pyGTF2bedGraph

pyGTF2bedGraph is part of the pyCRAC package. Generates bedgraph files for each chromosome. An homage to bedtools genomecoverage. Takes a pyReadCounters GTF file as input file. Can also output bedGraph files for substitutions and deletions.

Parameter list

File input options:

--gtf=readdata.gtf
                    type the path to the gtf file data file. Be default it
                    expects data from the standard input
-o converted
                    provide a name for an output file. A file extension or
                    strand information is not necessary.
-c yeast.txt, --chromfile=yeast.txt
                    Location of the chromosome info file. This file should
                    have two columns: first column is the names of the
                    chromosomes, second column is length of the
                    chromosomes. Default is yeast
-t TYPE, --type=TYPE
                    this tool can generate bedGraph files for reads,
                    substitutions or deletions. Please use
                    'reads','substitutions' or 'deletions' to indicate the
                    type of data. Default='reads'
--count
                    Takes the numbers in the 'score' column of the GTF
                    file as the total number of reads for each position.
                    Default is 1 for each interval.
--iCLIP
                    This turns on the iCLIP mode and the sgr reads or cDNA
                    files will report cross-linking site frequencies in
                    iCLIP data
-v, --verbose
                    to print status messages to a log file

These options can be used to add a track line for the UCSC genome browser:

--track
                    Use this flag to add a UCSC genome browser track line
                    to the beginning of your file
-n NAME, --name=NAME
                    For the USCS track line: provide a track name. Default
                    = 'User_supplied_track'
-d DESCRIPTION, --description=DESCRIPTION
                    For the USCS track line: provide a track description.
                    Default = 'User_supplied_track'
--color=COLOR
                    select the track color. Default = black
-s STRANDS, --colorstrands=STRANDS
                    select the colors for each strand. Default =
                    'red,blue'