; transcript_name "RP11-34P13.3-001"; transcript_source "havana"; transcript_biotype "lincRNA"; exon_id "ENSE00001922571"; exon_version "1"; tag "basic"; transcript_support_level "5";
+1	havana	exon	30976	31097	.	+	.	gene_id "ENSG00000243485"; gene_version "3"; transcript_id "ENST00000473358"; transcript_version "1"; exon_number "3"; gene_name "RP11-34P13.3"; gene_source "havana"; gene_biotype "lincRNA"; transcript_name "RP11-34P13.3-001"; transcript_source "havana"; transcript_biotype "lincRNA"; exon_id "ENSE00001827679"; exon_version "1"; tag "basic"; transcript_support_level "5";
+1	havana	transcript	30267	31109	.	+	.	gene_id "ENSG00000243485"; gene_version "3"; transcript_id "ENST00000469289"; transcript_version "1"; gene_name "RP11-34P13.3"; gene_source "havana"; gene_biotype "lincRNA"; transcript_name "RP11-34P13.3-002"; transcript_source "havana"; transcript_biotype "lincRNA"; transcript_support_level "5";
+1	havana	exon	30267	30667	.	+	.	gene_id "ENSG00000243485"; gene_version "3"; transcript_id "ENST00000469289"; transcript_version "1"; exon_number "1"; gene_name "RP11-34P13.3"; gene_source "havana"; gene_biotype "lincRNA"; transcript_name "RP11-34P13.3-002"; transcript_source "havana"; transcript_biotype "lincRNA"; exon_id "ENSE00001841699"; exon_version "1"; transcript_support_level "5";
+1	havana	exon	30976	31109	.	+	.	gene_id "ENSG00000243485"; gene_version "3"; transcript_id "ENST00000469289"; transcript_version "1"; exon_number "2"; gene_name "RP11-34P13.3"; gene_source "havana"; gene_biotype "lincRNA"; transcript_name "RP11-34P13.3-002"; transcript_source "havana"; transcript_biotype "lincRNA"; exon_id "ENSE00001890064"; exon_version "1"; transcript_support_level "5";
+1	ensembl	gene	30366	30503	.	+	.	gene_id "ENSG00000274890"; gene_version "1"; gene_name "MIR1302-2"; gene_source "ensembl"; gene_biotype "miRNA";
+1	ensembl	transcript	30366	30503	.	+	.	gene_id "ENSG00000274890"; gene_version "1"; transcript_id "ENST00000607096"; transcript_version "1"; gene_name "MIR1302-2"; gene_source "ensembl"; gene_biotype "miRNA"; transcript_name "MIR1302-2-201"; transcript_source "ensembl"; transcript_biotype "miRNA"; tag "basic"; transcript_support_level "NA";
+1	ensembl	exon	30366	30503	.	+	.	gene_id "ENSG00000274890"; gene_version "1"; transcript_id "ENST00000607096"; transcript_version "1"; exon_number "1"; gene_name "MIR1302-2"; gene_source "ensembl"; gene_biotype "miRNA"; transcript_name "MIR1302-2-201"; transcript_source "ensembl"; transcript_biotype "miRNA"; exon_id "ENSE00003695741"; exon_version "1"; tag "basic"; transcript_support_level "NA";
+1	havana	gene	34554	36081	.	-	.	gene_id "ENSG00000237613"; gene_version "2"; gene_name "FAM138A"; gene_source "havana"; gene_biotype "lincRNA";
+1	havana	transcript	34554	36081	.	-	.	gene_id "ENSG00000237613"; gene_version "2"; transcript_id "ENST00000417324"; transcript_version "1"; gene_name "FAM138A"; gene_source "havana"; gene_biotype "lincRNA"; transcript_name "FAM138A-001"; transcript_source "havana"; transcript_biotype "lincRNA"; tag "basic"; transcript_support_level "1";
