Homer Tag Directory Galaxy Composite Dataset

# HG changeset patch # User kevyin # Date 1355460124 18000 # Node ID 8cfd322a5907156570676b297324bc2a5bf2b122 # Parent 74c1fc7bb164d3028f73792e810f67af78c9b6f0 Deleted selected files diff -r 74c1fc7bb164 -r 8cfd322a5907 README --- a/README Tue Nov 27 02:34:33 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,13 +0,0 @@ -Homer wrapper for Galaxy - -Code repo: https://bitbucket.org/gvl/homer - -=========================================: -LICENSE for this wrapper: -=========================================: -Kevin Ying -Garvan Institute: http://www.garvan.org.au -GVL: https://genome.edu.au/wiki/GVL - -http://opensource.org/licenses/mit-license.php - diff -r 74c1fc7bb164 -r 8cfd322a5907 annotatePeaks.xml --- a/annotatePeaks.xml Tue Nov 27 02:34:33 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,41 +0,0 @@ - - - homer - - - - - annotatePeaks.pl $input_bed $genome_selector 1> $out_annotated - 2> $out_log || echo "Error running annotatePeaks." >&2 - - - - - - - - - - - - - - - - - - - - - - - .. class:: infomark - - **Homer annoatePeaks** - More information on accepted formats - http://biowhat.ucsd.edu/homer/ngs/annotation.html - - - - - diff -r 74c1fc7bb164 -r 8cfd322a5907 bed2pos.xml --- a/bed2pos.xml Tue Nov 27 02:34:33 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,34 +0,0 @@ - - - homer - - - - - bed2pos.pl $input_bed 1> $out_pos - 2> $out_log || echo "Error running bed2pos." >&2 - - - - - - - - - - - - - - - - - - - .. class:: infomark - - **Homer bed2pos.pl** - http://biowhat.ucsd.edu/homer/ngs/miscellaneous.html - - - diff -r 74c1fc7bb164 -r 8cfd322a5907 datatypes_conf.xml --- a/datatypes_conf.xml Tue Nov 27 02:34:33 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,9 +0,0 @@ - - - - - - - - - diff -r 74c1fc7bb164 -r 8cfd322a5907 findPeaks.xml --- a/findPeaks.xml Tue Nov 27 02:34:33 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,52 +0,0 @@ - - - homer - - Homer's peakcaller. Requires tag directories (see makeTagDirectory) - - - findPeaks $tagDir.extra_files_path $options -o $outputPeakFile - - #if $control_tagDir: - -i $control_tagDir.extra_files_path - #end if - - 2> $out_log || echo "Error running findPeaks." >&2 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - .. class:: infomark - - **Homer findPeaks** - http://biowhat.ucsd.edu/homer/ngs/peaks.html - - - - diff -r 74c1fc7bb164 -r 8cfd322a5907 homerDatatypes.py --- a/homerDatatypes.py Tue Nov 27 02:34:33 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,122 +0,0 @@ -""" -homer composite datatypes -NOTE: makeTagDirectory doesn't actually use this!!!! It uses html as the format - I've never got it to properly display the contents of the datatype for after - clicking the "eye" icon, so using html instead - -Use at your peril -Kevin Ying -for the homer wrapper - -Dec 2012 -""" - -import logging, os, sys, time, tempfile, shutil, string, glob -import data -from galaxy import util -from cgi import escape -import urllib, binascii -from galaxy.web import url_for -from galaxy.datatypes import metadata -from galaxy.datatypes.metadata import MetadataElement -from galaxy.datatypes.data import Text -from galaxy.datatypes.tabular import Tabular -from galaxy.datatypes.images import Html -from galaxy.datatypes.interval import Interval -from galaxy.util.hash_util import * - -gal_Log = logging.getLogger(__name__) -verbose = False - -class HomerTagDirectory(Html): - """ - base class to use for homer tag directory datatypes - composite datatype elements - stored in extra files path - """ - - #MetadataElement( name="base_name", desc="base name for all transformed versions of this genetic dataset", default='HomerTagDirectory', - #readonly=True, set_in_upload=False) - - composite_type = 'auto_primary_file' - #allow_datatype_change = False - file_ext = 'homerTagDirectory' - - def __init__(self, **kwd): - Html.__init__(self, **kwd) - self.add_composite_file('tagInfo.txt', description="tagInfo") - self.add_composite_file('tagAutocorrelation.txt', description="tagAutocorrelation") - self.add_composite_file('tagCountDistribution.txt', description="tagCountDistribution") - self.add_composite_file('tagLengthDistribution.txt', description="tagLengthDistribution") - - def generate_primary_file(self, dataset=None): - rval = ['Homer Tag Directory Galaxy Composite Dataset

'] - rval.append('

This composite dataset is composed of the following files:

%s (%s)%s
%s%s

' ) - return "\n".join( rval ) - - - def regenerate_primary_file(self,dataset): - """ - cannot do this until we are setting metadata - """ - #bn = dataset.metadata.base_name - efp = dataset.extra_files_path - flist = os.listdir(efp) - rval = ['Files for Composite Dataset %s

Composite %s contains:

%s

' ) - f = file(dataset.file_name,'w') - f.write("\n".join( rval )) - f.write('\n') - f.close() - - def get_mime(self): - """Returns the mime type of the datatype""" - return 'text/html' - - def set_meta( self, dataset, **kwd ): - - """ - for homer maketagdirectory eg - - """ - Html.set_meta( self, dataset, **kwd ) - if kwd.get('overwrite') == False: - if verbose: - gal_Log.debug('@@@ HomerTagDirectory set_meta called with overwrite = False') - return True - try: - efp = dataset.extra_files_path - except: - if verbose: - gal_Log.debug('@@@ HomerTagDirectory set_meta failed %s - dataset %s has no efp ?' % (sys.exc_info()[0], dataset.name)) - return False - try: - flist = os.listdir(efp) - except: - if verbose: gal_Log.debug('@@@ HomerTagDirectory set_meta failed %s - dataset %s has no efp ?' % (sys.exc_info()[0],dataset.name)) - return False - if len(flist) == 0: - if verbose: - gal_Log.debug('@@@ HomerTagDirectory set_meta failed - %s efp %s is empty?' % (dataset.name,efp)) - return False - self.regenerate_primary_file(dataset) - if not dataset.info: - dataset.info = 'Galaxy HomerTagDirectory datatype object' - if not dataset.blurb: - dataset.blurb = 'Composite file - Homer Galaxy toolkit' - return True - diff -r 74c1fc7bb164 -r 8cfd322a5907 makeTagDirectory.py --- a/makeTagDirectory.py Tue Nov 27 02:34:33 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,94 +0,0 @@ -""" - - -""" -import re -import os -import sys -import subprocess -import optparse -import shutil -import tempfile - -def getFileString(fpath, outpath): - """ - format a nice file size string - """ - size = '' - fp = os.path.join(outpath, fpath) - s = '? ?' - if os.path.isfile(fp): - n = float(os.path.getsize(fp)) - if n > 2**20: - size = ' (%1.1f MB)' % (n/2**20) - elif n > 2**10: - size = ' (%1.1f KB)' % (n/2**10) - elif n > 0: - size = ' (%d B)' % (int(n)) - s = '%s %s' % (fpath, size) - return s - -class makeTagDirectory(): - """wrapper - """ - - def __init__(self,opts=None, args=None): - self.opts = opts - self.args = args - - def run_makeTagDirectory(self): - """ - makeTagDirectory [options] [alignment file 2] - - """ - if self.opts.format != "bam": - cl = [self.opts.executable] + args + ["-format" , self.opts.format] - else: - cl = [self.opts.executable] + args - print cl - p = subprocess.Popen(cl) - retval = p.wait() - - - html = self.gen_html(args[0]) - #html = self.gen_html() - return html,retval - - def gen_html(self, dr=os.getcwd()): - flist = os.listdir(dr) - print flist - """ add a list of all files in the tagdirectory - """ - res = ['

Files created by makeTagDirectory

\n'] - - flist.sort() - for i,f in enumerate(flist): - if not(os.path.isdir(f)): - fn = os.path.split(f)[-1] - res.append('\n' % (fn,getFileString(fn, dr))) - - res.append('

\n') - - return res - -if __name__ == '__main__': - op = optparse.OptionParser() - op.add_option('-e', '--executable', default='makeTagDirectory') - op.add_option('-o', '--htmloutput', default=None) - op.add_option('-f', '--format', default="sam") - opts, args = op.parse_args() - #assert os.path.isfile(opts.executable),'## makeTagDirectory.py error - cannot find executable %s' % opts.executable - - #if not os.path.exists(opts.outputdir): - #os.makedirs(opts.outputdir) - f = makeTagDirectory(opts, args) - - html,retval = f.run_makeTagDirectory() - f = open(opts.htmloutput, 'w') - f.write(''.join(html)) - f.close() - if retval <> 0: - print >> sys.stderr, serr # indicate failure - - - diff -r 74c1fc7bb164 -r 8cfd322a5907 makeTagDirectory.xml --- a/makeTagDirectory.xml Tue Nov 27 02:34:33 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,50 +0,0 @@ - - - homer - - Simple wrapper for makeTagDirectory. Used by findPeaks - - makeTagDirectory.py ${tagDir.files_path} - #for $alignF in $alignmentFiles - $alignF.file -f $alignF.file.ext - #end for - -o $tagDir - 2> $out_log || echo "Error running homer_makeTagDirectory." >&2 - - - - - - - - - - - - - - - - - - - - - - - - - - - .. class:: infomark - - After the job finishes, save the zip file, unzip and open "index.html" - - The actual meme-chip command is displayed under "Command line summary" - - Defaults: - http://meme.nbcr.net/meme/doc/meme-chip.html - - - - diff -r 74c1fc7bb164 -r 8cfd322a5907 pos2bed.xml --- a/pos2bed.xml Tue Nov 27 02:34:33 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,34 +0,0 @@ - - - homer - - - - - pos2bed.pl $input_peak 1> $out_bed - 2> $out_log || echo "Error running pos2bed." >&2 - - - - - - - - - - - - - - - - - - - .. class:: infomark - - **Homer pos2bed.pl** - http://biowhat.ucsd.edu/homer/ngs/miscellaneous.html - - -