cummerbund: cuffdata.py annotate

annotate cuffdata.py @ 6:137aab1d9ac1

Add metadata to datatype: CuffDataDB

author	Jim Johnson <jj@umn.edu>
date	Mon, 18 Nov 2013 16:43:15 -0600
parents	da7241f92ecf
children	b5562b9a55c7

rev	line source
0 da7241f92ecf Uploaded jjohnson parents: diff changeset	1 """
da7241f92ecf Uploaded jjohnson parents: diff changeset	2 CuffData
da7241f92ecf Uploaded jjohnson parents: diff changeset	3 """
da7241f92ecf Uploaded jjohnson parents: diff changeset	4 import logging
6 137aab1d9ac1 Add metadata to datatype: CuffDataDB Jim Johnson <jj@umn.edu> parents: 0 diff changeset	5 import os,os.path,sys,re
137aab1d9ac1 Add metadata to datatype: CuffDataDB Jim Johnson <jj@umn.edu> parents: 0 diff changeset	6 import tempfile
137aab1d9ac1 Add metadata to datatype: CuffDataDB Jim Johnson <jj@umn.edu> parents: 0 diff changeset	7 from subprocess import Popen
0 da7241f92ecf Uploaded jjohnson parents: diff changeset	8 import galaxy.datatypes.data
da7241f92ecf Uploaded jjohnson parents: diff changeset	9 from galaxy.datatypes.images import Html
da7241f92ecf Uploaded jjohnson parents: diff changeset	10 from galaxy.datatypes.binary import Binary
da7241f92ecf Uploaded jjohnson parents: diff changeset	11 from galaxy import util
da7241f92ecf Uploaded jjohnson parents: diff changeset	12 from galaxy.datatypes.metadata import MetadataElement
da7241f92ecf Uploaded jjohnson parents: diff changeset	13
da7241f92ecf Uploaded jjohnson parents: diff changeset	14 log = logging.getLogger(__name__)
da7241f92ecf Uploaded jjohnson parents: diff changeset	15
da7241f92ecf Uploaded jjohnson parents: diff changeset	16 class CuffDiffData( Html ):
da7241f92ecf Uploaded jjohnson parents: diff changeset	17 """
da7241f92ecf Uploaded jjohnson parents: diff changeset	18 CuffDiff output files:
da7241f92ecf Uploaded jjohnson parents: diff changeset	19 run.info
da7241f92ecf Uploaded jjohnson parents: diff changeset	20 read_groups.info
da7241f92ecf Uploaded jjohnson parents: diff changeset	21 cds.count_tracking
da7241f92ecf Uploaded jjohnson parents: diff changeset	22 cds.diff
da7241f92ecf Uploaded jjohnson parents: diff changeset	23 cds.fpkm_tracking
da7241f92ecf Uploaded jjohnson parents: diff changeset	24 cds.read_group_tracking
da7241f92ecf Uploaded jjohnson parents: diff changeset	25 cds_exp.diff
da7241f92ecf Uploaded jjohnson parents: diff changeset	26 gene_exp.diff
da7241f92ecf Uploaded jjohnson parents: diff changeset	27 genes.count_tracking
da7241f92ecf Uploaded jjohnson parents: diff changeset	28 genes.fpkm_tracking
da7241f92ecf Uploaded jjohnson parents: diff changeset	29 genes.read_group_tracking
da7241f92ecf Uploaded jjohnson parents: diff changeset	30 isoform_exp.diff
da7241f92ecf Uploaded jjohnson parents: diff changeset	31 isoforms.count_tracking
da7241f92ecf Uploaded jjohnson parents: diff changeset	32 isoforms.fpkm_tracking
da7241f92ecf Uploaded jjohnson parents: diff changeset	33 isoforms.read_group_tracking
da7241f92ecf Uploaded jjohnson parents: diff changeset	34 promoters.diff
da7241f92ecf Uploaded jjohnson parents: diff changeset	35 splicing.diff
da7241f92ecf Uploaded jjohnson parents: diff changeset	36 tss_group_exp.diff
da7241f92ecf Uploaded jjohnson parents: diff changeset	37 tss_groups.count_tracking
da7241f92ecf Uploaded jjohnson parents: diff changeset	38 tss_groups.fpkm_tracking
da7241f92ecf Uploaded jjohnson parents: diff changeset	39 tss_groups.read_group_tracking
da7241f92ecf Uploaded jjohnson parents: diff changeset	40 """