+1	havana	exon	35721	36081	.	-	.	gene_id "ENSG00000237613"; gene_version "2"; transcript_id "ENST00000417324"; transcript_version "1"; exon_number "1"; gene_name "FAM138A"; gene_source "havana"; gene_biotype "lincRNA"; transcript_name "FAM138A-001"; transcript_source "havana"; transcript_biotype "lincRNA"; exon_id "ENSE00001656588"; exon_version "1"; tag "basic"; transcript_support_level "1";
+1	havana	exon	35277	35481	.	-	.	gene_id "ENSG00000237613"; gene_version "2"; transcript_id "ENST00000417324"; transcript_version "1"; exon_number "2"; gene_name "FAM138A"; gene_source "havana"; gene_biotype "lincRNA"; transcript_name "FAM138A-001"; transcript_source "havana"; transcript_biotype "lincRNA"; exon_id "ENSE00001669267"; exon_version "1"; tag "basic"; transcript_support_level "1";
+1	havana	exon	34554	35174	.	-	.	gene_id "ENSG00000237613"; gene_version "2"; transcript_id "ENST00000417324"; transcript_version "1"; exon_number "3"; gene_name "FAM138A"; gene_source "havana"; gene_biotype "lincRNA"; transcript_name "FAM138A-001"; transcript_source "havana"; transcript_biotype "lincRNA"; exon_id "ENSE00001727627"; exon_version "1"; tag "basic"; transcript_support_level "1";
+1	havana	transcript	35245	36073	.	-	.	gene_id "ENSG00000237613"; gene_version "2"; transcript_id "ENST00000461467"; transcript_version "1"; gene_name "FAM138A"; gene_source "havana"; gene_biotype "lincRNA"; transcript_name "FAM138A-002"; transcript_source "havana"; transcript_biotype "lincRNA"; transcript_support_level "3";
+1	havana	exon	35721	36073	.	-	.	gene_id "ENSG00000237613"; gene_version "2"; transcript_id "ENST00000461467"; transcript_version "1"; exon_number "1"; gene_name "FAM138A"; gene_source "havana"; gene_biotype "lincRNA"; transcript_name "FAM138A-002"; transcript_source "havana"; transcript_biotype "lincRNA"; exon_id "ENSE00001618781"; exon_version "2"; transcript_support_level "3";
+1	havana	exon	35245	35481	.	-	.	gene_id "ENSG00000237613"; gene_version "2"; transcript_id "ENST00000461467"; transcript_version "1"; exon_number "2"; gene_name "FAM138A"; gene_source "havana"; gene_biotype "lincRNA"; transcript_name "FAM138A-002"; transcript_source "havana"; transcript_biotype "lincRNA"; exon_id "ENSE00001874421"; exon_version "1"; transcript_support_level "3";
+1	havana	gene	52473	53312	.	+	.	gene_id "ENSG00000268020"; gene_version "3"; gene_name "OR4G4P"; gene_source "havana"; gene_biotype "unprocessed_pseudogene";
+1	havana	transcript	52473	53312	.	+	.	gene_id "ENSG00000268020"; gene_version "3"; transcript_id "ENST00000606857"; transcript_version "1"; gene_name "OR4G4P"; gene_source "havana"; gene_biotype "unprocessed_pseudogene"; transcript_name "OR4G4P-001"; transcript_source "havana"; transcript_biotype "unprocessed_pseudogene"; tag "basic"; transcript_support_level "NA";
+1	havana	exon	52473	53312	.	+	.	gene_id "ENSG00000268020"; gene_version "3"; transcript_id "ENST00000606857"; transcript_version "1"; exon_number "1"; gene_name "OR4G4P"; gene_source "havana"; gene_biotype "unprocessed_pseudogene"; transcript_name "OR4G4P-001"; transcript_source "havana"; transcript_biotype "unprocessed_pseudogene"; exon_id "ENSE00003698237"; exon_version "1"; tag "basic"; transcript_support_level "NA";
