| Previous changeset 0:040d4b3a19d5 (2019-04-03) Next changeset 2:e255c0e5dfca (2019-10-18) |
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Commit message:
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/util/.shed.yml commit 194d2e0af16624c9a3d1af92f7b3686d2e0ee552 |
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added:
gtf2featureAnnotation.R gtf2featureAnnotation.xml test-data/annotation.txt test-data/test.gtf |
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removed:
gtf2gene.R gtf2gene_list.xml |
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| diff -r 040d4b3a19d5 -r 247b439a78f7 gtf2featureAnnotation.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/gtf2featureAnnotation.R Fri Oct 18 10:10:54 2019 -0400 |
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| @@ -0,0 +1,195 @@ +#!/usr/bin/env Rscript + +# This script parses the GTF file to create a feature-wise annotation file with +# mitochondrial features flagged, to assist in annotation and QC of single-cell +# expression data analysis. + +suppressPackageStartupMessages(require(rtracklayer)) +suppressPackageStartupMessages(require(optparse)) + +ucfirst <- function (str) { + paste(toupper(substring(str, 1, 1)), tolower(substring(str, 2)), sep = "") +} + +die <- function(message){ + write(message, stderr()) + q(status = 1) +} + +cleanlist <- function(str){ + tolower(unlist(strsplit(str, ','))) +} + +cl <- commandArgs(trailingOnly = TRUE) + +option_list = list( + make_option( + c("-g", "--gtf-file"), + action = "store", + default = NA, + type = 'character', + help = "Path to a valid GTF file" + ), + make_option( + c("-t", "--feature-type"), + action = "store", + default = 'gene', + type = 'character', + help = 'Feature type to use (default: gene)' + ), + make_option( + c("-f", "--first-field"), + action = "store", + default = 'gene_id', + type = 'character', + help = 'Field to place first in output table (default: gene_id)' + ), + make_option( + c("-r", "--no-header"), + action = "store_false", + default = TRUE, + type = 'logical', + help = 'Suppress header on output' + ), + make_option( + c("-l", "--fields"), + action = "store", + default = NULL, + type = 'character', + help = 'Comma-separated list of output fields to retain (default: all)' + ), + make_option( + c("-m", "--mito"), + action = "store_true", + default = FALSE, + type = 'character', + help = 'Mark mitochondrial elements with reference to chromsomes and biotypes' + ), + make_option( + c("-n", "--mito-chr"), + action = "store", + default = 'mt,mitochondrion_genome,mito,m,chrM,chrMt', + type = 'character', + help = 'If specified, marks in a column called "mito" features on the specified chromosomes (case insensitive)' + ), + make_option( + c("-p", "--mito-biotypes"), + action = "store", + default = 'mt_trna,mt_rrna,mt_trna_pseudogene', + type = 'character', + help = 'If specified, marks in a column called "mito" features with the specified biotypes (case insensitve)' + ), + make_option( + c("-c", "--filter-cdnas"), + action = "store", + default = NULL, + type = 'character', + help = 'If specified, sequences in the provided FASTA-format cDNAs file will be filtered to remove entries not present in the annotation' + ), + make_option( + c("-d", "--filter-cdnas-field"), + action = "store", + default = 'transcript_id', + type = 'character', + help = 'Where --filter-cdnas is specified, what field should be used to compare to identfiers from the FASTA?' + ), + make_option( + c("-e", "--filter-cdnas-output"), + action = "store", + default = 'filtered.fa.gz', + type = 'character', + help = 'Where --filter-cdnas is specified, what file should the filtered sequences be output to?' + ), + make_option( + c("-u", "--version-transcripts"), + action = "store_true", + default = FALSE, + type = 'logical', + help = 'Where the GTF contains transcript versions, should these be appended to transcript identifiers? Useful when generating transcript/gene mappings for use with transcriptomes.' + ), + make_option( + c("-o", "--output-file"), + action = "store", + default = NA, + type = 'character', + help = 'Output file path' + ) +) + +opt <- parse_args(OptionParser(option_list = option_list), convert_hyphens_to_underscores = TRUE) + +if (is.na(opt$gtf_file)){ + die('ERROR: No input GTF file specified') +} + +if (is.na(opt$output_file)){ + die('ERROR: No output file specified') +} + +# Import the GTF + +print(paste('Reading', opt$gtf_file, 'elements of type', opt$feature_type)) +gtf <- import(opt$gtf_file, feature.type = opt$feature_type ) + +# Combine basic info (chromosomes, coordinates) with annotation found in GTF attributes + +anno <- cbind(chromosome = seqnames(gtf), as.data.frame(ranges(gtf)), elementMetadata(gtf)) +print(paste('Found', nrow(anno), 'features')) + +# Mark mitochondrial features + +if (opt$mito){ + anno$mito <- ucfirst(as.character(tolower(anno$gene_biotype) %in% cleanlist(opt$mito_biotypes) | tolower(anno$chromosome) %in% cleanlist(opt$mito_chr))) +} + +# If specified, put the desired field first + +if (! is.na(opt$first_field)){ + if (! opt$first_field %in% colnames(anno)){ + die(paste(first_field, 'is not a valid field')) + } + anno <- anno[,c(opt$first_field, colnames(anno)[colnames(anno) != opt$first_field])] +} + +# Version transcripts + +if ( opt$feature_type == 'transcript' && opt$version_transcripts && all(c('transcript_id', 'transcript_version') %in% colnames(anno) )){ + anno$transcript_id <- paste(anno$transcript_id, anno$transcript_version, sep='.') +} + +# If specified, filter down a provided cDNA FASTA file + +if (! is.null(opt$filter_cdnas)){ + + print(paste("Filtering", opt$filter_cdnas, "to match the GTF")) + + suppressPackageStartupMessages(require(Biostrings)) + + cdna <- readDNAStringSet(opt$filter_cdnas) + cdna_transcript_names <- unlist(lapply(names(cdna), function(x) unlist(strsplit(x, ' '))[1] )) + + # Filter out cDNAs without matching transcript entries in the GTF + + if (! any(cdna_transcript_names %in% anno[[opt$filter_cdnas_field]])){ + die(paste("ERROR: None of the input sequences have matching", opt$filter_cdnas_field, 'values in the GTF file')) + } + + cdna <- cdna[which(cdna_transcript_names %in% anno[[opt$filter_cdnas_field]])] + + print(paste('Storing filtered seqeunces to', opt$filter_cdnas_output)) + writeXStringSet(x = cdna, filepath = opt$filter_cdnas_output, compress = 'gzip') +} + +# If specified, subset to desired fields + +if (! is.null(opt$fields) && opt$fields != ''){ + fields <- unlist(strsplit(opt$fields, ',')) + if (any(! fields %in% colnames(anno))){ + die(paste('ERROR:', fields, 'contains invalid field(s)')) + } + anno <- anno[,fields, drop = FALSE] + anno <- anno[apply(anno, 1, function(x) all(! is.na(x))), ] +} + +print(paste('Storing output to', opt$output_file)) +write.table(anno, file = opt$output_file, sep = "\t", quote=FALSE, row.names = FALSE, col.names = opt$no_header) |
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| diff -r 040d4b3a19d5 -r 247b439a78f7 gtf2featureAnnotation.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/gtf2featureAnnotation.xml Fri Oct 18 10:10:54 2019 -0400 |