da7241f92ecf Uploaded jjohnson parents: diff changeset	41 file_ext = 'cuffdata'
da7241f92ecf Uploaded jjohnson parents: diff changeset	42 is_binary = False
da7241f92ecf Uploaded jjohnson parents: diff changeset	43 composite_type = 'auto_primary_file'
da7241f92ecf Uploaded jjohnson parents: diff changeset	44 allow_datatype_change = False
da7241f92ecf Uploaded jjohnson parents: diff changeset	45 def __init__( self, **kwd ):
da7241f92ecf Uploaded jjohnson parents: diff changeset	46 Html.__init__( self, **kwd )
da7241f92ecf Uploaded jjohnson parents: diff changeset	47 self.add_composite_file('run.info', description = 'run.info', mimetype = 'text/html', optional = True, is_binary = False )
da7241f92ecf Uploaded jjohnson parents: diff changeset	48 self.add_composite_file('read_groups.info', description = 'read_groups.info', mimetype = 'text/html', optional = True, is_binary = False )
da7241f92ecf Uploaded jjohnson parents: diff changeset	49 self.add_composite_file('cds.count_tracking', description = 'cds.count_tracking', mimetype = 'text/html', optional = True, is_binary = False )
da7241f92ecf Uploaded jjohnson parents: diff changeset	50 self.add_composite_file('cds.diff', description = 'cds.diff', mimetype = 'text/html', optional = True, is_binary = False )
da7241f92ecf Uploaded jjohnson parents: diff changeset	51 self.add_composite_file('cds.fpkm_tracking', description = 'cds.fpkm_tracking', mimetype = 'text/html', optional = True, is_binary = False )
da7241f92ecf Uploaded jjohnson parents: diff changeset	52 self.add_composite_file('cds.read_group_tracking', description = 'cds.read_group_tracking', mimetype = 'text/html', optional = True, is_binary = False )
da7241f92ecf Uploaded jjohnson parents: diff changeset	53 self.add_composite_file('cds_exp.diff', description = 'cds_exp.diff', mimetype = 'text/html', optional = True, is_binary = False )
da7241f92ecf Uploaded jjohnson parents: diff changeset	54 self.add_composite_file('gene_exp.diff', description = 'gene_exp.diff', mimetype = 'text/html', optional = True, is_binary = False )
da7241f92ecf Uploaded jjohnson parents: diff changeset	55 self.add_composite_file('genes.count_tracking', description = 'genes.count_tracking', mimetype = 'text/html', optional = True, is_binary = False )
da7241f92ecf Uploaded jjohnson parents: diff changeset	56 self.add_composite_file('genes.fpkm_tracking', description = 'genes.fpkm_tracking', mimetype = 'text/html', optional = True, is_binary = False )
da7241f92ecf Uploaded jjohnson parents: diff changeset	57 self.add_composite_file('genes.read_group_tracking', description = 'genes.read_group_tracking', mimetype = 'text/html', optional = True, is_binary = False )
da7241f92ecf Uploaded jjohnson parents: diff changeset	58 self.add_composite_file('isoform_exp.diff', description = 'isoform_exp.diff', mimetype = 'text/html', optional = True, is_binary = False )
da7241f92ecf Uploaded jjohnson parents: diff changeset	59 self.add_composite_file('isoforms.count_tracking', description = 'isoforms.count_tracking', mimetype = 'text/html', optional = True, is_binary = False )
da7241f92ecf Uploaded jjohnson parents: diff changeset	60 self.add_composite_file('isoforms.fpkm_tracking', description = 'isoforms.fpkm_tracking', mimetype = 'text/html', optional = True, is_binary = False )
da7241f92ecf Uploaded jjohnson parents: diff changeset	61 self.add_composite_file('isoforms.read_group_tracking', description = 'isoforms.read_group_tracking', mimetype = 'text/html', optional = True, is_binary = False )