+1	havana	gene	62948	63887	.	+	.	gene_id "ENSG00000240361"; gene_version "1"; gene_name "OR4G11P"; gene_source "havana"; gene_biotype "unprocessed_pseudogene";
+1	havana	transcript	62948	63887	.	+	.	gene_id "ENSG00000240361"; gene_version "1"; transcript_id "ENST00000492842"; transcript_version "1"; gene_name "OR4G11P"; gene_source "havana"; gene_biotype "unprocessed_pseudogene"; transcript_name "OR4G11P-001"; transcript_source "havana"; transcript_biotype "unprocessed_pseudogene"; tag "basic"; transcript_support_level "NA";
+1	havana	exon	62948	63887	.	+	.	gene_id "ENSG00000240361"; gene_version "1"; transcript_id "ENST00000492842"; transcript_version "1"; exon_number "1"; gene_name "OR4G11P"; gene_source "havana"; gene_biotype "unprocessed_pseudogene"; transcript_name "OR4G11P-001"; transcript_source "havana"; transcript_biotype "unprocessed_pseudogene"; exon_id "ENSE00001830178"; exon_version "1"; tag "basic"; transcript_support_level "NA";
+1	ensembl_havana	gene	69091	70008	.	+	.	gene_id "ENSG00000186092"; gene_version "4"; gene_name "OR4F5"; gene_source "ensembl_havana"; gene_biotype "protein_coding";
+1	ensembl_havana	transcript	69091	70008	.	+	.	gene_id "ENSG00000186092"; gene_version "4"; transcript_id "ENST00000335137"; transcript_version "3"; gene_name "OR4F5"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "OR4F5-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS30547"; tag "basic"; transcript_support_level "NA";
+1	ensembl_havana	exon	69091	70008	.	+	.	gene_id "ENSG00000186092"; gene_version "4"; transcript_id "ENST00000335137"; transcript_version "3"; exon_number "1"; gene_name "OR4F5"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "OR4F5-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS30547"; exon_id "ENSE00002319515"; exon_version "1"; tag "basic"; transcript_support_level "NA";
+1	ensembl_havana	CDS	69091	70005	.	+	0	gene_id "ENSG00000186092"; gene_version "4"; transcript_id "ENST00000335137"; transcript_version "3"; exon_number "1"; gene_name "OR4F5"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "OR4F5-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS30547"; protein_id "ENSP00000334393"; protein_version "3"; tag "basic"; transcript_support_level "NA";
+1	ensembl_havana	start_codon	69091	69093	.	+	0	gene_id "ENSG00000186092"; gene_version "4"; transcript_id "ENST00000335137"; transcript_version "3"; exon_number "1"; gene_name "OR4F5"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "OR4F5-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS30547"; tag "basic"; transcript_support_level "NA";
+1	ensembl_havana	stop_codon	70006	70008	.	+	0	gene_id "ENSG00000186092"; gene_version "4"; transcript_id "ENST00000335137"; transcript_version "3"; exon_number "1"; gene_name "OR4F5"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "OR4F5-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS30547"; tag "basic"; transcript_support_level "NA";
+1	ensembl_havana	gene	89295	133723	.	-	.	gene_id "ENSG00000238009"; gene_version "5"; gene_name "RP11-34P13.7"; gene_source "ensembl_havana"; gene_biotype "lincRNA";