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| @@ -0,0 +1,96 @@ +<tool id="_ensembl_gtf2gene_list" name="GTF2GeneAnnotationTable" version="1.42.1+galaxy1"> + <description>extracts a complete annotation table or subsets thereof from an Ensembl GTF using rtracklayer</description> + <requirements> + <requirement type="package" version="1.42.1">bioconductor-rtracklayer</requirement> + <requirement type="package">bioconductor-biostrings</requirement> + <requirement type="package">r-optparse</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + ln -s '$gtf_input' input.gtf; + $__tool_directory__/gtf2featureAnnotation.R --gtf-file input.gtf +#if $noheader +--no-header +#end if +#if $version_transcripts +--version-transcripts +#end if +#if $mito.mark_mito +--mito --mito-chr "${mito.mito_chr}" --mito-biotypes "${mito.mito_biotypes}" +#end if +#if $cdnas.filter_cdnas +--filter-cdnas "${cdnas.fasta_input}" --filter-cdnas-field "${cdnas.cdnas_field}" --filter-cdnas-output "${fasta_output}" +#end if +--feature-type "${feature_type}" --first-field "${first_field}" --output-file annotation.txt --fields "${fields}" + ]]></command> + + <inputs> + <param name="gtf_input" type="data" format="gff" label="Ensembl GTF file" /> + <param name="feature_type" type="text" optional='true' value="gene" label="Feature type for which to derive annotation"/> + <param name="first_field" type="text" optional='true' value="gene_id" label="Field to place first in output table"/> + <param name="noheader" type="boolean" checked="false" label="Suppress header line in output?"/> + <param name="fields" type="text" optional='true' value="" label="Comma-separated list of field names to extract from the GTF (default: use all fields)"/> + <param name="version_transcripts" type="boolean" checked="false" label="Append version to transcript identifiers?" help="For transcript feature type only: where the GTF contains transcript versions, should these be appended to transcript identifiers? Useful when generating transcript/gene mappings for use with transcriptomes"/> + <conditional name="mito"> + <param name="mark_mito" type="boolean" checked="true" label="Flag mitochondrial features?"/> + <when value="true"> + <param name="mito_chr" type="text" optional='true' value="mt,mitochondrion_genome,mito,m,chrM,chrMt" label="Comma-separated list of possible mitochondrial chromosome names (case insensitive)"/> + <param name="mito_biotypes" type="text" optional='true' value="mt_trna,mt_rrna,mt_trna_pseudogene" label="Comma-separated list of possible mitochondrial biotypes (case insensitive)"/> + </when> + <when value="false" /> + </conditional> + <conditional name="cdnas"> + <param name="filter_cdnas" type="boolean" checked="false" label="Filter a FASTA-format cDNA file to match annotations?" help="For some applications, e.g. transcriptome mappers, its useful to match a cDNAs file to an annotation list (e.g. transcript-to-gene mapping)"/> + <when value="true"> + <param name="fasta_input" type="data" format="fasta" label="FASTA-format cDNA/ transcript file" /> + <param name="cdnas_field" type="text" optional='true' value="transcript_id" label="Annotation field to match with sequences."/> + </when> + <when value="false" /> + </conditional> + </inputs> + + <outputs> + <data name="feature_annotation" format="tsv" from_work_dir="annotation.txt" label="${tool.name} on ${on_string}: annotation table"/> + <data name="fasta_output" format="fasta" from_work_dir="filtered.fa.gz" label="${tool.name} on ${on_string}: annotation-matched sequences"> + <filter>filter_cdnas</filter> + </data> + </outputs> + <tests> + <test> + <param name="gtf_input" ftype="gtf" value="test.gtf"/> + <output name="feature_annotation" file="annotation.txt"/> + </test> + </tests> + + + <help><![CDATA[ +.. class:: infomark + +**What it does** + +Given an Ensembl GTF file, it will extract all information on chromosomes, coordinates, and attributes provided at the specified feature level. Mitochondrial features can also be flagged. + +You can also supply a fasta-format file of sequences, which will be filtered by identifier to match annotation. This can be useful for tools such as