da7241f92ecf Uploaded jjohnson parents: diff changeset	62 self.add_composite_file('promoters.diff', description = 'promoters.diff', mimetype = 'text/html', optional = True, is_binary = False )
da7241f92ecf Uploaded jjohnson parents: diff changeset	63 self.add_composite_file('splicing.diff', description = 'splicing.diff', mimetype = 'text/html', optional = True, is_binary = False )
da7241f92ecf Uploaded jjohnson parents: diff changeset	64 self.add_composite_file('tss_group_exp.diff', description = 'tss_group_exp.diff', mimetype = 'text/html', optional = True, is_binary = False )
da7241f92ecf Uploaded jjohnson parents: diff changeset	65 self.add_composite_file('tss_groups.count_tracking', description = 'tss_groups.count_tracking', mimetype = 'text/html', optional = True, is_binary = False )
da7241f92ecf Uploaded jjohnson parents: diff changeset	66 self.add_composite_file('tss_groups.fpkm_tracking', description = 'tss_groups.fpkm_tracking', mimetype = 'text/html', optional = True, is_binary = False )
da7241f92ecf Uploaded jjohnson parents: diff changeset	67 self.add_composite_file('tss_groups.read_group_tracking', description = 'tss_groups.read_group_tracking', mimetype = 'text/html', optional = True, is_binary = False )
da7241f92ecf Uploaded jjohnson parents: diff changeset	68
da7241f92ecf Uploaded jjohnson parents: diff changeset	69 def generate_primary_file( self, dataset = None ):
da7241f92ecf Uploaded jjohnson parents: diff changeset	70 """
da7241f92ecf Uploaded jjohnson parents: diff changeset	71 This is called only at upload to write the html file
da7241f92ecf Uploaded jjohnson parents: diff changeset	72 cannot rename the datasets here - they come with the default unfortunately
da7241f92ecf Uploaded jjohnson parents: diff changeset	73 """
da7241f92ecf Uploaded jjohnson parents: diff changeset	74 rval = ['<html><head><title>CuffDiff Output</title></head>']
da7241f92ecf Uploaded jjohnson parents: diff changeset	75 rval.append('<body>')
da7241f92ecf Uploaded jjohnson parents: diff changeset	76 rval.append('<p/>CuffDiff Outputs:<p/><ul>')
da7241f92ecf Uploaded jjohnson parents: diff changeset	77 for composite_name, composite_file in self.get_composite_files( dataset = dataset ).iteritems():
da7241f92ecf Uploaded jjohnson parents: diff changeset	78 fn = composite_name
da7241f92ecf Uploaded jjohnson parents: diff changeset	79 log.debug( "Velvet log info %s %s %s" % ('JJ generate_primary_file',fn,composite_file))
da7241f92ecf Uploaded jjohnson parents: diff changeset	80 opt_text = ''
da7241f92ecf Uploaded jjohnson parents: diff changeset	81 if composite_file.optional:
da7241f92ecf Uploaded jjohnson parents: diff changeset	82 opt_text = ' (optional)'
da7241f92ecf Uploaded jjohnson parents: diff changeset	83 if composite_file.get('description'):
da7241f92ecf Uploaded jjohnson parents: diff changeset	84 rval.append( '<li><a href="%s" type="text/plain">%s (%s)</a>%s</li>' % ( fn, fn, composite_file.get('description'), opt_text ) )
da7241f92ecf Uploaded jjohnson parents: diff changeset	85 else:
da7241f92ecf Uploaded jjohnson parents: diff changeset	86 rval.append( '<li><a href="%s" type="text/plain">%s</a>%s</li>' % ( fn, fn, opt_text ) )
da7241f92ecf Uploaded jjohnson parents: diff changeset	87 rval.append( '</ul></body></html>' )
da7241f92ecf Uploaded jjohnson parents: diff changeset	88 return "\n".join( rval )
da7241f92ecf Uploaded jjohnson parents: diff changeset	89
da7241f92ecf Uploaded jjohnson parents: diff changeset	90 def regenerate_primary_file(self,dataset):