+1	havana	transcript	89295	120932	.	-	.	gene_id "ENSG00000238009"; gene_version "5"; transcript_id "ENST00000466430"; transcript_version "4"; gene_name "RP11-34P13.7"; gene_source "ensembl_havana"; gene_biotype "lincRNA"; transcript_name "RP11-34P13.7-001"; transcript_source "havana"; transcript_biotype "lincRNA"; tag "basic"; transcript_support_level "5 (assigned to previous version 3)";
+1	havana	exon	120775	120932	.	-	.	gene_id "ENSG00000238009"; gene_version "5"; transcript_id "ENST00000466430"; transcript_version "4"; exon_number "1"; gene_name "RP11-34P13.7"; gene_source "ensembl_havana"; gene_biotype "lincRNA"; transcript_name "RP11-34P13.7-001"; transcript_source "havana"; transcript_biotype "lincRNA"; exon_id "ENSE00001606755"; exon_version "2"; tag "basic"; transcript_support_level "5 (assigned to previous version 3)";
+1	havana	exon	112700	112804	.	-	.	gene_id "ENSG00000238009"; gene_version "5"; transcript_id "ENST00000466430"; transcript_version "4"; exon_number "2"; gene_name "RP11-34P13.7"; gene_source "ensembl_havana"; gene_biotype "lincRNA"; transcript_name "RP11-34P13.7-001"; transcript_source "havana"; transcript_biotype "lincRNA"; exon_id "ENSE00001957285"; exon_version "1"; tag "basic"; transcript_support_level "5 (assigned to previous version 3)";
+1	havana	exon	92091	92240	.	-	.	gene_id "ENSG00000238009"; gene_version "5"; transcript_id "ENST00000466430"; transcript_version "4"; exon_number "3"; gene_name "RP11-34P13.7"; gene_source "ensembl_havana"; gene_biotype "lincRNA"; transcript_name "RP11-34P13.7-001"; transcript_source "havana"; transcript_biotype "lincRNA"; exon_id "ENSE00001944529"; exon_version "1"; tag "basic"; transcript_support_level "5 (assigned to previous version 3)";
+1	havana	exon	89295	91629	.	-	.	gene_id "ENSG00000238009"; gene_version "5"; transcript_id "ENST00000466430"; transcript_version "4"; exon_number "4"; gene_name "RP11-34P13.7"; gene_source "ensembl_havana"; gene_biotype "lincRNA"; transcript_name "RP11-34P13.7-001"; transcript_source "havana"; transcript_biotype "lincRNA"; exon_id "ENSE00001846804"; exon_version "1"; tag "basic"; transcript_support_level "5 (assigned to previous version 3)";
+1	havana	transcript	92230	129217	.	-	.	gene_id "ENSG00000238009"; gene_version "5"; transcript_id "ENST00000477740"; transcript_version "4"; gene_name "RP11-34P13.7"; gene_source "ensembl_havana"; gene_biotype "lincRNA"; transcript_name "RP11-34P13.7-003"; transcript_source "havana"; transcript_biotype "lincRNA"; transcript_support_level "5 (assigned to previous version 3)";
+1	havana	exon	129055	129217	.	-	.	gene_id "ENSG00000238009"; gene_version "5"; transcript_id "ENST00000477740"; transcript_version "4"; exon_number "1"; gene_name "RP11-34P13.7"; gene_source "ensembl_havana"; gene_biotype "lincRNA"; transcript_name "RP11-34P13.7-003"; transcript_source "havana"; transcript_biotype "lincRNA"; exon_id "ENSE00001919246"; exon_version "1"; transcript_support_level "5 (assigned to previous version 3)";
+1	havana	exon	120721	120932	.	-	.	gene_id "ENSG00000238009"; gene_version "5"; transcript_id "ENST00000477740"; transcript_version "4"; exon_number "2"; gene_name "RP11-34P13.7"; gene_source "ensembl_havana"; gene_biotype "lincRNA"; transcript_name "RP11-34P13.7-003"; transcript_source "havana"; transcript_biotype "lincRNA"; exon_id "ENSE00001171005"; exon_version "3"; transcript_support_level "5 (assigned to previous version 3)";
