Mercurial > repos > iuc > length_and_gc_content
changeset 2:e3ba567abdf5 draft default tip
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/length_and_gc_content commit 7b6b07d22f3e6fed77b2c237de2b0d96fa939711"
| author | iuc |
|---|---|
| date | Fri, 11 Mar 2022 14:08:11 +0000 |
| parents | f088370d2a3c |
| children | |
| files | get_length_and_gc_content.r get_length_and_gc_content.xml macros.xml test-data/cached_locally/ref.fasta test-data/cached_locally/ref.gtf test-data/gc.tab test-data/in.fasta test-data/in.gtf test-data/length.tab |
| diffstat | 9 files changed, 523 insertions(+), 96 deletions(-) [+] |
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--- a/get_length_and_gc_content.r Sun Jan 28 04:04:58 2018 -0500 +++ b/get_length_and_gc_content.r Fri Mar 11 14:08:11 2022 +0000 @@ -1,59 +1,94 @@ # originally by Devon Ryan, https://www.biostars.org/p/84467/ -options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } ) +options(show.error.messages = F, + error = function() { + cat(geterrmessage(), file = stderr()) + q("no", 1, F) + }) # we need that to not crash galaxy with an UTF8 error on German LC settings. loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") suppressPackageStartupMessages({ - library("GenomicRanges") - library("rtracklayer") - library("Rsamtools") - library("optparse") - library("data.table") + library("GenomicRanges") + library("rtracklayer") + library("Rsamtools") + library("optparse") + library("data.table") }) option_list <- list( - make_option(c("-g","--gtf"), type="character", help="Input GTF file with gene / exon information."), - make_option(c("-f","--fasta"), type="character", default=FALSE, help="FASTA file that corresponds to the supplied GTF."), - make_option(c("-l","--length"), type="character", default=FALSE, help="Output file with Gene ID and length."), - make_option(c("-gc","--gc_content"), type="character", default=FALSE, help="Output file with Gene ID and GC content.") - ) + make_option(c("-g", "--gtf"), type = "character", + help = "Input gtf file with gene / exon information."), + make_option(c("-f", "--fasta"), type = "character", default = NULL, + help = "fasta file that corresponds to the supplied gtf."), + make_option(c("-l", "--length"), type = "character", default = NULL, + help = "Output file with Gene ID and length."), + make_option(c("-c", "--gc_content"), type = "character", default = NULL, + help = "Output file with Gene ID and GC content.") +) -parser <- OptionParser(usage = "%prog [options] file", option_list=option_list) -args = parse_args(parser) +parser <- OptionParser(usage = "%prog [options] file", + option_list = option_list) +args <- parse_args(parser) -GTFfile = args$gtf -FASTAfile = args$fasta -length = args$length -gc_content = args$gc_content +gtf_file <- args$gtf +fasta_file <- args$fasta +length <- args$length +gc_content <- args$gc_content + +# Check args: +if (is.null(fasta_file) & !is.null(gc_content)) { + stop("gc_content output requires fasta input") +} +if (is.null(length) & is.null(gc_content)) { + stop("neither gc_content nor length was set nothing to do.") +} #Load the annotation and reduce it -GTF <- import.gff(GTFfile, format="gtf", genome=NA, feature.type="exon") -grl <- reduce(split(GTF, elementMetadata(GTF)$gene_id)) -reducedGTF <- unlist(grl, use.names=T) -elementMetadata(reducedGTF)$gene_id <- rep(names(grl), elementNROWS(grl)) +gtf <- import.gff(gtf_file, format = "gtf", genome = NA, feature.type = "exon") +grl <- reduce(split(gtf, elementMetadata(gtf)$gene_id)) +reduced_gtf <- unlist(grl, use.names = T) +elementMetadata(reduced_gtf)$gene_id <- rep(names(grl), elementNROWS(grl)) -#Open the fasta file -FASTA <- FaFile(FASTAfile) -open(FASTA) +if (! is.null(gc_content)) { + #Open the fasta file + fasta <- FaFile(fasta_file) + open(fasta) -#Add the GC numbers -elementMetadata(reducedGTF)$nGCs <- letterFrequency(getSeq(FASTA, reducedGTF), "GC")[,1] -elementMetadata(reducedGTF)$widths <- width(reducedGTF) + #Add the GC numbers + elementMetadata(reduced_gtf)$n_gcs <- + letterFrequency(getSeq(fasta, reduced_gtf), "GC")[, 1] +} +elementMetadata(reduced_gtf)$widths <- width(reduced_gtf) #Create a list of the ensembl_id/GC/length -calc_GC_length <- function(x) { - nGCs = sum(elementMetadata(x)$nGCs) - width = sum(elementMetadata(x)$widths) - c(width, nGCs/width) +if (! is.null(gc_content)) { + calc_gc_length <- function(x) { + n_gcs <- sum(elementMetadata(x)$n_gcs) + width <- sum(elementMetadata(x)$widths) + c(width, n_gcs / width) + } + output <- t(sapply(split(reduced_gtf, elementMetadata(reduced_gtf)$gene_id), + calc_gc_length)) + output <- data.frame(setDT(data.frame(output), keep.rownames = TRUE)[]) + write.table(output[, c(1, 3)], file = gc_content, + col.names = FALSE, row.names = FALSE, + quote = FALSE, sep = "\t") +} else { + all_widths <- sapply(split(reduced_gtf, elementMetadata(reduced_gtf)$gene_id), + function(x) { + sum(elementMetadata(x)$widths) + }) + output <- data.frame(gene_id = names(all_widths), + length = all_widths) } -output <- t(sapply(split(reducedGTF, elementMetadata(reducedGTF)$gene_id), calc_GC_length)) -output <- data.frame(setDT(data.frame(output), keep.rownames = TRUE)[]) - -write.table(output[,c(1,2)], file=length, col.names=FALSE, row.names=FALSE, quote=FALSE, sep="\t") -write.table(output[,c(1,3)], file=gc_content, col.names=FALSE, row.names=FALSE, quote=FALSE, sep="\t") +if (! is.null(length)) { + write.table(output[, c(1, 2)], file = length, + col.names = FALSE, row.names = FALSE, + quote = FALSE, sep = "\t") +} sessionInfo()
--- a/get_length_and_gc_content.xml Sun Jan 28 04:04:58 2018 -0500 +++ b/get_length_and_gc_content.xml Fri Mar 11 14:08:11 2022 +0000 @@ -1,11 +1,9 @@ -<tool id="length_and_gc_content" name="Gene length and GC content" version="0.1.1"> +<tool id="length_and_gc_content" name="Gene length and GC content" version="0.1.2"> <description>from GTF and FASTA file</description> - <requirements> - <requirement type="package" version="1.3.2">r-optparse</requirement> - <requirement type="package" version="1.4.2">r-reshape2</requirement> - <requirement type="package" version="1.10.4">r-data.table</requirement> - <requirement type="package" version="1.34.2">bioconductor-rtracklayer</requirement> - </requirements> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> <stdio> <regex match="Execution halted" source="both" @@ -21,7 +19,7 @@ description="An undefined error occured, please check your input carefully and contact your administrator." /> </stdio> <version_command><![CDATA[ - echo $(R --version | grep version | grep -v GNU)", optparse version" $(R --vanilla --slave -e "library(optparse); cat(sessionInfo()\$otherPkgs\$optparse\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", reshape2 version" $(R --vanilla --slave -e "library(reshape2); cat(sessionInfo()\$otherPkgs\$reshape2\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", rtracklayer version" $(R --vanilla --slave -e "library(rtracklayer); cat(sessionInfo()\$otherPkgs\$rtracklayer\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", data.table version" $(R --vanilla --slave -e "library(data.table); cat(sessionInfo()\$otherPkgs\$data.table\$Version)" 2> /dev/null | grep -v -i "WARNING: ") + echo $(R --version | grep version | grep -v GNU)", optparse version" $(R --vanilla --slave -e "library(optparse); cat(sessionInfo()\$otherPkgs\$optparse\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", rtracklayer version" $(R --vanilla --slave -e "library(rtracklayer); cat(sessionInfo()\$otherPkgs\$rtracklayer\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", data.table version" $(R --vanilla --slave -e "library(data.table); cat(sessionInfo()\$otherPkgs\$data.table\$Version)" 2> /dev/null | grep -v -i "WARNING: ") ]]></version_command> <command><![CDATA[ @@ -37,24 +35,24 @@ ## Get FASTA -#if $fasta_file.fastaSource == 'indexed': - ln -s '$fasta_file.fasta_pre_installed.fields.path' fasta -#else: - ln -s '$fasta_file.fasta_history' fasta +#if $analysis.analysis_select != "length": + #if $analysis.fasta_file.fastaSource == 'indexed': + ln -s '$analysis.fasta_file.fasta_pre_installed.fields.path' fasta && + #else: + ln -s '$analysis.fasta_file.fasta_history' fasta && + #end if #end if -&& - Rscript '$__tool_directory__/get_length_and_gc_content.r' --gtf gtf ---fasta fasta -#if $length_out: +#if $analysis.analysis_select != "gc": --length '$length' #end if -#if $gc_out: +#if $analysis.analysis_select != "length": + --fasta fasta --gc_content '$gc_content' #end if @@ -79,39 +77,31 @@ </when> </conditional> - <conditional name="fasta_file"> - <param name="fastaSource" type="select" label="Select a built-in FASTA or one from your history" help="Choose history if you don't see the correct FASTA. The FASTA must be the same genome version as the GTF."> - <option value="indexed" selected="true">Use a built-in FASTA </option> - <option value="history">Use a FASTA from history</option> + <conditional name="analysis"> + <param name="analysis_select" type="select" label="Analysis to perform"> + <option value="all" selected="true">GC-content and gene lengths</option> + <option value="gc">GC-content only</option> + <option value="length">gene lengths only</option> </param> - <when value="indexed"> - <param name="fasta_pre_installed" type="select" help="Select the FASTA file from a list of pre-installed genomes" label="Select a FASTA file"> - <options from_data_table="all_fasta"> - <filter type="sort_by" column="2" /> - </options> - <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/> - </param> + <when value="all"> + <expand macro="fasta" /> </when> - <when value="history"> - <param name="fasta_history" type="data" format="fasta" label="Select a FASTA file that matches the supplied GTF file" /> + <when value="gc"> + <expand macro="fasta" /> </when> + <when value="length"/> </conditional> - - - <param name="length_out" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Output length file?" help="Default: Yes" /> - <param name="gc_out" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Output GC content file?" help="Default: Yes" /> - </inputs> <outputs> <data name="length" format="tabular" label="Gene length"> - <filter>length_out is True</filter> + <filter>analysis['analysis_select'] != "gc"</filter> <actions> <action name="column_names" type="metadata" default="GeneID,Length" /> </actions> </data> <data name="gc_content" format="tabular" label="Gene GC content"> - <filter>gc_out is True</filter> + <filter>analysis['analysis_select'] != "length"</filter> <actions> <action name="column_names" type="metadata" default="GeneID,GC_content" /> </actions> @@ -119,6 +109,8 @@ </outputs> <tests> + <!-- The gtf file was generated by + zcat gencode.v39.basic.annotation.gtf.gz | grep "HOXD" | awk -F "\t" -v OFS="\t" '$0~/HOXD10/ || $0~/HOXD9/ {$1="fake_chr2";$4-=176116521;$5-=176116521; print} --> <!-- Ensure length and GC files are output --> <test expect_num_outputs="2"> <param name="gtfSource" value="history" /> @@ -138,15 +130,14 @@ <!-- Ensure optional gc content works --> <test expect_num_outputs="1"> <param name="gtfSource" value="cached" /> - <param name="fastaSource" value="indexed" /> - <param name="gc_out" value="False" /> + <param name="analysis_select" value="length" /> <output name="length" file="length.tab" /> </test> <!-- Ensure optional length works --> <test expect_num_outputs="1"> <param name="gtfSource" value="cached" /> <param name="fastaSource" value="indexed" /> - <param name="length_out" value="False" /> + <param name="analysis_select" value="gc" /> <output name="gc_content" file="gc.tab" /> </test> </tests> @@ -156,14 +147,15 @@ .. class:: infomark -This tool calculates the length and GC content for the genes in a GTF file. It requires a FASTA file that is the same genome version as the GTF. +This tool calculates the length and/or GC content for the genes in a GTF file. +For the GC content, it requires a FASTA file that is the same genome version as the GTF. ----- **Inputs** - a GTF file -- a FASTA file +- a FASTA file (if GC content is requested) -----
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Fri Mar 11 14:08:11 2022 +0000 @@ -0,0 +1,28 @@ +<macros> + <xml name="requirements"> + <requirements> + <requirement type="package" version="1.7.1">r-optparse</requirement> + <requirement type="package" version="1.14.2">r-data.table</requirement> + <requirement type="package" version="1.54.0">bioconductor-rtracklayer</requirement> + </requirements> + </xml> + <xml name="fasta"> + <conditional name="fasta_file"> + <param name="fastaSource" type="select" label="Select a built-in FASTA or one from your history" help="Choose history if you don't see the correct FASTA. The FASTA must be the same genome version as the GTF."> + <option value="indexed" selected="true">Use a built-in FASTA </option> + <option value="history">Use a FASTA from history</option> + </param> + <when value="indexed"> + <param name="fasta_pre_installed" type="select" help="Select the FASTA file from a list of pre-installed genomes" label="Select a FASTA file"> + <options from_data_table="all_fasta"> + <filter type="sort_by" column="2" /> + </options> + <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/> + </param> + </when> + <when value="history"> + <param name="fasta_history" type="data" format="fasta" label="Select a FASTA file that matches the supplied GTF file" /> + </when> + </conditional> + </xml> +</macros>