da7241f92ecf Uploaded jjohnson parents: diff changeset	91 """
da7241f92ecf Uploaded jjohnson parents: diff changeset	92 cannot do this until we are setting metadata
da7241f92ecf Uploaded jjohnson parents: diff changeset	93 """
da7241f92ecf Uploaded jjohnson parents: diff changeset	94 flist = os.listdir(dataset.extra_files_path)
da7241f92ecf Uploaded jjohnson parents: diff changeset	95 rval = ['<html><head><title>CuffDiff Output</title></head>']
da7241f92ecf Uploaded jjohnson parents: diff changeset	96 rval.append('<body>')
da7241f92ecf Uploaded jjohnson parents: diff changeset	97 rval.append('<p/>CuffDiff Outputs:<p/><ul>')
da7241f92ecf Uploaded jjohnson parents: diff changeset	98 for i,fname in enumerate(flist):
da7241f92ecf Uploaded jjohnson parents: diff changeset	99 sfname = os.path.split(fname)[-1]
da7241f92ecf Uploaded jjohnson parents: diff changeset	100 rval.append( '<li><a href="%s" type="text/html">%s</a>' % ( sfname, sfname ) )
da7241f92ecf Uploaded jjohnson parents: diff changeset	101 rval.append( '</ul></body></html>' )
da7241f92ecf Uploaded jjohnson parents: diff changeset	102 f = file(dataset.file_name,'w')
da7241f92ecf Uploaded jjohnson parents: diff changeset	103 f.write("\n".join( rval ))
da7241f92ecf Uploaded jjohnson parents: diff changeset	104 f.write('\n')
da7241f92ecf Uploaded jjohnson parents: diff changeset	105 f.close()
da7241f92ecf Uploaded jjohnson parents: diff changeset	106
da7241f92ecf Uploaded jjohnson parents: diff changeset	107 def set_meta( self, dataset, **kwd ):
da7241f92ecf Uploaded jjohnson parents: diff changeset	108 Html.set_meta( self, dataset, **kwd )
da7241f92ecf Uploaded jjohnson parents: diff changeset	109 self.regenerate_primary_file(dataset)
da7241f92ecf Uploaded jjohnson parents: diff changeset	110
da7241f92ecf Uploaded jjohnson parents: diff changeset	111 def sniff( self, filename ):
da7241f92ecf Uploaded jjohnson parents: diff changeset	112 return False
da7241f92ecf Uploaded jjohnson parents: diff changeset	113
da7241f92ecf Uploaded jjohnson parents: diff changeset	114 class CuffDataDB( Binary ):
6 137aab1d9ac1 Add metadata to datatype: CuffDataDB Jim Johnson <jj@umn.edu> parents: 0 diff changeset	115 file_ext = 'cuffdatadb'
0 da7241f92ecf Uploaded jjohnson parents: diff changeset	116 is_binary = True
da7241f92ecf Uploaded jjohnson parents: diff changeset	117 allow_datatype_change = False
6 137aab1d9ac1 Add metadata to datatype: CuffDataDB Jim Johnson <jj@umn.edu> parents: 0 diff changeset	118 MetadataElement( name="sample_names", default=[], desc="Sample names", readonly=True, visible=True, optional=True, no_value=[] )
137aab1d9ac1 Add metadata to datatype: CuffDataDB Jim Johnson <jj@umn.edu> parents: 0 diff changeset	119 MetadataElement( name="replicate_names", default=[], desc="Replicate names", readonly=True, visible=True, optional=True, no_value=[] )
137aab1d9ac1 Add metadata to datatype: CuffDataDB Jim Johnson <jj@umn.edu> parents: 0 diff changeset	120 MetadataElement( name="gene_ids", default=[], desc="Gene Ids", readonly=True, visible=True, optional=True, no_value=[] )
137aab1d9ac1 Add metadata to datatype: CuffDataDB Jim Johnson <jj@umn.edu> parents: 0 diff changeset	121
137aab1d9ac1 Add metadata to datatype: CuffDataDB Jim Johnson <jj@umn.edu> parents: 0 diff changeset	122 def __init__( self, **kwd ):
137aab1d9ac1 Add metadata to datatype: CuffDataDB Jim Johnson <jj@umn.edu> parents: 0 diff changeset	123 Binary.__init__( self, **kwd )
137aab1d9ac1 Add metadata to datatype: CuffDataDB Jim Johnson <jj@umn.edu> parents: 0 diff changeset	124 log.info('Creating cummeRbund CuffDataDB')