+1	havana	exon	112700	112804	.	-	.	gene_id "ENSG00000238009"; gene_version "5"; transcript_id "ENST00000477740"; transcript_version "4"; exon_number "3"; gene_name "RP11-34P13.7"; gene_source "ensembl_havana"; gene_biotype "lincRNA"; transcript_name "RP11-34P13.7-003"; transcript_source "havana"; transcript_biotype "lincRNA"; exon_id "ENSE00001957285"; exon_version "1"; transcript_support_level "5 (assigned to previous version 3)";
+1	havana	exon	92230	92240	.	-	.	gene_id "ENSG00000238009"; gene_version "5"; transcript_id "ENST00000477740"; transcript_version "4"; exon_number "4"; gene_name "RP11-34P13.7"; gene_source "ensembl_havana"; gene_biotype "lincRNA"; transcript_name "RP11-34P13.7-003"; transcript_source "havana"; transcript_biotype "lincRNA"; exon_id "ENSE00001896976"; exon_version "1"; transcript_support_level "5 (assigned to previous version 3)";
+1	havana	transcript	110953	129173	.	-	.	gene_id "ENSG00000238009"; gene_version "5"; transcript_id "ENST00000471248"; transcript_version "1"; gene_name "RP11-34P13.7"; gene_source "ensembl_havana"; gene_biotype "lincRNA"; transcript_name "RP11-34P13.7-002"; transcript_source "havana"; transcript_biotype "lincRNA"; transcript_support_level "5";
+1	havana	exon	129055	129173	.	-	.	gene_id "ENSG00000238009"; gene_version "5"; transcript_id "ENST00000471248"; transcript_version "1"; exon_number "1"; gene_name "RP11-34P13.7"; gene_source "ensembl_havana"; gene_biotype "lincRNA"; transcript_name "RP11-34P13.7-002"; transcript_source "havana"; transcript_biotype "lincRNA"; exon_id "ENSE00001934975"; exon_version "1"; transcript_support_level "5";
+1	havana	exon	112700	112804	.	-	.	gene_id "ENSG00000238009"; gene_version "5"; transcript_id "ENST00000471248"; transcript_version "1"; exon_number "2"; gene_name "RP11-34P13.7"; gene_source "ensembl_havana"; gene_biotype "lincRNA"; transcript_name "RP11-34P13.7-002"; transcript_source "havana"; transcript_biotype "lincRNA"; exon_id "ENSE00001957285"; exon_version "1"; transcript_support_level "5";
+1	havana	exon	110953	111357	.	-	.	gene_id "ENSG00000238009"; gene_version "5"; transcript_id "ENST00000471248"; transcript_version "1"; exon_number "3"; gene_name "RP11-34P13.7"; gene_source "ensembl_havana"; gene_biotype "lincRNA"; transcript_name "RP11-34P13.7-002"; transcript_source "havana"; transcript_biotype "lincRNA"; exon_id "ENSE00001879696"; exon_version "1"; transcript_support_level "5";
+1	ensembl	transcript	120725	133723	.	-	.	gene_id "ENSG00000238009"; gene_version "5"; transcript_id "ENST00000610542"; transcript_version "1"; gene_name "RP11-34P13.7"; gene_source "ensembl_havana"; gene_biotype "lincRNA"; transcript_name "RP11-34P13.7-201"; transcript_source "ensembl"; transcript_biotype "lincRNA"; transcript_support_level "5";