Alevin which need a transcript-to-gene mapping and a transcriptome file without any missing entries (with respect to annotation). + + +**Inputs** + + * Ensembl GTF file + +----- + +**Outputs** + + * Gene annotations in tsv. +]]></help> +<citations> + <citation type="bibtex"> +@misc{github-hinxton-single-cell, +author = {Jonathan Manning, EBI Gene Expression Team}, +year = {2019}, +title = {Hinxton Single Cell Anlysis Environment}, +publisher = {GitHub}, +journal = {GitHub repository}, +url = {https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary}, + }</citation> +</citations> +</tool> |
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| diff -r 040d4b3a19d5 -r 247b439a78f7 gtf2gene.R --- a/gtf2gene.R Wed Apr 03 12:05:26 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,8 +0,0 @@ -#!/usr/bin/env Rscript - -suppressPackageStartupMessages(require(rtracklayer)) -args <- commandArgs(TRUE) - -annotation <- elementMetadata(import( args[1] )) -genes <- unique(annotation[['gene_id']]) -writeLines(genes[ ! is.na(genes)], con = 'genes.txt') |
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| diff -r 040d4b3a19d5 -r 247b439a78f7 gtf2gene_list.xml --- a/gtf2gene_list.xml Wed Apr 03 12:05:26 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,54 +0,0 @@ -<tool id="_ensembl_gtf2gene_list" name="GTF2GeneList" version="1.42.1+galaxy0"> - <description>extracts gene ids from Ensembl GTF using rtracklayer</description> - <requirements> - <requirement type="package" version="1.42.1">bioconductor-rtracklayer</requirement> - </requirements> - <command detect_errors="exit_code"><![CDATA[ - ln -s '$gtf_input' input.gtf; - Rscript $__tool_directory__/gtf2gene.R input.gtf - ]]></command> - - <inputs> - <param name="gtf_input" type="data" format="gff" label="Ensembl GTF file" /> - </inputs> - - <outputs> - <data name="gene_list" format="tsv" from_work_dir="genes.txt" label="${tool.name} on ${on_string}"/> - </outputs> - <tests> - <test> - <param name="gtf_input" ftype="data" value="short_ensembl_gtf.gtf"/> - <output name="gene_list" ftype="data" value="genes.txt" compare="sim_size"/> - </test> - </tests> - - - <help><![CDATA[ -.. class:: infomark - -**What it does** - -Given an Ensembl GTF file, it will extract the list of all gene identifiers in the GTF to a simple tsv file. - -**Inputs** - - * Ensembl GTF file - ------ - -**Outputs** - - * Gene identifier list in tsv. -]]></help> -<citations> - <citation type="bibtex"> -@misc{github-hinxton-single-cell, -author = {Pablo Moreno, EBI Gene Expression Team}, -year = {2019}, -title = {Hinxton Single Cell Anlysis Environment}, -publisher = {GitHub}, -journal = {GitHub repository}, -url = {https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary}, - }</citation> -</citations> -</tool> |
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| diff -r 040d4b3a19d5 -r 247b439a78f7 test-data/annotation.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/annotation.txt Fri Oct 18 10:10:54 2019 -0400 |
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| @@ -0,0 +1,11 @@ +gene_id chromosome start end width source type score phase gene_version gene_name gene_source gene_biotype mito +ENSG00000223972 1 11869 14409 2541 havana gene NA NA 5 DDX11L1 havana transcribed_unprocessed_pseudogene False +ENSG00000227232 1 14404 29570 15167 havana gene NA NA 5 WASH7P havana unprocessed_pseudogene False +ENSG00000278267 1 17369 17436 68 mirbase gene NA NA 1 MIR6859-1 mirbase miRNA False +ENSG00000243485 1 29554 31109 1556 havana gene NA NA 5 MIR1302-2HG havana lncRNA False +ENSG00000284332 1 30366 30503 138 mirbase gene NA NA 1 MIR1302-2 mirbase miRNA False +ENSG00000237613 1 34554 36081 1528 havana gene NA NA 2 FAM138A havana lncRNA False +ENSG00000268020 1 52473 53312 840 havana gene NA NA 3 OR4G4P havana unprocessed_pseudogene False +ENSG00000240361 1 57598 64116 6519 havana gene NA NA 2 OR4G11P havana transcribed_unprocessed_pseudogene False +ENSG00000186092 1 65419 71585 6167 ensembl_havana gene NA NA 6 OR4F5 ensembl_havana protein_coding False +ENSG00000238009 1 89295 133723 44429 ensembl_havana gene NA NA 6 AL627309.1 ensembl_havana lncRNA False |