137aab1d9ac1 Add metadata to datatype: CuffDataDB Jim Johnson <jj@umn.edu> parents: 0 diff changeset	125
137aab1d9ac1 Add metadata to datatype: CuffDataDB Jim Johnson <jj@umn.edu> parents: 0 diff changeset	126 def set_meta( self, dataset, **kwd ):
137aab1d9ac1 Add metadata to datatype: CuffDataDB Jim Johnson <jj@umn.edu> parents: 0 diff changeset	127 def get_contents(fname):
137aab1d9ac1 Add metadata to datatype: CuffDataDB Jim Johnson <jj@umn.edu> parents: 0 diff changeset	128 contents = ''
137aab1d9ac1 Add metadata to datatype: CuffDataDB Jim Johnson <jj@umn.edu> parents: 0 diff changeset	129 with open(fname,'r') as fh:
137aab1d9ac1 Add metadata to datatype: CuffDataDB Jim Johnson <jj@umn.edu> parents: 0 diff changeset	130 contents = fh.read()
137aab1d9ac1 Add metadata to datatype: CuffDataDB Jim Johnson <jj@umn.edu> parents: 0 diff changeset	131 return contents
137aab1d9ac1 Add metadata to datatype: CuffDataDB Jim Johnson <jj@umn.edu> parents: 0 diff changeset	132 if not dataset.has_data():
137aab1d9ac1 Add metadata to datatype: CuffDataDB Jim Johnson <jj@umn.edu> parents: 0 diff changeset	133 return
137aab1d9ac1 Add metadata to datatype: CuffDataDB Jim Johnson <jj@umn.edu> parents: 0 diff changeset	134 try:
137aab1d9ac1 Add metadata to datatype: CuffDataDB Jim Johnson <jj@umn.edu> parents: 0 diff changeset	135 ## Create a tmpdir
137aab1d9ac1 Add metadata to datatype: CuffDataDB Jim Johnson <jj@umn.edu> parents: 0 diff changeset	136 ## create an Rscript to write out info about the CuffData, e.g. samples replicates gene_ids
137aab1d9ac1 Add metadata to datatype: CuffDataDB Jim Johnson <jj@umn.edu> parents: 0 diff changeset	137 ## define file names to use as sinks for each type of data
137aab1d9ac1 Add metadata to datatype: CuffDataDB Jim Johnson <jj@umn.edu> parents: 0 diff changeset	138 # tmp_dir = tempfile.mkdtemp()
137aab1d9ac1 Add metadata to datatype: CuffDataDB Jim Johnson <jj@umn.edu> parents: 0 diff changeset	139 tmp_dir = '/tmp/gx/cuffdb'
137aab1d9ac1 Add metadata to datatype: CuffDataDB Jim Johnson <jj@umn.edu> parents: 0 diff changeset	140 if not os.path.isdir(tmp_dir):
137aab1d9ac1 Add metadata to datatype: CuffDataDB Jim Johnson <jj@umn.edu> parents: 0 diff changeset	141 os.makedirs(tmp_dir)
137aab1d9ac1 Add metadata to datatype: CuffDataDB Jim Johnson <jj@umn.edu> parents: 0 diff changeset	142 rscript = tempfile.NamedTemporaryFile( dir=tmp_dir,suffix='.r' ).name
137aab1d9ac1 Add metadata to datatype: CuffDataDB Jim Johnson <jj@umn.edu> parents: 0 diff changeset	143 rscript_fh = open( rscript, 'wb' )
137aab1d9ac1 Add metadata to datatype: CuffDataDB Jim Johnson <jj@umn.edu> parents: 0 diff changeset	144 rscript_fh.write('library(cummeRbund)\n')
137aab1d9ac1 Add metadata to datatype: CuffDataDB Jim Johnson <jj@umn.edu> parents: 0 diff changeset	145 rscript_fh.write('cuff<-readCufflinks(dir = "", dbFile = "%s", rebuild = F)\n' % (dataset.file_name))
137aab1d9ac1 Add metadata to datatype: CuffDataDB Jim Johnson <jj@umn.edu> parents: 0 diff changeset	146 rscript_fh.write('sink("%s")\n' % ("out.blurb"))
137aab1d9ac1 Add metadata to datatype: CuffDataDB Jim Johnson <jj@umn.edu> parents: 0 diff changeset	147 rscript_fh.write('print(cuff)\n')
137aab1d9ac1 Add metadata to datatype: CuffDataDB Jim Johnson <jj@umn.edu> parents: 0 diff changeset	148 rscript_fh.write('sink()\n')
137aab1d9ac1 Add metadata to datatype: CuffDataDB Jim Johnson <jj@umn.edu> parents: 0 diff changeset	149 rscript_fh.write('sink("%s")\n' % ("out.samples"))