+1	ensembl	exon	133374	133723	.	-	.	gene_id "ENSG00000238009"; gene_version "5"; transcript_id "ENST00000610542"; transcript_version "1"; exon_number "1"; gene_name "RP11-34P13.7"; gene_source "ensembl_havana"; gene_biotype "lincRNA"; transcript_name "RP11-34P13.7-201"; transcript_source "ensembl"; transcript_biotype "lincRNA"; exon_id "ENSE00003748456"; exon_version "1"; transcript_support_level "5";
+1	ensembl	exon	129055	129223	.	-	.	gene_id "ENSG00000238009"; gene_version "5"; transcript_id "ENST00000610542"; transcript_version "1"; exon_number "2"; gene_name "RP11-34P13.7"; gene_source "ensembl_havana"; gene_biotype "lincRNA"; transcript_name "RP11-34P13.7-201"; transcript_source "ensembl"; transcript_biotype "lincRNA"; exon_id "ENSE00003734824"; exon_version "1"; transcript_support_level "5";
+1	ensembl	exon	120874	120932	.	-	.	gene_id "ENSG00000238009"; gene_version "5"; transcript_id "ENST00000610542"; transcript_version "1"; exon_number "3"; gene_name "RP11-34P13.7"; gene_source "ensembl_havana"; gene_biotype "lincRNA"; transcript_name "RP11-34P13.7-201"; transcript_source "ensembl"; transcript_biotype "lincRNA"; exon_id "ENSE00003740919"; exon_version "1"; transcript_support_level "5";
+1	ensembl	exon	120725	120869	.	-	.	gene_id "ENSG00000238009"; gene_version "5"; transcript_id "ENST00000610542"; transcript_version "1"; exon_number "4"; gene_name "RP11-34P13.7"; gene_source "ensembl_havana"; gene_biotype "lincRNA"; transcript_name "RP11-34P13.7-201"; transcript_source "ensembl"; transcript_biotype "lincRNA"; exon_id "ENSE00003749543"; exon_version "1"; transcript_support_level "5";
+1	havana	transcript	129081	133566	.	-	.	gene_id "ENSG00000238009"; gene_version "5"; transcript_id "ENST00000453576"; transcript_version "2"; gene_name "RP11-34P13.7"; gene_source "ensembl_havana"; gene_biotype "lincRNA"; transcript_name "RP11-34P13.7-004"; transcript_source "havana"; transcript_biotype "lincRNA"; transcript_support_level "2";
+1	havana	exon	133374	133566	.	-	.	gene_id "ENSG00000238009"; gene_version "5"; transcript_id "ENST00000453576"; transcript_version "2"; exon_number "1"; gene_name "RP11-34P13.7"; gene_source "ensembl_havana"; gene_biotype "lincRNA"; transcript_name "RP11-34P13.7-004"; transcript_source "havana"; transcript_biotype "lincRNA"; exon_id "ENSE00001737600"; exon_version "2"; transcript_support_level "2";
+1	havana	exon	129081	129223	.	-	.	gene_id "ENSG00000238009"; gene_version "5"; transcript_id "ENST00000453576"; transcript_version "2"; exon_number "2"; gene_name "RP11-34P13.7"; gene_source "ensembl_havana"; gene_biotype "lincRNA"; transcript_name "RP11-34P13.7-004"; transcript_source "havana"; transcript_biotype "lincRNA"; exon_id "ENSE00001827073"; exon_version "1"; transcript_support_level "2";
+1	havana	gene	89551	91105	.	-	.	gene_id "ENSG00000239945"; gene_version "1"; gene_name "RP11-34P13.8"; gene_source "havana"; gene_biotype "lincRNA";
+1	havana	transcript	89551	91105	.	-	.	gene_id "ENSG00000239945"; gene_version "1"; transcript_id "ENST00000495576"; transcript_version "1"; gene_name "RP11-34P13.8"; gene_source "havana"; gene_biotype "lincRNA"; transcript_name "RP11-34P13.8-001"; transcript_source "havana"; transcript_biotype "lincRNA"; tag "basic"; transcript_support_level "5";