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| diff -r 040d4b3a19d5 -r 247b439a78f7 test-data/test.gtf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test.gtf Fri Oct 18 10:10:54 2019 -0400 |
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| b'@@ -0,0 +1,100 @@\n+#!genome-build GRCh38.p13\n+#!genome-version GRCh38\n+#!genome-date 2013-12\n+#!genome-build-accession NCBI:GCA_000001405.28\n+#!genebuild-last-updated 2019-06\n+1\thavana\tgene\t11869\t14409\t.\t+\t.\tgene_id "ENSG00000223972"; gene_version "5"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene";\n+1\thavana\ttranscript\t11869\t14409\t.\t+\t.\tgene_id "ENSG00000223972"; gene_version "5"; transcript_id "ENST00000456328"; transcript_version "2"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; transcript_name "DDX11L1-202"; transcript_source "havana"; transcript_biotype "lncRNA"; tag "basic"; transcript_support_level "1";\n+1\thavana\texon\t11869\t12227\t.\t+\t.\tgene_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 "DDX11L1-202"; transcript_source "havana"; transcript_biotype "lncRNA"; exon_id "ENSE00002234944"; exon_version "1"; tag "basic"; transcript_support_level "1";\n+1\thavana\texon\t12613\t12721\t.\t+\t.\tgene_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 "DDX11L1-202"; transcript_source "havana"; transcript_biotype "lncRNA"; exon_id "ENSE00003582793"; exon_version "1"; tag "basic"; transcript_support_level "1";\n+1\thavana\texon\t13221\t14409\t.\t+\t.\tgene_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 "DDX11L1-202"; transcript_source "havana"; transcript_biotype "lncRNA"; exon_id "ENSE00002312635"; exon_version "1"; tag "basic"; transcript_support_level "1";\n+1\thavana\ttranscript\t12010\t13670\t.\t+\t.\tgene_id "ENSG00000223972"; gene_version "5"; transcript_id "ENST00000450305"; transcript_version "2"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; transcript_name "DDX11L1-201"; transcript_source "havana"; transcript_biotype "transcribed_unprocessed_pseudogene"; tag "basic"; transcript_support_level "NA";\n+1\thavana\texon\t12010\t12057\t.\t+\t.\tgene_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 "DDX11L1-201"; transcript_source "havana"; transcript_biotype "transcribed_unprocessed_pseudogene"; exon_id "ENSE00001948541"; exon_version "1"; tag "basic"; transcript_support_level "NA";\n+1\thavana\texon\t12179\t12227\t.\t+\t.\tgene_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 "DDX11L1-201"; transcript_source "havana"; transcript_biotype "transcribed_unprocessed_pseudogene"; exon_id "ENSE00001671638"; exon_version "2"; tag "basic"; transcript_support_level "NA";\n+1\thavana\texon\t12613\t12697\t.\t+\t.\tgene_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 "DDX11L1-201"; transcript_source "havana"; transcript_biotype "transcribed_unprocessed_pseudogene"; exon_id "ENSE00001758273"; exon_version "2"; tag "basic"; transcript_support_level "NA";\n+1\thavana\texon\t12975\t13052\t.\t+\t.\tgene_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 "DDX11L1-2'..b'ncRNA"; exon_id "ENSE00001171005"; exon_version "3"; transcript_support_level "5";\n+1\thavana\texon\t112700\t112804\t.\t-\t.\tgene_id "ENSG00000238009"; gene_version "6"; transcript_id "ENST00000477740"; transcript_version "5"; exon_number "3"; gene_name "AL627309.1"; gene_source "ensembl_havana"; gene_biotype "lncRNA"; transcript_name "AL627309.1-202"; transcript_source "havana"; transcript_biotype "lncRNA"; exon_id "ENSE00001957285"; exon_version "1"; transcript_support_level "5";\n+1\thavana\texon\t92230\t92240\t.