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GTF to BEDGraph converter.
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Jeremy Goecks
@@ -79,6 +79,7 @@
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<tool file="fastx_toolkit/fastq_to_fasta.xml" />
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<tool file="filters/wiggle_to_simple.xml" />
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<tool file="filters/sff_extractor.xml" />
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<tool file="filters/gtf2bedgraph.xml" />
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</section>
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<section name="Extract Features" id="features">
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<tool file="filters/ucsc_gene_bed_to_exon_bed.xml" />
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@@ -0,0 +1,79 @@
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<tool id="gtf2bedgraph" name="GTF-to-BEDGraph">
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<description>converter</description>
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<command interpreter="python">gtf_to_bedgraph_converter.py $input $out_file1 $attribute_name</command>
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<inputs>
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<param format="gtf" name="input" type="data" label="Convert this query"/>
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<param name="attribute_name" type="text" label="Attribute to Use for Value"/>
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</inputs>
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<outputs>
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<data format="bedgraph" name="out_file1" />
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</outputs>
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<tests>
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<test>
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<param name="input" value="gtf2bedgraph_in.gtf" ftype="gtf"/>
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<param name="attribute_name" value="FPKM"/>
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<output name="out_file1" file="gtf2bedgraph_out.bedgraph" ftype="bedgraph"/>
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</test>
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</tests>
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<help>
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**What it does**
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This tool converts data from GTF format to BEDGraph format (scroll down for format description).
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--------
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**Example**
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The following data in GFF format::
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chr22 GeneA enhancer 10000000 10001000 500 + . gene_id "GeneA"; transcript_id "TranscriptAlpha"; FPKM "2.75"; frac "1.000000";
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chr22 GeneA promoter 10010000 10010100 900 + . gene_id "GeneA"; transcript_id "TranscriptsAlpha"; FPKM "2.25"; frac "1.000000";
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using the attribute name 'FPKM' will be converted to BEDGraph (**note** that 1 is subtracted from the start coordinate)::
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chr22 9999999 10001000 2.75
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chr22 10009999 10010100 2.25
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------
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.. class:: infomark
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**About formats**
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**GTF format** Gene Transfer Format is a format for describing genes and other features associated with DNA, RNA and Protein sequences. GTF lines have nine tab-separated fields::
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1. seqname - Must be a chromosome or scaffold.
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2. source - The program that generated this feature.
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3. feature - The name of this type of feature. Some examples of standard feature types are "CDS", "start_codon", "stop_codon", and "exon".
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4. start - The starting position of the feature in the sequence. The first base is numbered 1.
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5. end - The ending position of the feature (inclusive).
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6. score - A score between 0 and 1000. If there is no score value, enter ".".
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7. strand - Valid entries include '+', '-', or '.' (for don't know/care).
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8. frame - If the feature is a coding exon, frame should be a number between 0-2 that represents the reading frame of the first base. If the feature is not a coding exon, the value should be '.'.
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9. group - The group field is a list of attributes. Each attribute consists of a type/value pair. Attributes must end in a semi-colon, and be separated from any following attribute by exactly one space. The attribute list must begin with the two mandatory attributes: (i) gene_id value - A globally unique identifier for the genomic source of the sequence and (ii) transcript_id value - A globally unique identifier for the predicted transcript.
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**BEDGraph format**
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The bedGraph format is line-oriented. Bedgraph data are preceeded by a track definition line, which adds a number of options for controlling the default display of this track.
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For the track definition line, all options are placed in a single line separated by spaces:
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track type=bedGraph name=track_label description=center_label
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visibility=display_mode color=r,g,b altColor=r,g,b
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priority=priority autoScale=on|off alwaysZero=on|off
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gridDefault=on|off maxHeightPixels=max:default:min
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graphType=bar|points viewLimits=lower:upper
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yLineMark=real-value yLineOnOff=on|off
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windowingFunction=maximum|mean|minimum smoothingWindow=off|2-16
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The track type is REQUIRED, and must be bedGraph:
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type=bedGraph
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Following the track definition line are the track data in four column BED format::
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chromA chromStartA chromEndA dataValueA
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chromB chromStartB chromEndB dataValueB
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</help>
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</tool>
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@@ -0,0 +1,73 @@
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#!/usr/bin/env python
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import os, sys, tempfile
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assert sys.version_info[:2] >= ( 2, 4 )
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def __main__():
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# Read parms.
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input_name = sys.argv[1]
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output_name = sys.argv[2]
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attribute_name = sys.argv[3]
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# Create temp file.
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tmp_name = tempfile.NamedTemporaryFile().name
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# Do conversion.
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skipped_lines = 0
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first_skipped_line = 0
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out = open( tmp_name, 'w' )
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# Write track definition line.
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out.write( "track type=bedGraph\n")
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# Write track data to temporary file.
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i = 0
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for i, line in enumerate( file( input_name ) ):
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line = line.rstrip( '\r\n' )
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if line and not line.startswith( '#' ):
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try:
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elems = line.split( '\t' )
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start = str( int( elems[3] ) - 1 ) # GTF coordinates are 1-based, BedGraph are 0-based.
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strand = elems[6]
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if strand not in ['+', '-']:
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strand = '+'
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attributes_list = elems[8].split(";")
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attributes = {}
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for name_value_pair in attributes_list:
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pair = name_value_pair.strip().split(" ")
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name = pair[0].strip()
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if name == '':
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continue
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# Need to strip double quote from values
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value = pair[1].strip(" \"")
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attributes[name] = value
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value = attributes[ attribute_name ]
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# GTF format: chrom source, name, chromStart, chromEnd, score, strand, frame, attributes.
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# BedGraph format: chrom, chromStart, chromEnd, value
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out.write( "%s\t%s\t%s\t%s\n" %( elems[0], start, elems[4], value ) )
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except:
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skipped_lines += 1
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if not first_skipped_line:
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first_skipped_line = i + 1
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else:
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skipped_lines += 1
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if not first_skipped_line:
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first_skipped_line = i + 1
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out.close()
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# Sort tmp file to create bedgraph file; sort by chromosome name and chromosome start.
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cmd = "sort -k1,1 -k2,2n < %s > %s" % ( tmp_name, output_name )
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try:
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os.system(cmd)
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os.remove(tmp_name)
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except Exception, ex:
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sys.stderr.write( "%s\n" % ex )
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sys.exit(1)
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info_msg = "%i lines converted to BEDGraph. " % ( i + 1 - skipped_lines )
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if skipped_lines > 0:
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info_msg += "Skipped %d blank/comment/invalid lines starting with line #%d." %( skipped_lines, first_skipped_line )
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print info_msg
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if __name__ == "__main__": __main__()
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