--- a/test-data/cached_locally/ref.fasta Sun Jan 28 04:04:58 2018 -0500 +++ b/test-data/cached_locally/ref.fasta Fri Mar 11 14:08:11 2022 +0000 @@ -1,2 +1,173 @@ ->1 -AAAAAAAAAATTTTTTTTTTCCCCCCCCCCGGGGGGGGGGAAAAAAAAAAAAAAAAAAAATTTTTTTTTTCCCCCCCCCCGGGGGGGGGGAAAAAAAAAATTTTT \ No newline at end of file +>fake_chr2 hg38_dna range=chr2:176116522-176125113 5'pad=0 3'pad=0 strand=+ repeatMasking=none +TGGGGCGGGCTGGCCGAGCGAGCCCTGGAGAGGCGGACAGGAGGGCGGCG +GAGAGCGCTGGGCCGGTTGTCTCCAGCGCGCACTATCGCGGGCGCGTAGT +AGATGTCGCTGTTGTCCGTGCTTACCCGGCCGGCCGGCCAGGCTCTGGAG +CACGTGACCCGAGAGGAGGCTGCGGCTCAAGGCCATTTTCAAATCTCATT +GGCTTGGTTGTCATGTGGTCGGCAGAGGCATCCACAATTACACGGGGAAT +GTTTTCCTAGAGATGTCAGCCTACAAAGGACACAATCTCTCTTCTTCAAA +TTCTTCCCCAAAATGTCCTTTCCCAACAGCTCTCCTGCTGCTAATACTTT +TTTAGTAGATTCCTTGATCAGTGCCTGCAGGAGTGACAGTTTTTATTCCA +GCAGCGCCAGCATGTACATGCCACCACCTAGCGCAGACATGGGGACCTAT +GGAATGCAAACCTGTGGACTGCTCCCGTCTCTGGCCAAAAGAGAAGTGAA +CCACCAAAATATGGGTATGAATGTGCATCCTTATATACCTCAAGTAGACA +GTTGGACAGATCCGAACAGATCTTGTCGAATAGAGCAACCTGTTACACAG +CAAGTCCCCACTTGCTCCTTCACCACCAACATTAAGGAAGAATCCAATTG +CTGCATGTATTCTGATAAGCGCAACAAACTCATTTCGGCCGAGGTCCCTT +CGTACCAGAGGCTGGTCCCTGAGTCTTGTCCCGTTGAGAACCCTGAGGTT +CCCGTCCCTGGATATTTTAGACTGAGTCAGACCTACGCCACCGGGAAAAC +CCAAGAGTACAATAATAGCCCCGAAGGCAGCTCCACTGTCATGCTCCAGC +TCAACCCTCGTGGCGCGGCCAAGCCGCAGCTCTCCGCTGCCCAGCTGCAG +ATGGAAAAGAAGATGAACGAGCCCGTGAGCGGCCAGGAGCCCACCAAAGT +CTCCCAGGTGGAGAGCCCCGAGGCCAAAGGCGGCCTTCCCGAAGAGAGGA +GCTGCCTGGCTGAGGTCTCCGTGTCCAGTCCCGAAGTGCAGGAGAAGGAA +AGCAAAGGTCGGTATGAGCAGAGTTGCCACCCCAGCGGGGCGCGCAGCCC +GGGAACCCGGCAGAGAGGGAGTGCCGGGGTGCCCAGCGCCGAGCCGGAGC +CCGACTTGGCAGGTGCTGCTCCGCCTGGTTTTAGAGGGGTGATCTCAGCC +CTGAGATAGTCCCCGCTTCTCCCCTGCTGCCCTGGCCCTCTCCGCCAGTC +CTGGCCCCACGCTGATGGCGCCCGGGCAGAGGAAAAGCTTGCCGGTTTTA +TTTTTCCTGAGCTAGACCTGAACACAACAAAAGAGCGCAAAGGAGACCTG +CGGCTCATAAACACGACCACAGAGCCTCTTTTCTCCTGCTCAGATTTGCA +GTTCCAGTTTTGCCTTGAGCCCAATGATCATGTTAAGGTGATCCAGGGCA +CCGTGTTCGTGTTCAAGTGTATGCACCCCGCATCCTGCGAGCTTGGGGGT +GGTGAGGGGAAAGAGATGGCTGGGCTGGTTGGTGCTTGAGTTGGGAAACA +GGGCTTACTGCCTTTGCTGGGCTAGGTAACCTTGGCTTTGTTTAGGAAAA +GTGCTGCAGTCTTTGCAATCCGTCGGCAAAGAGGGCAAAGGCGGAGGGGG +AGAGTGGAACCCGCATTGCCCTCCCTGCAAGGCCAGCCTTAGGGCTGGGC +TAAGGCAAAGAGCCAGGGATCTGGCTTTTTGAGAAGGAACCCTCCTCCTC +TCCCCCAGTGCTTAGAGGTGGGCCACAGTAGGGGGCTCCCTTTCTGGGGG +AATGCTTTAGTGTGGGGGCAAGAAGACATGAAAATTAAGGAAATTCTGGG +GAATGCAACAATACCCAGGCAAGGTGGGGGAAGGTGTCTCGCTTCCCCAT +TTATCTTTTGAAAGAGAATGGGCACCTATAAACCTGACTGTCAGGATTCC +TGACTGCCTAGGAGAGGTGGGGAAGAAGTGGCAGATTTGGGGACCTGAGG +CAGCAGTGGGGTTGGTAGGCTTGTCCAGGTCGTGGCGTATTCCCCTCCGT +CCCTGTTAGGAGCTGAACCCTTAGAATGTTGCTGGGGAGATCTGGAAAGT +TTACTATTCTACTAATGTTTTGTACAAGTGAGAAAGTTGAAAGAGAGAGC +GAGAACCCAAATGCAGACTGTCCTGCCATCATGTCATTTAAGTAATGTGG +CATCAATGTAAGATTCCCTTCCAAGGCCCACTTCATGTGAGTAATGTTTA +ATACTAGCATTTTCCAAAGCGGCCTGGCTGCCAGCAGGGTCACGGCCAAG +GGTACATTTGAACAGTCTGAAGAAAAAAACAAAAACGAAAACCAAAACCA +AAACCAAAACAAAAACAAAAACAAAAACAAACAAACAAAAAACCTCTTGA +TTTTTTTCTTCTTCTCCCTTTAATTTTGTTAGAGGAAATCAAGTCTGATA +CACCAACCAGCAATTGGCTCACTGCAAAGAGTGGCAGAAAGAAGAGGTGC +CCTTACACTAAGCACCAAACGCTGGAATTAGAAAAAGAGTTCTTGTTCAA +TATGTACCTCACCCGCGAGCGCCGCCTAGAGATCAGTAAGAGCGTTAACC +TCACCGACAGGCAGGTCAAGATTTGGTTTCAAAACCGCCGAATGAAACTC +AAGAAGATGAGCCGAGAGAACCGGATCCGAGAACTGACCGCCAACCTCAC +GTTTTCTTAGGTCTGAGGCCGGTCTGAGGCCGGTCAGAGGCCAGGATTGG +AGAGGGGGCACCGCGTTCCAGGGCCCAGTGCTGGAGGACTGGGAAAGCGG +AAACAAAACCTTCACCGCTCTTTGTTTGTTGTTTTGTTGTATTTTGTTTT +CCTGCTAGAATGTGACTTTGGGGTCATTATGTTCGTGCTGCAAGTGATCT +GTAATCCCTATGAGTATATATATATATATATATATATATATATAAAAACT +TAGCACGTGTAATTTATTATTTTTTCATCGTAATGCAGGGTAACTATTAT +TGCGCATTTTCATTTGGGTCTTAACTTATTGGAACTGTAGAGCATCCATC +CATCCATCCATCCAGCAATGTGACTTTTTCATGTCTTTCCTAACACAAAA +GGTCTATGTGTGTGGTTAGTCCATGAACTCATGGCATTTTGAATACATCC +AGTACTTTAAAAATGACATATATATTTAAAAAAAAAAGATTAAGAAAACC +CACAAGTTGGAGGGAGGGGGACTTAAAAAGCACATTACAATGTATCTTTT +CACAAATGAATTTAGCAGTTGTCCTTGGTGAGATGGGATATTGGCGATTT +ATGCCTTGTAGCCTTTCCCTTGTGGTGCATCTGTGGTTTGGTAGAAGTAC +AACAGCAACCTGTCCTTTCTGTGCATGTTCTGGTCGCATGTATAATGCAA +TAAACTCTGGAAATGAGTTCACTCCCTCTGCTTTCTGAAATGGAAATATG +TTATGGTGGAAATGAAAGCCTATGGTGAGATTATCTTCTGGTTACACTCC +CTGTTTGGGGCATTTGGGCAGGGGAGTGATAGACTAGTAGGGGAAGGGAG +ATGGGGGAGAAAAGCTGGAGGAGGCCTAGGGTGTTGGATTTTGGCAGTGG +TTGGGGGAGAGGAATTATAAGCTAGCTTGAGAGTGAAGTTTTCATAATTG +GGAGGAAGGGGAGTCTCCTCTTTCCTTTCCCAGTCCCCAGTGATAGTAAC +ATAATTGCGCTCTCAATGGGTGTGAGCTTTCCTCTGGCCTGAACCTGGTA +AGTAAGCCTATACCCCAAGCCACTTTCTCCTCAAAGCTTCCCATTTGTGT +GTTTTCTCCTCTTTGGTTTTGGTTGTGTTGTTTTTAATGCTTTCAGTGGC +ATCTTGGTGATTTCTGGCTGGCGAGCAATCATCAGGGGCTAGGTTGAAGC +TAGTCTTGCCCACCTGGAAGTTGCCGGCCTCCATTACAGGAGCAAGGACA +AACAGCAGTGTAGCACTGCAGCGGATCCAATTCTGCCCCCTTTCCCTCAG +CCCTACCCCCATCCCAAGCGCAAGACAGCCAGACCCCAGAGAAGCCGAGG +ATGGGTGAGTTTTCCCATCCCACTTCGCCTTGATCTCCTTGTGGACGGGT +TTTATGCTCAGTCATTACCTTTTAGTGGCCCACATGAAATTTTGTTAAAG +GAAGAAATGAAAAGATTTTCCCCAGTCAGTCTTTCCTCTATTTAATTACA +AAATGCTGGTGGGAACTGCTGCATCTGGGATGCAAGAAAATGCAGAAAGG +GTGACTGAAAATTTTGCAAATGAACATGACTTCCCATGAAGTCTAATGTT +CCATTCGCTGCCATGGTCCAGGGGACTCCCACCAGCTTCCACCGGCTTCA +ACAGGATCTCCACTAGAGAGCCCAGACTTATCTAGTCCTGTCGGGGAAAA +GGGAGAAGAGGCCTTGCAGGAGAAAGCTAACAGAAAATTCGTTACCTGAG +GTCCTGCCTGCAGTTTCAAATAGCTTCCAGCAGTTTTACAAAACACATCC +TTTCCATTTCTTCCTTTTAAATGTTTCCCTAAGAACGATCCATTTAGGTG +CTATAAGTCCTCAGCCAGGGAGTCTCTGGGACACTGGCATTCAAAATTTT +AAACTTCCGCCCCAAAACCAGGAACATTCCAAGACAGAACTCTTTTAGGG +GGCCATTTCCTGGGGGTGGGGGAGAGGGCTTGGAATCAATGCTAGATTGA +AAACGTTGTAATAGCTTTGCCCCAGACTTAACACCGGTTGGGCAGGAGGA +GGGTAATTTTTATTTAGCCGTTTCTCCGATCATGTGGGGAATACCATTAG +CTGTTGATAGCGGGCCATGTATCCGAGGAAAGCCTGAGCTACAAGGCAAA +GGCATCCCATCTGGAACAAAATCAGAAAGCTATTGGCAAAGGTAATCAAT +CAGGCCATAAATAGCCATTTACCCGCTTCCTTTTCGGGGCTGGAGGTGGG +CCGGGAGCCCTCCAAGGGTGAGCTGGGCAACTTGTAGAGCAAGGAATATG +CCCTCCGCTGCCGGCGCCCCGGCCGCTTTTGTCTGGGCTCCCAGCCGGGC +TTCCGAGGCTTTGTACCATGGATTTGGGAGTGACAATGGGCATTTCCCTC +AGATTCAAGGCTGCTCAACCTCACCTCTGTAGGGGGAAAAAAATCAGAAG +GGAGTGTCCCAAGGACCTAGCCATTCGGCCGAATTTTTTAGACATTTTGG +GAGTCTCCTCCGAGGCCTTTAAGTGCGAACCGCGCGAAGCGGCCCTGCCC +GGGGAGACTCGCTGAGGCAGGGCTGAGGCGGCGGGCGGGAGCAAGCTGCT +CTAGCATTTGGGTTCTGCCCTGTGGCGTGTTCTCTTCCAGGGCCTTTCCA +GCATCATCGGAGAAGACGAAGCACCCTGGCCGCCACTGTCCGTGCTGCGC +CAACTCGCCCGGCCGCCCGCCCTTCCGAGGGCAGGCAGAAGCCCCTCTGT +GTCCTCCACCGCCGCGCCCCGGCTCGCCCCTCGGGCCGCGGCGTGTGCCC +AGCCTCACGTCGGGGTGTGTGTGGCCGCGCGGGCGTGTGTGAGTGTGGCA +GGGGGAGGGGGCCCTCCGATCTGCTCCATCCGTCCGTTTTATTAGGGACA +CATTAATCTATAATCAAATACACCTCATAAAATTTTTATTGAAAGGCATA +ATATCATTACAGAGGTCTTCCACCTGTTTTAAACAACACGACAAGCTGTG +AGCAAGCGTGTGTGTGGGGATGTGTGGGGAGGGGTGGGTGTGAGTAGGGA +GAGAGGCGAGGGGAGAACAGCTCCCCTCGGGCGCTAGGGGCCGCCCCGAG +GGCCCGCCTGCCTCGGGCGACACCGGCCTGGCGCCCCCGCGGCCGCTCCG +TGTGCCCTGGACTCGCCGCCCGCGGCTCGGAAGCTGGAGAGTCAGCGACG +GGGCCCGACTGCGGGACCGAGGGCTGCAAGAAGAAGCGAACAAATAGTCC +CCAGCGCCTCCTCTGGATGCGGTCGCGTCTGTGGTCCTGGCAGCCGCTGG +GCGGGCCAGGCCAGGTCGGGCCGGGCCGAGCCGGGCACATGGACCTGGGC +CTGCGGGCTCTAATTGCGGCGCTTATGTTGATGATTTTTTTTTTAATCAC +AGCAGCCCCCAGTTTAGCGGACTGATTTACTCCCGGTATTGGTAAATATG +ATCACGTGGGCCGCGCGACCAATGGTGGAGGCTGCAGCCTGCGAACTAGT +CGGTGGCTCGGGCGCCGGCGGGGAGCTGCTCGGCGGCGGACAGTGTAATG +TTGGGTGGGAGTGCGGGACGCCTCAAAATGTCTTCCAGTGGCACCCTCAG +CAACTACTACGTGGACTCGCTTATAGGCCATGAGGGCGACGAGGTGTTCG +CGGCGCGCTTCGGGCCGCCGGGGCCAGGCGCGCAGGGCCGGCCTGCAGGT +GTGGCTGATGGCCCGGCCGCCACCGCCGCCGAGTTCGCCTCGTGTAGTTT +TGCCCCCAGATCGGCCGTGTTCTCTGCCTCGTGGTCCGCGGTGCCCTCCC +AGCCCCCGGCAGCGGCGGCGATGAGCGGCCTCTACCACCCGTACGTTCCC +CCGCCGCCCCTGGCCGCCTCTGCCTCCGAGCCCGGCCGCTACGTGCGCTC +CTGGATGGAGCCGCTGCCCGGCTTCCCGGGCGGTGCGGGCGGTGGCGGTG +GTGGTGGAGGCGGCGGTCCGGGCCGCGGTCCCAGCCCTGGCCCCAGCGGC +CCAGCCAACGGGCGCCACTACGGGATTAAGCCTGAAACCCGAGCGGCCCC +GGCCCCCGCCACGGCCGCCTCCACCACCTCCTCCTCCTCCACTTCCTTAT +CCTCCTCCTCCAAACGGACTGAGTGCTCCGTGGCCCGGGAGTCCCAGGGG +AGCAGCGGCCCCGAGTTCTCGTGCAACTCGTTCCTGCAGGAGAAGGCGGC +AGCGGCGACGGGGGGAACCGGGCCTGGGGCAGGGATCGGGGCCGCGACTG +GGACGGGCGGCTCGTCGGAGCCCTCAGCTTGCAGCGACCACCCGATCCCA +GGCTGTTCGCTGAAGGAGGAGGAGAAGCAGCATTCGCAGCCGCAGCAGCA +GCAACTTGACCCAAGTAAGTGCAAAAGAAATTGCCCCCTGATTTATTGCT +GAAACCTGTAAGGCTCGAATGTGCAAAACTGATAGTTTTACTAACCTATA +AAAACGTCTAGACGCCTACCCAAGCCTAGGCGAACAACATGCATCCATAA +AAAGAGCTTCCCATAACCACCTACCCTGGGCGCTCAGTTAGTACGGTAAA +CAGAGCGCGAGCATTAAGGCTTTTTATGATAATTCCCCACAAGTTGTGAA +AAGCGACCATCCTTGGTGAAATTAATTTAACGACCTCTCTTCCCCACCCT +GTGGTCTCTCCCTGCCTCCCCTCCTCTCCTCTCTCCCCGTCTCCAAACCT +CCCTCTTTGTAGACAACCCCGCCGCGAACTGGATCCACGCTCGCTCCACC +CGGAAAAAGCGCTGTCCCTACACCAAATACCAGACGCTTGAGCTGGAGAA +AGAATTCCTCTTCAACATGTACCTCACCCGGGACCGGCGCTACGAGGTGG +CCAGGATTCTCAACCTAACAGAGAGACAGGTCAAAATCTGGTTTCAGAAC +CGTAGGATGAAAATGAAAAAGATGAGCAAGGAGAAATGCCCCAAAGGAGA +CTGACCCGGCGCGGTGCTGGCGGGAGCGCTCAAGGGCAGCGGATTTGTTG +TTGTTGCTGTTTTCCTTTGTGGGTGTTTGGTGCTTGATTTCCAGAAACTC +TCCAGCGACTTGGACTTCTTCTTCTTTTTTTTTTTCTTTTTAGATAGAAG +TGACTGTGTGGTTGGTCTCTGAGGTATTTGGGGGACTCTGTATTTGCTCG +TTTACGTGTTGGAAAAACCAAGTGGCTTTGGGGTTTCGCCCTATCCCACT +CCCTCTCTTTCCTGCTCCATTGGTTCCTTAAGAAATGCTATATTTTGTGA +GTGCAAGCTGGCTTGGGGAGCCCTCTCTTGTGTAAATGTCCCCCATGTTT +CTGAAAAGTGCTGTAGTTTAGTCCCCTCACCCCCAGCACTGCCCAAACAG +GGGCCAAGTGCGCCCCAATTCCAAGAATGAAGGCAGAGCGACAACAGTGC +GGACACCCCGGCTGCTAGCCCACGGTGAAGCCCGGCGGGGTTGCCCACCA +GTTGCGAAAGCCCCCTTTCCTCAGGGAGCACGCGGGACCTCGGTGGAGAT +CTCCAGTGAGGCTTAGAGGAGCCCAGGGCCTCGGGCGGGTTGGGGTTTGT +CCTCAGTGCATTGGACGCGCTGCTCTCTCCCCTGAAGGCTGGGCTCGCGT +GGGCGGCCGCGGGTGGTGGCCCTCCCGGTTCCTGCCCGAGGACCAGTTGT +AAATGTTACTGCTTCCTACTAATAAATGCTGACCTGATCAAATGGAGCCC +AGACGCTGGCCCTAAACATTGTGTGCCTGCTTTCTCTGCCTCTCTGCAAA +ATATCACACTCAGGATATTTCTCCTCTACCCCTGGGAGTGAGACATTGTT +AAAAATTCAGGGCCCTTCCACCTGACAGATCTCTCTGATGTGTCTCTGCC +TTCTCTGCCTCACATCCCTTTGTGTAGGCAGATGCAGCAGCA
--- a/test-data/cached_locally/ref.gtf Sun Jan 28 04:04:58 2018 -0500 +++ b/test-data/cached_locally/ref.gtf Fri Mar 11 14:08:11 2022 +0000 @@ -1,6 +1,20 @@ -1 ensembl_havana gene 1 103 . + . gene_id "ENSG00000162526"; gene_version "4"; gene_name "OR4F5"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000001094"; havana_gene_version "1"; -1 ensembl_havana transcript 1 103 . + . gene_id "ENSG00000162526"; gene_version "4"; transcript_id "ENST00000335137"; transcript_version "3"; gene_name "OR4F5"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000001094"; havana_gene_version "1"; transcript_name "OR4F5-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS30547"; havana_transcript "OTTHUMT00000003223"; havana_transcript_version "1"; tag "basic"; transcript_support_level "NA"; -1 ensembl_havana exon 1 103 . + . gene_id "ENSG00000162526"; gene_version "4"; transcript_id "ENST00000335137"; transcript_version "3"; exon_number "1"; gene_name "OR4F5"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000001094"; havana_gene_version "1"; transcript_name "OR4F5-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS30547"; havana_transcript "OTTHUMT00000003223"; havana_transcript_version "1"; exon_id "ENSE00002319515"; exon_version "1"; tag "basic"; transcript_support_level "NA"; -1 ensembl_havana CDS 1 100 . + 0 gene_id "ENSG00000162526"; gene_version "4"; transcript_id "ENST00000335137"; transcript_version "3"; exon_number "1"; gene_name "OR4F5"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000001094"; havana_gene_version "1"; transcript_name "OR4F5-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS30547"; havana_transcript "OTTHUMT00000003223"; havana_transcript_version "1"; protein_id "ENSP00000334393"; protein_version "3"; tag "basic"; transcript_support_level "NA"; -1 ensembl_havana start_codon 1 3 . + 0 gene_id "ENSG00000162526"; gene_version "4"; transcript_id "ENST00000335137"; transcript_version "3"; exon_number "1"; gene_name "OR4F5"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000001094"; havana_gene_version "1"; transcript_name "OR4F5-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS30547"; havana_transcript "OTTHUMT00000003223"; havana_transcript_version "1"; tag "basic"; transcript_support_level "NA"; -1 ensembl_havana stop_codon 101 103 . + 0 gene_id "ENSG00000162526"; gene_version "4"; transcript_id "ENST00000335137"; transcript_version "3"; exon_number "1"; gene_name "OR4F5"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000001094"; havana_gene_version "1"; transcript_name "OR4F5-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS30547"; havana_transcript "OTTHUMT00000003223"; havana_transcript_version "1"; tag "basic"; transcript_support_level "NA"; +fake_chr2 HAVANA gene 257 3416 . + . gene_id "ENSG00000128710.6"; gene_type "protein_coding"; gene_name "HOXD10"; level 1; hgnc_id "HGNC:5133"; tag "overlapping_locus"; havana_gene "OTTHUMG00000132511.5"; +fake_chr2 HAVANA transcript 257 3416 . + . gene_id "ENSG00000128710.6"; transcript_id "ENST00000249501.5"; gene_type "protein_coding"; gene_name "HOXD10"; transcript_type "protein_coding"; transcript_name "HOXD10-201"; level 2; protein_id "ENSP00000249501.4"; transcript_support_level "1"; hgnc_id "HGNC:5133"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_1"; tag "CCDS"; ccdsid "CCDS2266.1"; havana_gene "OTTHUMG00000132511.5"; havana_transcript "OTTHUMT00000255692.3"; +fake_chr2 HAVANA exon 257 1057 . + . gene_id "ENSG00000128710.6"; transcript_id "ENST00000249501.5"; gene_type "protein_coding"; gene_name "HOXD10"; transcript_type "protein_coding"; transcript_name "HOXD10-201"; exon_number 1; exon_id "ENSE00000882912.6"; level 2; protein_id "ENSP00000249501.4"; transcript_support_level "1"; hgnc_id "HGNC:5133"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_1"; tag "CCDS"; ccdsid "CCDS2266.1"; havana_gene "OTTHUMG00000132511.5"; havana_transcript "OTTHUMT00000255692.3"; +fake_chr2 HAVANA CDS 313 1057 . + 0 gene_id "ENSG00000128710.6"; transcript_id "ENST00000249501.5"; gene_type "protein_coding"; gene_name "HOXD10"; transcript_type "protein_coding"; transcript_name "HOXD10-201"; exon_number 1; exon_id "ENSE00000882912.6"; level 2; protein_id "ENSP00000249501.4"; transcript_support_level "1"; hgnc_id "HGNC:5133"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_1"; tag "CCDS"; ccdsid "CCDS2266.1"; havana_gene "OTTHUMG00000132511.5"; havana_transcript "OTTHUMT00000255692.3"; +fake_chr2 HAVANA start_codon 313 315 . + 0 gene_id "ENSG00000128710.6"; transcript_id "ENST00000249501.5"; gene_type "protein_coding"; gene_name "HOXD10"; transcript_type "protein_coding"; transcript_name "HOXD10-201"; exon_number 1; exon_id "ENSE00000882912.6"; level 2; protein_id "ENSP00000249501.4"; transcript_support_level "1"; hgnc_id "HGNC:5133"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_1"; tag "CCDS"; ccdsid "CCDS2266.1"; havana_gene "OTTHUMG00000132511.5"; havana_transcript "OTTHUMT00000255692.3"; +fake_chr2 HAVANA exon 2433 3416 . + . gene_id "ENSG00000128710.6"; transcript_id "ENST00000249501.5"; gene_type "protein_coding"; gene_name "HOXD10"; transcript_type "protein_coding"; transcript_name "HOXD10-201"; exon_number 2; exon_id "ENSE00001816717.3"; level 2; protein_id "ENSP00000249501.4"; transcript_support_level "1"; hgnc_id "HGNC:5133"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_1"; tag "CCDS"; ccdsid "CCDS2266.1"; havana_gene "OTTHUMG00000132511.5"; havana_transcript "OTTHUMT00000255692.3"; +fake_chr2 HAVANA CDS 2433 2707 . + 2 gene_id "ENSG00000128710.6"; transcript_id "ENST00000249501.5"; gene_type "protein_coding"; gene_name "HOXD10"; transcript_type "protein_coding"; transcript_name "HOXD10-201"; exon_number 2; exon_id "ENSE00001816717.3"; level 2; protein_id "ENSP00000249501.4"; transcript_support_level "1"; hgnc_id "HGNC:5133"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_1"; tag "CCDS"; ccdsid "CCDS2266.1"; havana_gene "OTTHUMG00000132511.5"; havana_transcript "OTTHUMT00000255692.3"; +fake_chr2 HAVANA stop_codon 2708 2710 . + 0 gene_id "ENSG00000128710.6"; transcript_id "ENST00000249501.5"; gene_type "protein_coding"; gene_name "HOXD10"; transcript_type "protein_coding"; transcript_name "HOXD10-201"; exon_number 2; exon_id "ENSE00001816717.3"; level 2; protein_id "ENSP00000249501.4"; transcript_support_level "1"; hgnc_id "HGNC:5133"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_1"; tag "CCDS"; ccdsid "CCDS2266.1"; havana_gene "OTTHUMG00000132511.5"; havana_transcript "OTTHUMT00000255692.3"; +fake_chr2 HAVANA UTR 257 312 . + . gene_id "ENSG00000128710.6"; transcript_id "ENST00000249501.5"; gene_type "protein_coding"; gene_name "HOXD10"; transcript_type "protein_coding"; transcript_name "HOXD10-201"; exon_number 1; exon_id "ENSE00000882912.6"; level 2; protein_id "ENSP00000249501.4"; transcript_support_level "1"; hgnc_id "HGNC:5133"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_1"; tag "CCDS"; ccdsid "CCDS2266.1"; havana_gene "OTTHUMG00000132511.5"; havana_transcript "OTTHUMT00000255692.3"; +fake_chr2 HAVANA UTR 2708 3416 . + . gene_id "ENSG00000128710.6"; transcript_id "ENST00000249501.5"; gene_type "protein_coding"; gene_name "HOXD10"; transcript_type "protein_coding"; transcript_name "HOXD10-201"; exon_number 2; exon_id "ENSE00001816717.3"; level 2; protein_id "ENSP00000249501.4"; transcript_support_level "1"; hgnc_id "HGNC:5133"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_1"; tag "CCDS"; ccdsid "CCDS2266.1"; havana_gene "OTTHUMG00000132511.5"; havana_transcript "OTTHUMT00000255692.3"; +fake_chr2 HAVANA gene 6198 8416 . + . gene_id "ENSG00000128709.13"; gene_type "protein_coding"; gene_name "HOXD9"; level 2; hgnc_id "HGNC:5140"; havana_gene "OTTHUMG00000132516.6"; +fake_chr2 HAVANA transcript 6198 8416 . + . gene_id "ENSG00000128709.13"; transcript_id "ENST00000249499.8"; gene_type "protein_coding"; gene_name "HOXD9"; transcript_type "protein_coding"; transcript_name "HOXD9-201"; level 2; protein_id "ENSP00000249499.6"; transcript_support_level "1"; hgnc_id "HGNC:5140"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_1"; tag "CCDS"; ccdsid "CCDS2267.2"; havana_gene "OTTHUMG00000132516.6"; havana_transcript "OTTHUMT00000255698.6"; +fake_chr2 HAVANA exon 6198 7064 . + . gene_id "ENSG00000128709.13"; transcript_id "ENST00000249499.8"; gene_type "protein_coding"; gene_name "HOXD9"; transcript_type "protein_coding"; transcript_name "HOXD9-201"; exon_number 1; exon_id "ENSE00000882914.5"; level 2; protein_id "ENSP00000249499.6"; transcript_support_level "1"; hgnc_id "HGNC:5140"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_1"; tag "CCDS"; ccdsid "CCDS2267.2"; havana_gene "OTTHUMG00000132516.6"; havana_transcript "OTTHUMT00000255698.6"; +fake_chr2 HAVANA CDS 6248 7064 . + 0 gene_id "ENSG00000128709.13"; transcript_id "ENST00000249499.8"; gene_type "protein_coding"; gene_name "HOXD9"; transcript_type "protein_coding"; transcript_name "HOXD9-201"; exon_number 1; exon_id "ENSE00000882914.5"; level 2; protein_id "ENSP00000249499.6"; transcript_support_level "1"; hgnc_id "HGNC:5140"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_1"; tag "CCDS"; ccdsid "CCDS2267.2"; havana_gene "OTTHUMG00000132516.6"; havana_transcript "OTTHUMT00000255698.6"; +fake_chr2 HAVANA start_codon 6248 6250 . + 0 gene_id "ENSG00000128709.13"; transcript_id "ENST00000249499.8"; gene_type "protein_coding"; gene_name "HOXD9"; transcript_type "protein_coding"; transcript_name "HOXD9-201"; exon_number 1; exon_id "ENSE00000882914.5"; level 2; protein_id "ENSP00000249499.6"; transcript_support_level "1"; hgnc_id "HGNC:5140"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_1"; tag "CCDS"; ccdsid "CCDS2267.2"; havana_gene "OTTHUMG00000132516.6"; havana_transcript "OTTHUMT00000255698.6"; +fake_chr2 HAVANA exon 7413 8416 . + . gene_id "ENSG00000128709.13"; transcript_id "ENST00000249499.8"; gene_type "protein_coding"; gene_name "HOXD9"; transcript_type "protein_coding"; transcript_name "HOXD9-201"; exon_number 2; exon_id "ENSE00001845001.4"; level 2; protein_id "ENSP00000249499.6"; transcript_support_level "1"; hgnc_id "HGNC:5140"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_1"; tag "CCDS"; ccdsid "CCDS2267.2"; havana_gene "OTTHUMG00000132516.6"; havana_transcript "OTTHUMT00000255698.6"; +fake_chr2 HAVANA CDS 7413 7651 . + 2 gene_id "ENSG00000128709.13"; transcript_id "ENST00000249499.8"; gene_type "protein_coding"; gene_name "HOXD9"; transcript_type "protein_coding"; transcript_name "HOXD9-201"; exon_number 2; exon_id "ENSE00001845001.4"; level 2; protein_id "ENSP00000249499.6"; transcript_support_level "1"; hgnc_id "HGNC:5140"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_1"; tag "CCDS"; ccdsid "CCDS2267.2"; havana_gene "OTTHUMG00000132516.6"; havana_transcript "OTTHUMT00000255698.6"; +fake_chr2 HAVANA stop_codon 7652 7654 . + 0 gene_id "ENSG00000128709.13"; transcript_id "ENST00000249499.8"; gene_type "protein_coding"; gene_name "HOXD9"; transcript_type "protein_coding"; transcript_name "HOXD9-201"; exon_number 2; exon_id "ENSE00001845001.4"; level 2; protein_id "ENSP00000249499.6"; transcript_support_level "1"; hgnc_id "HGNC:5140"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_1"; tag "CCDS"; ccdsid "CCDS2267.2"; havana_gene "OTTHUMG00000132516.6"; havana_transcript "OTTHUMT00000255698.6"; +fake_chr2 HAVANA UTR 6198 6247 . + . gene_id "ENSG00000128709.13"; transcript_id "ENST00000249499.8"; gene_type "protein_coding"; gene_name "HOXD9"; transcript_type "protein_coding"; transcript_name "HOXD9-201"; exon_number 1; exon_id "ENSE00000882914.5"; level 2; protein_id "ENSP00000249499.6"; transcript_support_level "1"; hgnc_id "HGNC:5140"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_1"; tag "CCDS"; ccdsid "CCDS2267.2"; havana_gene "OTTHUMG00000132516.6"; havana_transcript "OTTHUMT00000255698.6"; +fake_chr2 HAVANA UTR 7652 8416 . + . gene_id "ENSG00000128709.13"; transcript_id "ENST00000249499.8"; gene_type "protein_coding"; gene_name "HOXD9"; transcript_type "protein_coding"; transcript_name "HOXD9-201"; exon_number 2; exon_id "ENSE00001845001.4"; level 2; protein_id "ENSP00000249499.6"; transcript_support_level "1"; hgnc_id "HGNC:5140"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_1"; tag "CCDS"; ccdsid "CCDS2267.2"; havana_gene "OTTHUMG00000132516.6"; havana_transcript "OTTHUMT00000255698.6";
--- a/test-data/gc.tab Sun Jan 28 04:04:58 2018 -0500 +++ b/test-data/gc.tab Fri Mar 11 14:08:11 2022 +0000 @@ -1,1 +1,2 @@ -ENSG00000162526 0.388349514563107 +ENSG00000128709.13 0.626402993051844 +ENSG00000128710.6 0.467226890756303
