comparison cuffdata.py @ 6:137aab1d9ac1

Add metadata to datatype: CuffDataDB

5:2bb88bf1c1dd

"""
CuffData 
"""
import logging
import os,os.path,re
import galaxy.datatypes.data
from galaxy.datatypes.images import Html
from galaxy.datatypes.binary import Binary
from galaxy import util
from galaxy.datatypes.metadata import MetadataElement

    def sniff( self, filename ):
        return False

class CuffDataDB( Binary ):
    file_ext = 'cuffdata'
    is_binary = True
    allow_datatype_change = False

6:137aab1d9ac1

"""
CuffData 
"""
import logging
import os,os.path,sys,re
import tempfile
from subprocess import Popen
import galaxy.datatypes.data
from galaxy.datatypes.images import Html
from galaxy.datatypes.binary import Binary
from galaxy import util
from galaxy.datatypes.metadata import MetadataElement

    def sniff( self, filename ):
        return False

class CuffDataDB( Binary ):
    file_ext = 'cuffdatadb'
    is_binary = True
    allow_datatype_change = False
    MetadataElement( name="sample_names", default=[], desc="Sample names", readonly=True, visible=True, optional=True, no_value=[] )
    MetadataElement( name="replicate_names", default=[], desc="Replicate names", readonly=True, visible=True, optional=True, no_value=[] )
    MetadataElement( name="gene_ids", default=[], desc="Gene Ids", readonly=True, visible=True, optional=True, no_value=[] )

    def __init__( self, **kwd ):
        Binary.__init__( self, **kwd )
        log.info('Creating cummeRbund CuffDataDB')

    def set_meta( self, dataset, **kwd ):
        def get_contents(fname):
            contents = ''
            with open(fname,'r') as fh:
                contents = fh.read()
            return contents
        if not dataset.has_data():
            return
        try:
            ## Create a tmpdir
            ## create an Rscript to write out info about the CuffData, e.g. samples replicates gene_ids
            ## define file names to use as sinks for each type of data
            # tmp_dir = tempfile.mkdtemp()
            tmp_dir = '/tmp/gx/cuffdb'
            if not os.path.isdir(tmp_dir):
                os.makedirs(tmp_dir)
            rscript = tempfile.NamedTemporaryFile( dir=tmp_dir,suffix='.r' ).name
            rscript_fh = open( rscript, 'wb' )
            rscript_fh.write('library(cummeRbund)\n')
            rscript_fh.write('cuff<-readCufflinks(dir = "", dbFile = "%s", rebuild = F)\n' % (dataset.file_name))
            rscript_fh.write('sink("%s")\n' % ("out.blurb"))
            rscript_fh.write('print(cuff)\n')
            rscript_fh.write('sink()\n')
            rscript_fh.write('sink("%s")\n' % ("out.samples"))
            rscript_fh.write('cat(samples(cuff)[[2]],sep=",")\n')
            rscript_fh.write('sink()\n')
            rscript_fh.write('sink("%s")\n' % ("out.replicates"))
            rscript_fh.write('cat(replicates(cuff)[[4]],sep=",")\n')
            rscript_fh.write('sink()\n')
            rscript_fh.write('sink("%s")\n' % ("out.gene_ids"))
            rscript_fh.write('cat(annotation(genes(cuff))[[1]],sep=",")\n')
            rscript_fh.write('sink()\n')
            rscript_fh.close()
            cmd = ( "Rscript --vanilla %s" % rscript )
            tmp_stderr_name = tempfile.NamedTemporaryFile( dir=tmp_dir,suffix='.err' ).name
            tmp_stderr = open( tmp_stderr_name, 'wb' )
            proc = Popen( args=cmd, shell=True, cwd=tmp_dir, stderr=tmp_stderr.fileno() )
            returncode = proc.wait()
            tmp_stderr.close()
            flist = os.listdir(tmp_dir)
            for i,fname in enumerate(flist):
                sfname = os.path.split(fname)[-1]
                if sfname == 'out.blurb':
                    dataset.blurb = get_contents(os.path.join(tmp_dir,fname))
                elif sfname == 'out.samples':
                    dataset.metadata.sample_names = get_contents(os.path.join(tmp_dir,fname)).split(',')
                elif sfname == 'out.replicates':
                    dataset.metadata.replicate_names = get_contents(os.path.join(tmp_dir,fname)).split(',')
                elif sfname == 'out.gene_ids':
                    dataset.metadata.gene_ids = get_contents(os.path.join(tmp_dir,fname)).split(',')
        except Exception, e:
            log.error('Error setting cummeRbund CuffDataDB metadata : %s' % str(e))