\t-\t.\tgene_id "ENSG00000238009"; gene_version "6"; transcript_id "ENST00000477740"; transcript_version "5"; exon_number "4"; gene_name "AL627309.1"; gene_source "ensembl_havana"; gene_biotype "lncRNA"; transcript_name "AL627309.1-202"; transcript_source "havana"; transcript_biotype "lncRNA"; exon_id "ENSE00001896976"; exon_version "1"; transcript_support_level "5";\n+1\thavana\ttranscript\t110953\t129173\t.\t-\t.\tgene_id "ENSG00000238009"; gene_version "6"; transcript_id "ENST00000471248"; transcript_version "1"; gene_name "AL627309.1"; gene_source "ensembl_havana"; gene_biotype "lncRNA"; transcript_name "AL627309.1-203"; transcript_source "havana"; transcript_biotype "lncRNA"; transcript_support_level "5";\n+1\thavana\texon\t129055\t129173\t.\t-\t.\tgene_id "ENSG00000238009"; gene_version "6"; transcript_id "ENST00000471248"; transcript_version "1"; exon_number "1"; gene_name "AL627309.1"; gene_source "ensembl_havana"; gene_biotype "lncRNA"; transcript_name "AL627309.1-203"; transcript_source "havana"; transcript_biotype "lncRNA"; exon_id "ENSE00001934975"; exon_version "1"; transcript_support_level "5";\n+1\thavana\texon\t112700\t112804\t.\t-\t.\tgene_id "ENSG00000238009"; gene_version "6"; transcript_id "ENST00000471248"; transcript_version "1"; exon_number "2"; gene_name "AL627309.1"; gene_source "ensembl_havana"; gene_biotype "lncRNA"; transcript_name "AL627309.1-203"; transcript_source "havana"; transcript_biotype "lncRNA"; exon_id "ENSE00001957285"; exon_version "1"; transcript_support_level "5";\n+1\thavana\texon\t110953\t111357\t.\t-\t.\tgene_id "ENSG00000238009"; gene_version "6"; transcript_id "ENST00000471248"; transcript_version "1"; exon_number "3"; gene_name "AL627309.1"; gene_source "ensembl_havana"; gene_biotype "lncRNA"; transcript_name "AL627309.1-203"; transcript_source "havana"; transcript_biotype "lncRNA"; exon_id "ENSE00001879696"; exon_version "1"; transcript_support_level "5";\n+1\tensembl\ttranscript\t120725\t133723\t.\t-\t.\tgene_id "ENSG00000238009"; gene_version "6"; transcript_id "ENST00000610542"; transcript_version "1"; gene_name "AL627309.1"; gene_source "ensembl_havana"; gene_biotype "lncRNA"; transcript_name "AL627309.1-205"; transcript_source "ensembl"; transcript_biotype "lncRNA"; tag "basic"; transcript_support_level "5";\n+1\tensembl\texon\t133374\t133723\t.\t-\t.\tgene_id "ENSG00000238009"; gene_version "6"; transcript_id "ENST00000610542"; transcript_version "1"; exon_number "1"; gene_name "AL627309.1"; gene_source "ensembl_havana"; gene_biotype "lncRNA"; transcript_name "AL627309.1-205"; transcript_source "ensembl"; transcript_biotype "lncRNA"; exon_id "ENSE00003748456"; exon_version "1"; tag "basic"; transcript_support_level "5";\n+1\tensembl\texon\t129055\t129223\t.\t-\t.\tgene_id "ENSG00000238009"; gene_version "6"; transcript_id "ENST00000610542"; transcript_version "1"; exon_number "2"; gene_name "AL627309.1"; gene_source "ensembl_havana"; gene_biotype "lncRNA"; transcript_name "AL627309.1-205"; transcript_source "ensembl"; transcript_biotype "lncRNA"; exon_id "ENSE00003734824"; exon_version "1"; tag "basic"; transcript_support_level "5";\n+1\tensembl\texon\t120874\t120932\t.\t-\t.\tgene_id "ENSG00000238009"; gene_version "6"; transcript_id "ENST00000610542"; transcript_version "1"; exon_number "3"; gene_name "AL627309.1"; gene_source "ensembl_havana"; gene_biotype "lncRNA"; transcript_name "AL627309.1-205"; transcript_source "ensembl"; transcript_biotype "lncRNA"; exon_id "ENSE00003740919"; exon_version "1"; tag "basic"; transcript_support_level "5";\n' |