+1	havana	exon	90287	91105	.	-	.	gene_id "ENSG00000239945"; gene_version "1"; transcript_id "ENST00000495576"; transcript_version "1"; exon_number "1"; gene_name "RP11-34P13.8"; gene_source "havana"; gene_biotype "lincRNA"; transcript_name "RP11-34P13.8-001"; transcript_source "havana"; transcript_biotype "lincRNA"; exon_id "ENSE00001907785"; exon_version "1"; tag "basic"; transcript_support_level "5";
+1	havana	exon	89551	90050	.	-	.	gene_id "ENSG00000239945"; gene_version "1"; transcript_id "ENST00000495576"; transcript_version "1"; exon_number "2"; gene_name "RP11-34P13.8"; gene_source "havana"; gene_biotype "lincRNA"; transcript_name "RP11-34P13.8-001"; transcript_source "havana"; transcript_biotype "lincRNA"; exon_id "ENSE00001927725"; exon_version "1"; tag "basic"; transcript_support_level "5";
+1	havana	gene	131025	134836	.	+	.	gene_id "ENSG00000233750"; gene_version "3"; gene_name "CICP27"; gene_source "havana"; gene_biotype "processed_pseudogene";
+1	havana	transcript	131025	134836	.	+	.	gene_id "ENSG00000233750"; gene_version "3"; transcript_id "ENST00000442987"; transcript_version "3"; gene_name "CICP27"; gene_source "havana"; gene_biotype "processed_pseudogene"; transcript_name "CICP27-001"; transcript_source "havana"; transcript_biotype "processed_pseudogene"; tag "basic"; transcript_support_level "NA";
+1	havana	exon	131025	134836	.	+	.	gene_id "ENSG00000233750"; gene_version "3"; transcript_id "ENST00000442987"; transcript_version "3"; exon_number "1"; gene_name "CICP27"; gene_source "havana"; gene_biotype "processed_pseudogene"; transcript_name "CICP27-001"; transcript_source "havana"; transcript_biotype "processed_pseudogene"; exon_id "ENSE00001625118"; exon_version "3"; tag "basic"; transcript_support_level "NA";
+1	havana	gene	135141	135895	.	-	.	gene_id "ENSG00000268903"; gene_version "1"; gene_name "RP11-34P13.15"; gene_source "havana"; gene_biotype "processed_pseudogene";
+1	havana	transcript	135141	135895	.	-	.	gene_id "ENSG00000268903"; gene_version "1"; transcript_id "ENST00000494149"; transcript_version "2"; gene_name "RP11-34P13.15"; gene_source "havana"; gene_biotype "processed_pseudogene"; transcript_name "RP11-34P13.15-001"; transcript_source "havana"; transcript_biotype "processed_pseudogene"; tag "basic"; transcript_support_level "NA";
+1	havana	exon	135141	135895	.	-	.	gene_id "ENSG00000268903"; gene_version "1"; transcript_id "ENST00000494149"; transcript_version "2"; exon_number "1"; gene_name "RP11-34P13.15"; gene_source "havana"; gene_biotype "processed_pseudogene"; transcript_name "RP11-34P13.15-001"; transcript_source "havana"; transcript_biotype "processed_pseudogene"; exon_id "ENSE00001879101"; exon_version "2"; tag "basic"; transcript_support_level "NA";
+1	havana	gene	137682	137965	.	-	.	gene_id "ENSG00000269981"; gene_version "1"; gene_name "RP11-34P13.16"; gene_source "havana"; gene_biotype "processed_pseudogene";
+1	havana	transcript	137682	137965	.	-	.	gene_id "ENSG00000269981"; gene_version "1"; transcript_id "ENST00000595919"; transcript_version "1"; gene_name "RP11-34P13.16"; gene_source "havana"; gene_biotype "processed_pseudogene"; transcript_name "RP11-34P13.16-001"; transcript_source "havana"; transcript_biotype "processed_pseudogene"; tag "basic"; transcript_support_level "NA";
