Mercurial > repos > iuc > length_and_gc_content

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/all_fasta.loc.sample	Thu Nov 17 16:41:06 2016 -0500
@@ -0,0 +1,18 @@
+#This file lists the locations and dbkeys of all the fasta files
+#under the "genome" directory (a directory that contains a directory
+#for each build). The script extract_fasta.py will generate the file
+#all_fasta.loc. This file has the format (white space characters are
+#TAB characters):
+#
+#<unique_build_id>	<dbkey>	<display_name>	<file_path>
+#
+#So, all_fasta.loc could look something like this:
+#
+#apiMel3	apiMel3	Honeybee (Apis mellifera): apiMel3	/path/to/genome/apiMel3/apiMel3.fa
+#hg19canon	hg19	Human (Homo sapiens): hg19 Canonical	/path/to/genome/hg19/hg19canon.fa
+#hg19full	hg19	Human (Homo sapiens): hg19 Full	/path/to/genome/hg19/hg19full.fa
+#
+#Your all_fasta.loc file should contain an entry for each individual
+#fasta file. So there will be multiple fasta files for each build,
+#such as with hg19 above.
+#
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/get_length_and_gc_content.r	Thu Nov 17 16:41:06 2016 -0500
@@ -0,0 +1,59 @@
+# 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 ) } )
+
+# 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")
+})
+
+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 name and length."),
+    make_option(c("-gc","--gc_content"), type="character", default=FALSE, help="Output file with gene name and GC content.")
+  )
+
+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
+
+#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))
+
+#Open the fasta file
+FASTA <- FaFile(FASTAfile)
+open(FASTA)
+
+#Add the GC numbers
+elementMetadata(reducedGTF)$nGCs <- letterFrequency(getSeq(FASTA, reducedGTF), "GC")[,1]
+elementMetadata(reducedGTF)$widths <- width(reducedGTF)
+
+#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)
+}
+output <- t(sapply(split(reducedGTF, elementMetadata(reducedGTF)$gene_id), calc_GC_length))
+output <- data.frame(setDT(data.frame(output), keep.rownames = TRUE)[])
+
+
+write.table(output[,c(1,2)], file=length, col.names=FALSE, row.names=FALSE, quote=FALSE, sep="\t")
+write.table(output[,c(1,3)], file=gc_content, col.names=FALSE, row.names=FALSE, quote=FALSE, sep="\t")
+
+
+sessionInfo()
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/get_length_and_gc_content.xml	Thu Nov 17 16:41:06 2016 -0500
@@ -0,0 +1,89 @@
+<tool id="length_and_gc_content" name="Gene length and gc content" version="0.1.0">
+    <description>from GTF file</description>
+    <requirements>
+        <requirement type="package" version="1.3.2">r-optparse</requirement>
+        <requirement type="package" version="1.4.1">r-reshape2</requirement>
+        <requirement type="package" version="1.9.6">r-data.table</requirement>
+        <requirement type="package" version="1.34.1">bioconductor-rtracklayer</requirement>
+    </requirements>
+    <stdio>
+        <regex match="Execution halted"
+               source="both"
+               level="fatal"
+               description="Execution halted." />
+        <regex match="Error in"
+               source="both"
+               level="fatal"
+               description="An undefined error occured, please check your input carefully and contact your administrator." />
+        <regex match="Fatal error"
+               source="both"
+               level="fatal"
+               description="An undefined error occured, please check your input carefully and contact your administrator." />
+    </stdio>
+    <command><![CDATA[
+        Rscript '$__tool_directory__'/get_length_and_gc_content.r --gtf '$gtf'
+        #if $fastaSource.genomeSource == 'indexed':
+            --fasta '$fastaSource.fasta_pre_installed.fields.path'
+        #else:
+            --fasta '$fastaSource.fasta_history'
+        #end if
+        --length '$length'
+        --gc_content '$gc_content'
+    ]]></command>
+    <inputs>
+        <param name="gtf" type="data" format="gtf" help="The GTF must match the FASTA file" label="GTF file for length and GC calculation"/>
+        <conditional name="fastaSource">
+            <param help="choose history if you don't see the correct genome fasta" label="Select a reference fasta from your history or use a built-in fasta?" name="genomeSource" type="select">
+                <option value="indexed">Use a built-in fasta</option>
+                <option value="history">Use 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 sequence">
+                    <options from_data_table="all_fasta">
+                        <filter type="data_meta" key="dbkey" ref="gtf" column="0"/>
+                    </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">
+                <options>
+                    <filter type="data_meta" key="dbkey" ref="gtf"/>
+                </options>
+                <validator type="no_options" message="The current history does not include a fasta dataset with the build associated with the selected input file"/>
+            </param>
+        </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data name="length" format="tabular" label="gene length">
+            <actions>
+                <action name="column_names" type="metadata" default="gene,length" />
+            </actions>
+        </data>
+        <data name="gc_content" format="tabular" label="gene gc content">
+             <actions>
+                <action name="column_names" type="metadata" default="gene,gc_content" />
+            </actions>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <param name="gtf" value="in.gtf" ftype="gtf"></param>
+            <param name="fastaSource|genomeSource" value="history"></param>
+            <param name="fastaSource|fasta_history" value="in.fasta" ftype="fasta"></param>
+            <output name="length" file="length.tab"></output>
+            <output name="gc_content" file="gc.tab"></output>
+        </test>
+    </tests>
+    <help>
+
+        **What it does**
+
+        Returns a tabular file with gene id and length and a tabular file with gene id and GC content, based on a supplied GTF and a FASTA file.
+
+
+        </help>
+    <citations>
+    </citations>
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gc.tab	Thu Nov 17 16:41:06 2016 -0500
@@ -0,0 +1,1 @@
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gene_length.tab	Thu Nov 17 16:41:06 2016 -0500
@@ -0,0 +1,948 @@
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+ENSG00000240392	575
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+ENSG00000240821	579
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+ENSG00000241370	1606
+ENSG00000241494	438
+ENSG00000241680	375
+ENSG00000241697	2611
+ENSG00000241772	1051
+ENSG00000241923	622
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+ENSG00000242140	231
+ENSG00000242349	1427
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/in.fasta	Thu Nov 17 16:41:06 2016 -0500
@@ -0,0 +1,2 @@
+>1
+AAAAAAAAAATTTTTTTTTTCCCCCCCCCCGGGGGGGGGGAAAAAAAAAAAAAAAAAAAATTTTTTTTTTCCCCCCCCCCGGGGGGGGGGAAAAAAAAAATTTTT
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/in.gtf	Thu Nov 17 16:41:06 2016 -0500
@@ -0,0 +1,6 @@
+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";
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/length.tab	Thu Nov 17 16:41:06 2016 -0500
@@ -0,0 +1,1 @@
+ENSG00000162526	103
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample	Thu Nov 17 16:41:06 2016 -0500
@@ -0,0 +1,7 @@
+<tables>
+    <!-- Locations of all fasta files under genome directory -->
+    <table name="all_fasta" comment_char="#">
+        <columns>value, dbkey, name, path</columns>
+        <file path="tool-data/all_fasta.loc" />
+    </table>
+</tables>