--- a/test-data/in.fasta Sun Jan 28 04:04:58 2018 -0500 +++ b/test-data/in.fasta Fri Mar 11 14:08:11 2022 +0000 @@ -1,2 +1,173 @@ ->1 -AAAAAAAAAATTTTTTTTTTCCCCCCCCCCGGGGGGGGGGAAAAAAAAAAAAAAAAAAAATTTTTTTTTTCCCCCCCCCCGGGGGGGGGGAAAAAAAAAATTTTT \ No newline at end of file +>fake_chr2 hg38_dna range=chr2:176116522-176125113 5'pad=0 3'pad=0 strand=+ repeatMasking=none +TGGGGCGGGCTGGCCGAGCGAGCCCTGGAGAGGCGGACAGGAGGGCGGCG +GAGAGCGCTGGGCCGGTTGTCTCCAGCGCGCACTATCGCGGGCGCGTAGT +AGATGTCGCTGTTGTCCGTGCTTACCCGGCCGGCCGGCCAGGCTCTGGAG +CACGTGACCCGAGAGGAGGCTGCGGCTCAAGGCCATTTTCAAATCTCATT +GGCTTGGTTGTCATGTGGTCGGCAGAGGCATCCACAATTACACGGGGAAT +GTTTTCCTAGAGATGTCAGCCTACAAAGGACACAATCTCTCTTCTTCAAA +TTCTTCCCCAAAATGTCCTTTCCCAACAGCTCTCCTGCTGCTAATACTTT +TTTAGTAGATTCCTTGATCAGTGCCTGCAGGAGTGACAGTTTTTATTCCA +GCAGCGCCAGCATGTACATGCCACCACCTAGCGCAGACATGGGGACCTAT +GGAATGCAAACCTGTGGACTGCTCCCGTCTCTGGCCAAAAGAGAAGTGAA +CCACCAAAATATGGGTATGAATGTGCATCCTTATATACCTCAAGTAGACA +GTTGGACAGATCCGAACAGATCTTGTCGAATAGAGCAACCTGTTACACAG +CAAGTCCCCACTTGCTCCTTCACCACCAACATTAAGGAAGAATCCAATTG +CTGCATGTATTCTGATAAGCGCAACAAACTCATTTCGGCCGAGGTCCCTT +CGTACCAGAGGCTGGTCCCTGAGTCTTGTCCCGTTGAGAACCCTGAGGTT +CCCGTCCCTGGATATTTTAGACTGAGTCAGACCTACGCCACCGGGAAAAC +CCAAGAGTACAATAATAGCCCCGAAGGCAGCTCCACTGTCATGCTCCAGC +TCAACCCTCGTGGCGCGGCCAAGCCGCAGCTCTCCGCTGCCCAGCTGCAG +ATGGAAAAGAAGATGAACGAGCCCGTGAGCGGCCAGGAGCCCACCAAAGT +CTCCCAGGTGGAGAGCCCCGAGGCCAAAGGCGGCCTTCCCGAAGAGAGGA +GCTGCCTGGCTGAGGTCTCCGTGTCCAGTCCCGAAGTGCAGGAGAAGGAA +AGCAAAGGTCGGTATGAGCAGAGTTGCCACCCCAGCGGGGCGCGCAGCCC +GGGAACCCGGCAGAGAGGGAGTGCCGGGGTGCCCAGCGCCGAGCCGGAGC +CCGACTTGGCAGGTGCTGCTCCGCCTGGTTTTAGAGGGGTGATCTCAGCC +CTGAGATAGTCCCCGCTTCTCCCCTGCTGCCCTGGCCCTCTCCGCCAGTC +CTGGCCCCACGCTGATGGCGCCCGGGCAGAGGAAAAGCTTGCCGGTTTTA +TTTTTCCTGAGCTAGACCTGAACACAACAAAAGAGCGCAAAGGAGACCTG +CGGCTCATAAACACGACCACAGAGCCTCTTTTCTCCTGCTCAGATTTGCA +GTTCCAGTTTTGCCTTGAGCCCAATGATCATGTTAAGGTGATCCAGGGCA +CCGTGTTCGTGTTCAAGTGTATGCACCCCGCATCCTGCGAGCTTGGGGGT +GGTGAGGGGAAAGAGATGGCTGGGCTGGTTGGTGCTTGAGTTGGGAAACA +GGGCTTACTGCCTTTGCTGGGCTAGGTAACCTTGGCTTTGTTTAGGAAAA +GTGCTGCAGTCTTTGCAATCCGTCGGCAAAGAGGGCAAAGGCGGAGGGGG +AGAGTGGAACCCGCATTGCCCTCCCTGCAAGGCCAGCCTTAGGGCTGGGC +TAAGGCAAAGAGCCAGGGATCTGGCTTTTTGAGAAGGAACCCTCCTCCTC +TCCCCCAGTGCTTAGAGGTGGGCCACAGTAGGGGGCTCCCTTTCTGGGGG +AATGCTTTAGTGTGGGGGCAAGAAGACATGAAAATTAAGGAAATTCTGGG +GAATGCAACAATACCCAGGCAAGGTGGGGGAAGGTGTCTCGCTTCCCCAT +TTATCTTTTGAAAGAGAATGGGCACCTATAAACCTGACTGTCAGGATTCC +TGACTGCCTAGGAGAGGTGGGGAAGAAGTGGCAGATTTGGGGACCTGAGG +CAGCAGTGGGGTTGGTAGGCTTGTCCAGGTCGTGGCGTATTCCCCTCCGT +CCCTGTTAGGAGCTGAACCCTTAGAATGTTGCTGGGGAGATCTGGAAAGT +TTACTATTCTACTAATGTTTTGTACAAGTGAGAAAGTTGAAAGAGAGAGC +GAGAACCCAAATGCAGACTGTCCTGCCATCATGTCATTTAAGTAATGTGG +CATCAATGTAAGATTCCCTTCCAAGGCCCACTTCATGTGAGTAATGTTTA +ATACTAGCATTTTCCAAAGCGGCCTGGCTGCCAGCAGGGTCACGGCCAAG +GGTACATTTGAACAGTCTGAAGAAAAAAACAAAAACGAAAACCAAAACCA +AAACCAAAACAAAAACAAAAACAAAAACAAACAAACAAAAAACCTCTTGA +TTTTTTTCTTCTTCTCCCTTTAATTTTGTTAGAGGAAATCAAGTCTGATA +CACCAACCAGCAATTGGCTCACTGCAAAGAGTGGCAGAAAGAAGAGGTGC +CCTTACACTAAGCACCAAACGCTGGAATTAGAAAAAGAGTTCTTGTTCAA +TATGTACCTCACCCGCGAGCGCCGCCTAGAGATCAGTAAGAGCGTTAACC +TCACCGACAGGCAGGTCAAGATTTGGTTTCAAAACCGCCGAATGAAACTC +AAGAAGATGAGCCGAGAGAACCGGATCCGAGAACTGACCGCCAACCTCAC +GTTTTCTTAGGTCTGAGGCCGGTCTGAGGCCGGTCAGAGGCCAGGATTGG +AGAGGGGGCACCGCGTTCCAGGGCCCAGTGCTGGAGGACTGGGAAAGCGG +AAACAAAACCTTCACCGCTCTTTGTTTGTTGTTTTGTTGTATTTTGTTTT +CCTGCTAGAATGTGACTTTGGGGTCATTATGTTCGTGCTGCAAGTGATCT +GTAATCCCTATGAGTATATATATATATATATATATATATATATAAAAACT +TAGCACGTGTAATTTATTATTTTTTCATCGTAATGCAGGGTAACTATTAT +TGCGCATTTTCATTTGGGTCTTAACTTATTGGAACTGTAGAGCATCCATC +CATCCATCCATCCAGCAATGTGACTTTTTCATGTCTTTCCTAACACAAAA +GGTCTATGTGTGTGGTTAGTCCATGAACTCATGGCATTTTGAATACATCC +AGTACTTTAAAAATGACATATATATTTAAAAAAAAAAGATTAAGAAAACC +CACAAGTTGGAGGGAGGGGGACTTAAAAAGCACATTACAATGTATCTTTT +CACAAATGAATTTAGCAGTTGTCCTTGGTGAGATGGGATATTGGCGATTT +ATGCCTTGTAGCCTTTCCCTTGTGGTGCATCTGTGGTTTGGTAGAAGTAC +AACAGCAACCTGTCCTTTCTGTGCATGTTCTGGTCGCATGTATAATGCAA +TAAACTCTGGAAATGAGTTCACTCCCTCTGCTTTCTGAAATGGAAATATG +TTATGGTGGAAATGAAAGCCTATGGTGAGATTATCTTCTGGTTACACTCC +CTGTTTGGGGCATTTGGGCAGGGGAGTGATAGACTAGTAGGGGAAGGGAG +ATGGGGGAGAAAAGCTGGAGGAGGCCTAGGGTGTTGGATTTTGGCAGTGG +TTGGGGGAGAGGAATTATAAGCTAGCTTGAGAGTGAAGTTTTCATAATTG +GGAGGAAGGGGAGTCTCCTCTTTCCTTTCCCAGTCCCCAGTGATAGTAAC +ATAATTGCGCTCTCAATGGGTGTGAGCTTTCCTCTGGCCTGAACCTGGTA +AGTAAGCCTATACCCCAAGCCACTTTCTCCTCAAAGCTTCCCATTTGTGT +GTTTTCTCCTCTTTGGTTTTGGTTGTGTTGTTTTTAATGCTTTCAGTGGC +ATCTTGGTGATTTCTGGCTGGCGAGCAATCATCAGGGGCTAGGTTGAAGC +TAGTCTTGCCCACCTGGAAGTTGCCGGCCTCCATTACAGGAGCAAGGACA +AACAGCAGTGTAGCACTGCAGCGGATCCAATTCTGCCCCCTTTCCCTCAG +CCCTACCCCCATCCCAAGCGCAAGACAGCCAGACCCCAGAGAAGCCGAGG +ATGGGTGAGTTTTCCCATCCCACTTCGCCTTGATCTCCTTGTGGACGGGT +TTTATGCTCAGTCATTACCTTTTAGTGGCCCACATGAAATTTTGTTAAAG +GAAGAAATGAAAAGATTTTCCCCAGTCAGTCTTTCCTCTATTTAATTACA +AAATGCTGGTGGGAACTGCTGCATCTGGGATGCAAGAAAATGCAGAAAGG +GTGACTGAAAATTTTGCAAATGAACATGACTTCCCATGAAGTCTAATGTT +CCATTCGCTGCCATGGTCCAGGGGACTCCCACCAGCTTCCACCGGCTTCA +ACAGGATCTCCACTAGAGAGCCCAGACTTATCTAGTCCTGTCGGGGAAAA +GGGAGAAGAGGCCTTGCAGGAGAAAGCTAACAGAAAATTCGTTACCTGAG +GTCCTGCCTGCAGTTTCAAATAGCTTCCAGCAGTTTTACAAAACACATCC +TTTCCATTTCTTCCTTTTAAATGTTTCCCTAAGAACGATCCATTTAGGTG +CTATAAGTCCTCAGCCAGGGAGTCTCTGGGACACTGGCATTCAAAATTTT +AAACTTCCGCCCCAAAACCAGGAACATTCCAAGACAGAACTCTTTTAGGG +GGCCATTTCCTGGGGGTGGGGGAGAGGGCTTGGAATCAATGCTAGATTGA +AAACGTTGTAATAGCTTTGCCCCAGACTTAACACCGGTTGGGCAGGAGGA +GGGTAATTTTTATTTAGCCGTTTCTCCGATCATGTGGGGAATACCATTAG +CTGTTGATAGCGGGCCATGTATCCGAGGAAAGCCTGAGCTACAAGGCAAA +GGCATCCCATCTGGAACAAAATCAGAAAGCTATTGGCAAAGGTAATCAAT +CAGGCCATAAATAGCCATTTACCCGCTTCCTTTTCGGGGCTGGAGGTGGG +CCGGGAGCCCTCCAAGGGTGAGCTGGGCAACTTGTAGAGCAAGGAATATG +CCCTCCGCTGCCGGCGCCCCGGCCGCTTTTGTCTGGGCTCCCAGCCGGGC +TTCCGAGGCTTTGTACCATGGATTTGGGAGTGACAATGGGCATTTCCCTC +AGATTCAAGGCTGCTCAACCTCACCTCTGTAGGGGGAAAAAAATCAGAAG +GGAGTGTCCCAAGGACCTAGCCATTCGGCCGAATTTTTTAGACATTTTGG +GAGTCTCCTCCGAGGCCTTTAAGTGCGAACCGCGCGAAGCGGCCCTGCCC +GGGGAGACTCGCTGAGGCAGGGCTGAGGCGGCGGGCGGGAGCAAGCTGCT +CTAGCATTTGGGTTCTGCCCTGTGGCGTGTTCTCTTCCAGGGCCTTTCCA +GCATCATCGGAGAAGACGAAGCACCCTGGCCGCCACTGTCCGTGCTGCGC +CAACTCGCCCGGCCGCCCGCCCTTCCGAGGGCAGGCAGAAGCCCCTCTGT +GTCCTCCACCGCCGCGCCCCGGCTCGCCCCTCGGGCCGCGGCGTGTGCCC +AGCCTCACGTCGGGGTGTGTGTGGCCGCGCGGGCGTGTGTGAGTGTGGCA +GGGGGAGGGGGCCCTCCGATCTGCTCCATCCGTCCGTTTTATTAGGGACA +CATTAATCTATAATCAAATACACCTCATAAAATTTTTATTGAAAGGCATA +ATATCATTACAGAGGTCTTCCACCTGTTTTAAACAACACGACAAGCTGTG +AGCAAGCGTGTGTGTGGGGATGTGTGGGGAGGGGTGGGTGTGAGTAGGGA +GAGAGGCGAGGGGAGAACAGCTCCCCTCGGGCGCTAGGGGCCGCCCCGAG +GGCCCGCCTGCCTCGGGCGACACCGGCCTGGCGCCCCCGCGGCCGCTCCG +TGTGCCCTGGACTCGCCGCCCGCGGCTCGGAAGCTGGAGAGTCAGCGACG +GGGCCCGACTGCGGGACCGAGGGCTGCAAGAAGAAGCGAACAAATAGTCC +CCAGCGCCTCCTCTGGATGCGGTCGCGTCTGTGGTCCTGGCAGCCGCTGG +GCGGGCCAGGCCAGGTCGGGCCGGGCCGAGCCGGGCACATGGACCTGGGC +CTGCGGGCTCTAATTGCGGCGCTTATGTTGATGATTTTTTTTTTAATCAC +AGCAGCCCCCAGTTTAGCGGACTGATTTACTCCCGGTATTGGTAAATATG +ATCACGTGGGCCGCGCGACCAATGGTGGAGGCTGCAGCCTGCGAACTAGT +CGGTGGCTCGGGCGCCGGCGGGGAGCTGCTCGGCGGCGGACAGTGTAATG +TTGGGTGGGAGTGCGGGACGCCTCAAAATGTCTTCCAGTGGCACCCTCAG +CAACTACTACGTGGACTCGCTTATAGGCCATGAGGGCGACGAGGTGTTCG +CGGCGCGCTTCGGGCCGCCGGGGCCAGGCGCGCAGGGCCGGCCTGCAGGT +GTGGCTGATGGCCCGGCCGCCACCGCCGCCGAGTTCGCCTCGTGTAGTTT +TGCCCCCAGATCGGCCGTGTTCTCTGCCTCGTGGTCCGCGGTGCCCTCCC +AGCCCCCGGCAGCGGCGGCGATGAGCGGCCTCTACCACCCGTACGTTCCC +CCGCCGCCCCTGGCCGCCTCTGCCTCCGAGCCCGGCCGCTACGTGCGCTC +CTGGATGGAGCCGCTGCCCGGCTTCCCGGGCGGTGCGGGCGGTGGCGGTG +GTGGTGGAGGCGGCGGTCCGGGCCGCGGTCCCAGCCCTGGCCCCAGCGGC +CCAGCCAACGGGCGCCACTACGGGATTAAGCCTGAAACCCGAGCGGCCCC +GGCCCCCGCCACGGCCGCCTCCACCACCTCCTCCTCCTCCACTTCCTTAT +CCTCCTCCTCCAAACGGACTGAGTGCTCCGTGGCCCGGGAGTCCCAGGGG +AGCAGCGGCCCCGAGTTCTCGTGCAACTCGTTCCTGCAGGAGAAGGCGGC +AGCGGCGACGGGGGGAACCGGGCCTGGGGCAGGGATCGGGGCCGCGACTG +GGACGGGCGGCTCGTCGGAGCCCTCAGCTTGCAGCGACCACCCGATCCCA +GGCTGTTCGCTGAAGGAGGAGGAGAAGCAGCATTCGCAGCCGCAGCAGCA +GCAACTTGACCCAAGTAAGTGCAAAAGAAATTGCCCCCTGATTTATTGCT +GAAACCTGTAAGGCTCGAATGTGCAAAACTGATAGTTTTACTAACCTATA +AAAACGTCTAGACGCCTACCCAAGCCTAGGCGAACAACATGCATCCATAA +AAAGAGCTTCCCATAACCACCTACCCTGGGCGCTCAGTTAGTACGGTAAA +CAGAGCGCGAGCATTAAGGCTTTTTATGATAATTCCCCACAAGTTGTGAA +AAGCGACCATCCTTGGTGAAATTAATTTAACGACCTCTCTTCCCCACCCT +GTGGTCTCTCCCTGCCTCCCCTCCTCTCCTCTCTCCCCGTCTCCAAACCT +CCCTCTTTGTAGACAACCCCGCCGCGAACTGGATCCACGCTCGCTCCACC +CGGAAAAAGCGCTGTCCCTACACCAAATACCAGACGCTTGAGCTGGAGAA +AGAATTCCTCTTCAACATGTACCTCACCCGGGACCGGCGCTACGAGGTGG +CCAGGATTCTCAACCTAACAGAGAGACAGGTCAAAATCTGGTTTCAGAAC +CGTAGGATGAAAATGAAAAAGATGAGCAAGGAGAAATGCCCCAAAGGAGA +CTGACCCGGCGCGGTGCTGGCGGGAGCGCTCAAGGGCAGCGGATTTGTTG +TTGTTGCTGTTTTCCTTTGTGGGTGTTTGGTGCTTGATTTCCAGAAACTC +TCCAGCGACTTGGACTTCTTCTTCTTTTTTTTTTTCTTTTTAGATAGAAG +TGACTGTGTGGTTGGTCTCTGAGGTATTTGGGGGACTCTGTATTTGCTCG +TTTACGTGTTGGAAAAACCAAGTGGCTTTGGGGTTTCGCCCTATCCCACT +CCCTCTCTTTCCTGCTCCATTGGTTCCTTAAGAAATGCTATATTTTGTGA +GTGCAAGCTGGCTTGGGGAGCCCTCTCTTGTGTAAATGTCCCCCATGTTT +CTGAAAAGTGCTGTAGTTTAGTCCCCTCACCCCCAGCACTGCCCAAACAG +GGGCCAAGTGCGCCCCAATTCCAAGAATGAAGGCAGAGCGACAACAGTGC +GGACACCCCGGCTGCTAGCCCACGGTGAAGCCCGGCGGGGTTGCCCACCA +GTTGCGAAAGCCCCCTTTCCTCAGGGAGCACGCGGGACCTCGGTGGAGAT +CTCCAGTGAGGCTTAGAGGAGCCCAGGGCCTCGGGCGGGTTGGGGTTTGT +CCTCAGTGCATTGGACGCGCTGCTCTCTCCCCTGAAGGCTGGGCTCGCGT +GGGCGGCCGCGGGTGGTGGCCCTCCCGGTTCCTGCCCGAGGACCAGTTGT +AAATGTTACTGCTTCCTACTAATAAATGCTGACCTGATCAAATGGAGCCC +AGACGCTGGCCCTAAACATTGTGTGCCTGCTTTCTCTGCCTCTCTGCAAA +ATATCACACTCAGGATATTTCTCCTCTACCCCTGGGAGTGAGACATTGTT +AAAAATTCAGGGCCCTTCCACCTGACAGATCTCTCTGATGTGTCTCTGCC +TTCTCTGCCTCACATCCCTTTGTGTAGGCAGATGCAGCAGCA
--- a/test-data/in.gtf Sun Jan 28 04:04:58 2018 -0500 +++ b/test-data/in.gtf Fri Mar 11 14:08:11 2022 +0000 @@ -1,6 +1,20 @@ -1 ensembl_havana gene 1 103 . + . gene_id "ENSG00000162526"; gene_version "4"; gene_name "OR4F5"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000001094"; havana_gene_version "1"; -1 ensembl_havana transcript 1 103 . + . gene_id "ENSG00000162526"; gene_version "4"; transcript_id "ENST00000335137"; transcript_version "3"; gene_name "OR4F5"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000001094"; havana_gene_version "1"; transcript_name "OR4F5-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS30547"; havana_transcript "OTTHUMT00000003223"; havana_transcript_version "1"; tag "basic"; transcript_support_level "NA"; -1 ensembl_havana exon 1 103 . + . gene_id "ENSG00000162526"; gene_version "4"; transcript_id "ENST00000335137"; transcript_version "3"; exon_number "1"; gene_name "OR4F5"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000001094"; havana_gene_version "1"; transcript_name "OR4F5-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS30547"; havana_transcript "OTTHUMT00000003223"; havana_transcript_version "1"; exon_id "ENSE00002319515"; exon_version "1"; tag "basic"; transcript_support_level "NA"; -1 ensembl_havana CDS 1 100 . + 0 gene_id "ENSG00000162526"; gene_version "4"; transcript_id "ENST00000335137"; transcript_version "3"; exon_number "1"; gene_name "OR4F5"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000001094"; havana_gene_version "1"; transcript_name "OR4F5-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS30547"; havana_transcript "OTTHUMT00000003223"; havana_transcript_version "1"; protein_id "ENSP00000334393"; protein_version "3"; tag "basic"; transcript_support_level "NA"; -1 ensembl_havana start_codon 1 3 . + 0 gene_id "ENSG00000162526"; gene_version "4"; transcript_id "ENST00000335137"; transcript_version "3"; exon_number "1"; gene_name "OR4F5"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000001094"; havana_gene_version "1"; transcript_name "OR4F5-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS30547"; havana_transcript "OTTHUMT00000003223"; havana_transcript_version "1"; tag "basic"; transcript_support_level "NA"; -1 ensembl_havana stop_codon 101 103 . + 0 gene_id "ENSG00000162526"; gene_version "4"; transcript_id "ENST00000335137"; transcript_version "3"; exon_number "1"; gene_name "OR4F5"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTHUMG00000001094"; havana_gene_version "1"; transcript_name "OR4F5-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS30547"; havana_transcript "OTTHUMT00000003223"; havana_transcript_version "1"; tag "basic"; transcript_support_level "NA"; +fake_chr2 HAVANA gene 257 3416 . + . gene_id "ENSG00000128710.6"; gene_type "protein_coding"; gene_name "HOXD10"; level 1; hgnc_id "HGNC:5133"; tag "overlapping_locus"; havana_gene "OTTHUMG00000132511.5"; +fake_chr2 HAVANA transcript 257 3416 . + . gene_id "ENSG00000128710.6"; transcript_id "ENST00000249501.5"; gene_type "protein_coding"; gene_name "HOXD10"; transcript_type "protein_coding"; transcript_name "HOXD10-201"; level 2; protein_id "ENSP00000249501.4"; transcript_support_level "1"; hgnc_id "HGNC:5133"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_1"; tag "CCDS"; ccdsid "CCDS2266.1"; havana_gene "OTTHUMG00000132511.5"; havana_transcript "OTTHUMT00000255692.3"; +fake_chr2 HAVANA exon 257 1057 . + . gene_id "ENSG00000128710.6"; transcript_id "ENST00000249501.5"; gene_type "protein_coding"; gene_name "HOXD10"; transcript_type "protein_coding"; transcript_name "HOXD10-201"; exon_number 1; exon_id "ENSE00000882912.6"; level 2; protein_id "ENSP00000249501.4"; transcript_support_level "1"; hgnc_id "HGNC:5133"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_1"; tag "CCDS"; ccdsid "CCDS2266.1"; havana_gene "OTTHUMG00000132511.5"; havana_transcript "OTTHUMT00000255692.3"; +fake_chr2 HAVANA CDS 313 1057 . + 0 gene_id "ENSG00000128710.6"; transcript_id "ENST00000249501.5"; gene_type "protein_coding"; gene_name "HOXD10"; transcript_type "protein_coding"; transcript_name "HOXD10-201"; exon_number 1; exon_id "ENSE00000882912.6"; level 2; protein_id "ENSP00000249501.4"; transcript_support_level "1"; hgnc_id "HGNC:5133"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_1"; tag "CCDS"; ccdsid "CCDS2266.1"; havana_gene "OTTHUMG00000132511.5"; havana_transcript "OTTHUMT00000255692.3"; +fake_chr2 HAVANA start_codon 313 315 . + 0 gene_id "ENSG00000128710.6"; transcript_id "ENST00000249501.5"; gene_type "protein_coding"; gene_name "HOXD10"; transcript_type "protein_coding"; transcript_name "HOXD10-201"; exon_number 1; exon_id "ENSE00000882912.6"; level 2; protein_id "ENSP00000249501.4"; transcript_support_level "1"; hgnc_id "HGNC:5133"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_1"; tag "CCDS"; ccdsid "CCDS2266.1"; havana_gene "OTTHUMG00000132511.5"; havana_transcript "OTTHUMT00000255692.3"; +fake_chr2 HAVANA exon 2433 3416 . + . gene_id "ENSG00000128710.6"; transcript_id "ENST00000249501.5"; gene_type "protein_coding"; gene_name "HOXD10"; transcript_type "protein_coding"; transcript_name "HOXD10-201"; exon_number 2; exon_id "ENSE00001816717.3"; level 2; protein_id "ENSP00000249501.4"; transcript_support_level "1"; hgnc_id "HGNC:5133"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_1"; tag "CCDS"; ccdsid "CCDS2266.1"; havana_gene "OTTHUMG00000132511.5"; havana_transcript "OTTHUMT00000255692.3"; +fake_chr2 HAVANA CDS 2433 2707 . + 2 gene_id "ENSG00000128710.6"; transcript_id "ENST00000249501.5"; gene_type "protein_coding"; gene_name "HOXD10"; transcript_type "protein_coding"; transcript_name "HOXD10-201"; exon_number 2; exon_id "ENSE00001816717.3"; level 2; protein_id "ENSP00000249501.4"; transcript_support_level "1"; hgnc_id "HGNC:5133"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_1"; tag "CCDS"; ccdsid "CCDS2266.1"; havana_gene "OTTHUMG00000132511.5"; havana_transcript "OTTHUMT00000255692.3"; +fake_chr2 HAVANA stop_codon 2708 2710 . + 0 gene_id "ENSG00000128710.6"; transcript_id "ENST00000249501.5"; gene_type "protein_coding"; gene_name "HOXD10"; transcript_type "protein_coding"; transcript_name "HOXD10-201"; exon_number 2; exon_id "ENSE00001816717.3"; level 2; protein_id "ENSP00000249501.4"; transcript_support_level "1"; hgnc_id "HGNC:5133"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_1"; tag "CCDS"; ccdsid "CCDS2266.1"; havana_gene "OTTHUMG00000132511.5"; havana_transcript "OTTHUMT00000255692.3"; +fake_chr2 HAVANA UTR 257 312 . + . gene_id "ENSG00000128710.6"; transcript_id "ENST00000249501.5"; gene_type "protein_coding"; gene_name "HOXD10"; transcript_type "protein_coding"; transcript_name "HOXD10-201"; exon_number 1; exon_id "ENSE00000882912.6"; level 2; protein_id "ENSP00000249501.4"; transcript_support_level "1"; hgnc_id "HGNC:5133"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_1"; tag "CCDS"; ccdsid "CCDS2266.1"; havana_gene "OTTHUMG00000132511.5"; havana_transcript "OTTHUMT00000255692.3"; +fake_chr2 HAVANA UTR 2708 3416 . + . gene_id "ENSG00000128710.6"; transcript_id "ENST00000249501.5"; gene_type "protein_coding"; gene_name "HOXD10"; transcript_type "protein_coding"; transcript_name "HOXD10-201"; exon_number 2; exon_id "ENSE00001816717.3"; level 2; protein_id "ENSP00000249501.4"; transcript_support_level "1"; hgnc_id "HGNC:5133"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_1"; tag "CCDS"; ccdsid "CCDS2266.1"; havana_gene "OTTHUMG00000132511.5"; havana_transcript "OTTHUMT00000255692.3"; +fake_chr2 HAVANA gene 6198 8416 . + . gene_id "ENSG00000128709.13"; gene_type "protein_coding"; gene_name "HOXD9"; level 2; hgnc_id "HGNC:5140"; havana_gene "OTTHUMG00000132516.6"; +fake_chr2 HAVANA transcript 6198 8416 . + . gene_id "ENSG00000128709.13"; transcript_id "ENST00000249499.8"; gene_type "protein_coding"; gene_name "HOXD9"; transcript_type "protein_coding"; transcript_name "HOXD9-201"; level 2; protein_id "ENSP00000249499.6"; transcript_support_level "1"; hgnc_id "HGNC:5140"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_1"; tag "CCDS"; ccdsid "CCDS2267.2"; havana_gene "OTTHUMG00000132516.6"; havana_transcript "OTTHUMT00000255698.6"; +fake_chr2 HAVANA exon 6198 7064 . + . gene_id "ENSG00000128709.13"; transcript_id "ENST00000249499.8"; gene_type "protein_coding"; gene_name "HOXD9"; transcript_type "protein_coding"; transcript_name "HOXD9-201"; exon_number 1; exon_id "ENSE00000882914.5"; level 2; protein_id "ENSP00000249499.6"; transcript_support_level "1"; hgnc_id "HGNC:5140"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_1"; tag "CCDS"; ccdsid "CCDS2267.2"; havana_gene "OTTHUMG00000132516.6"; havana_transcript "OTTHUMT00000255698.6"; +fake_chr2 HAVANA CDS 6248 7064 . + 0 gene_id "ENSG00000128709.13"; transcript_id "ENST00000249499.8"; gene_type "protein_coding"; gene_name "HOXD9"; transcript_type "protein_coding"; transcript_name "HOXD9-201"; exon_number 1; exon_id "ENSE00000882914.5"; level 2; protein_id "ENSP00000249499.6"; transcript_support_level "1"; hgnc_id "HGNC:5140"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_1"; tag "CCDS"; ccdsid "CCDS2267.2"; havana_gene "OTTHUMG00000132516.6"; havana_transcript "OTTHUMT00000255698.6"; +fake_chr2 HAVANA start_codon 6248 6250 . + 0 gene_id "ENSG00000128709.13"; transcript_id "ENST00000249499.8"; gene_type "protein_coding"; gene_name "HOXD9"; transcript_type "protein_coding"; transcript_name "HOXD9-201"; exon_number 1; exon_id "ENSE00000882914.5"; level 2; protein_id "ENSP00000249499.6"; transcript_support_level "1"; hgnc_id "HGNC:5140"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_1"; tag "CCDS"; ccdsid "CCDS2267.2"; havana_gene "OTTHUMG00000132516.6"; havana_transcript "OTTHUMT00000255698.6"; +fake_chr2 HAVANA exon 7413 8416 . + . gene_id "ENSG00000128709.13"; transcript_id "ENST00000249499.8"; gene_type "protein_coding"; gene_name "HOXD9"; transcript_type "protein_coding"; transcript_name "HOXD9-201"; exon_number 2; exon_id "ENSE00001845001.4"; level 2; protein_id "ENSP00000249499.6"; transcript_support_level "1"; hgnc_id "HGNC:5140"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_1"; tag "CCDS"; ccdsid "CCDS2267.2"; havana_gene "OTTHUMG00000132516.6"; havana_transcript "OTTHUMT00000255698.6"; +fake_chr2 HAVANA CDS 7413 7651 . + 2 gene_id "ENSG00000128709.13"; transcript_id "ENST00000249499.8"; gene_type "protein_coding"; gene_name "HOXD9"; transcript_type "protein_coding"; transcript_name "HOXD9-201"; exon_number 2; exon_id "ENSE00001845001.4"; level 2; protein_id "ENSP00000249499.6"; transcript_support_level "1"; hgnc_id "HGNC:5140"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_1"; tag "CCDS"; ccdsid "CCDS2267.2"; havana_gene "OTTHUMG00000132516.6"; havana_transcript "OTTHUMT00000255698.6"; +fake_chr2 HAVANA stop_codon 7652 7654 . + 0 gene_id "ENSG00000128709.13"; transcript_id "ENST00000249499.8"; gene_type "protein_coding"; gene_name "HOXD9"; transcript_type "protein_coding"; transcript_name "HOXD9-201"; exon_number 2; exon_id "ENSE00001845001.4"; level 2; protein_id "ENSP00000249499.6"; transcript_support_level "1"; hgnc_id "HGNC:5140"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_1"; tag "CCDS"; ccdsid "CCDS2267.2"; havana_gene "OTTHUMG00000132516.6"; havana_transcript "OTTHUMT00000255698.6"; +fake_chr2 HAVANA UTR 6198 6247 . + . gene_id "ENSG00000128709.13"; transcript_id "ENST00000249499.8"; gene_type "protein_coding"; gene_name "HOXD9"; transcript_type "protein_coding"; transcript_name "HOXD9-201"; exon_number 1; exon_id "ENSE00000882914.5"; level 2; protein_id "ENSP00000249499.6"; transcript_support_level "1"; hgnc_id "HGNC:5140"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_1"; tag "CCDS"; ccdsid "CCDS2267.2"; havana_gene "OTTHUMG00000132516.6"; havana_transcript "OTTHUMT00000255698.6"; +fake_chr2 HAVANA UTR 7652 8416 . + . gene_id "ENSG00000128709.13"; transcript_id "ENST00000249499.8"; gene_type "protein_coding"; gene_name "HOXD9"; transcript_type "protein_coding"; transcript_name "HOXD9-201"; exon_number 2; exon_id "ENSE00001845001.4"; level 2; protein_id "ENSP00000249499.6"; transcript_support_level "1"; hgnc_id "HGNC:5140"; tag "basic"; tag "Ensembl_canonical"; tag "MANE_Select"; tag "appris_principal_1"; tag "CCDS"; ccdsid "CCDS2267.2"; havana_gene "OTTHUMG00000132516.6"; havana_transcript "OTTHUMT00000255698.6";