+1	havana	exon	137682	137965	.	-	.	gene_id "ENSG00000269981"; gene_version "1"; transcript_id "ENST00000595919"; transcript_version "1"; exon_number "1"; gene_name "RP11-34P13.16"; gene_source "havana"; gene_biotype "processed_pseudogene"; transcript_name "RP11-34P13.16-001"; transcript_source "havana"; transcript_biotype "processed_pseudogene"; exon_id "ENSE00001936432"; exon_version "2"; tag "basic"; transcript_support_level "NA";
diff -r 000000000000 -r 75a14cc16d4d test-data/gtf2bed_test_transcript_info.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gtf2bed_test_transcript_info.txt	Fri May 18 15:10:34 2018 -0400
@@ -0,0 +1,22 @@
+#transId	geneId	source	chrom	start	end	strand	proteinId	geneName	transcriptName	geneType	transcriptType
+ENST00000456328	ENSG00000223972	havana	1	11868	14409	+		DDX11L1	DDX11L1-002	transcribed_unprocessed_pseudogene	processed_transcript
+ENST00000450305	ENSG00000223972	havana	1	12009	13670	+		DDX11L1	DDX11L1-001	transcribed_unprocessed_pseudogene	transcribed_unprocessed_pseudogene
+ENST00000488147	ENSG00000227232	havana	1	14403	29570	-		WASH7P	WASH7P-001	unprocessed_pseudogene	unprocessed_pseudogene
+ENST00000619216	ENSG00000278267	ensembl	1	17368	17436	-		MIR6859-1	MIR6859-1-201	miRNA	miRNA
+ENST00000473358	ENSG00000243485	havana	1	29553	31097	+		RP11-34P13.3	RP11-34P13.3-001	lincRNA	lincRNA
+ENST00000469289	ENSG00000243485	havana	1	30266	31109	+		RP11-34P13.3	RP11-34P13.3-002	lincRNA	lincRNA
+ENST00000607096	ENSG00000274890	ensembl	1	30365	30503	+		MIR1302-2	MIR1302-2-201	miRNA	miRNA
+ENST00000417324	ENSG00000237613	havana	1	34553	36081	-		FAM138A	FAM138A-001	lincRNA	lincRNA
+ENST00000461467	ENSG00000237613	havana	1	35244	36073	-		FAM138A	FAM138A-002	lincRNA	lincRNA
+ENST00000606857	ENSG00000268020	havana	1	52472	53312	+		OR4G4P	OR4G4P-001	unprocessed_pseudogene	unprocessed_pseudogene
+ENST00000492842	ENSG00000240361	havana	1	62947	63887	+		OR4G11P	OR4G11P-001	unprocessed_pseudogene	unprocessed_pseudogene
+ENST00000335137	ENSG00000186092	ensembl_havana	1	69090	70008	+	ENSP00000334393	OR4F5	OR4F5-001	protein_coding	protein_coding
+ENST00000466430	ENSG00000238009	havana	1	89294	120932	-		RP11-34P13.7	RP11-34P13.7-001	lincRNA	lincRNA
+ENST00000477740	ENSG00000238009	havana	1	92229	129217	-		RP11-34P13.7	RP11-34P13.7-003	lincRNA	lincRNA
+ENST00000471248	ENSG00000238009	havana	1	110952	129173	-		RP11-34P13.7	RP11-34P13.7-002	lincRNA	lincRNA
+ENST00000610542	ENSG00000238009	ensembl	1	120724	133723	-		RP11-34P13.7	RP11-34P13.7-201	lincRNA	lincRNA
+ENST00000453576	ENSG00000238009	havana	1	129080	133566	-		RP11-34P13.7	RP11-34P13.7-004	lincRNA	lincRNA
+ENST00000495576	ENSG00000239945	havana	1	89550	91105	-		RP11-34P13.8	RP11-34P13.8-001	lincRNA	lincRNA
+ENST00000442987	ENSG00000233750	havana	1	131024	134836	+		CICP27	CICP27-001	processed_pseudogene	processed_pseudogene
+ENST00000494149	ENSG00000268903	havana	1	135140	135895	-		RP11-34P13.15	RP11-34P13.15-001	processed_pseudogene	processed_pseudogene
+ENST00000595919	ENSG00000269981	havana	1	137681	137965	-		RP11-34P13.16	RP11-34P13.16-001	processed_pseudogene	processed_pseudogene