137aab1d9ac1 Add metadata to datatype: CuffDataDB Jim Johnson <jj@umn.edu> parents: 0 diff changeset	150 rscript_fh.write('cat(samples(cuff)[[2]],sep=",")\n')
137aab1d9ac1 Add metadata to datatype: CuffDataDB Jim Johnson <jj@umn.edu> parents: 0 diff changeset	151 rscript_fh.write('sink()\n')
137aab1d9ac1 Add metadata to datatype: CuffDataDB Jim Johnson <jj@umn.edu> parents: 0 diff changeset	152 rscript_fh.write('sink("%s")\n' % ("out.replicates"))
137aab1d9ac1 Add metadata to datatype: CuffDataDB Jim Johnson <jj@umn.edu> parents: 0 diff changeset	153 rscript_fh.write('cat(replicates(cuff)[[4]],sep=",")\n')
137aab1d9ac1 Add metadata to datatype: CuffDataDB Jim Johnson <jj@umn.edu> parents: 0 diff changeset	154 rscript_fh.write('sink()\n')
137aab1d9ac1 Add metadata to datatype: CuffDataDB Jim Johnson <jj@umn.edu> parents: 0 diff changeset	155 rscript_fh.write('sink("%s")\n' % ("out.gene_ids"))
137aab1d9ac1 Add metadata to datatype: CuffDataDB Jim Johnson <jj@umn.edu> parents: 0 diff changeset	156 rscript_fh.write('cat(annotation(genes(cuff))[[1]],sep=",")\n')
137aab1d9ac1 Add metadata to datatype: CuffDataDB Jim Johnson <jj@umn.edu> parents: 0 diff changeset	157 rscript_fh.write('sink()\n')
137aab1d9ac1 Add metadata to datatype: CuffDataDB Jim Johnson <jj@umn.edu> parents: 0 diff changeset	158 rscript_fh.close()
137aab1d9ac1 Add metadata to datatype: CuffDataDB Jim Johnson <jj@umn.edu> parents: 0 diff changeset	159 cmd = ( "Rscript --vanilla %s" % rscript )
137aab1d9ac1 Add metadata to datatype: CuffDataDB Jim Johnson <jj@umn.edu> parents: 0 diff changeset	160 tmp_stderr_name = tempfile.NamedTemporaryFile( dir=tmp_dir,suffix='.err' ).name
137aab1d9ac1 Add metadata to datatype: CuffDataDB Jim Johnson <jj@umn.edu> parents: 0 diff changeset	161 tmp_stderr = open( tmp_stderr_name, 'wb' )
137aab1d9ac1 Add metadata to datatype: CuffDataDB Jim Johnson <jj@umn.edu> parents: 0 diff changeset	162 proc = Popen( args=cmd, shell=True, cwd=tmp_dir, stderr=tmp_stderr.fileno() )
137aab1d9ac1 Add metadata to datatype: CuffDataDB Jim Johnson <jj@umn.edu> parents: 0 diff changeset	163 returncode = proc.wait()
137aab1d9ac1 Add metadata to datatype: CuffDataDB Jim Johnson <jj@umn.edu> parents: 0 diff changeset	164 tmp_stderr.close()
137aab1d9ac1 Add metadata to datatype: CuffDataDB Jim Johnson <jj@umn.edu> parents: 0 diff changeset	165 flist = os.listdir(tmp_dir)
137aab1d9ac1 Add metadata to datatype: CuffDataDB Jim Johnson <jj@umn.edu> parents: 0 diff changeset	166 for i,fname in enumerate(flist):
137aab1d9ac1 Add metadata to datatype: CuffDataDB Jim Johnson <jj@umn.edu> parents: 0 diff changeset	167 sfname = os.path.split(fname)[-1]
137aab1d9ac1 Add metadata to datatype: CuffDataDB Jim Johnson <jj@umn.edu> parents: 0 diff changeset	168 if sfname == 'out.blurb':
137aab1d9ac1 Add metadata to datatype: CuffDataDB Jim Johnson <jj@umn.edu> parents: 0 diff changeset	169 dataset.blurb = get_contents(os.path.join(tmp_dir,fname))
137aab1d9ac1 Add metadata to datatype: CuffDataDB Jim Johnson <jj@umn.edu> parents: 0 diff changeset	170 elif sfname == 'out.samples':
137aab1d9ac1 Add metadata to datatype: CuffDataDB Jim Johnson <jj@umn.edu> parents: 0 diff changeset	171 dataset.metadata.sample_names = get_contents(os.path.join(tmp_dir,fname)).split(',')
137aab1d9ac1 Add metadata to datatype: CuffDataDB Jim Johnson <jj@umn.edu> parents: 0 diff changeset	172 elif sfname == 'out.replicates':
137aab1d9ac1 Add metadata to datatype: CuffDataDB Jim Johnson <jj@umn.edu> parents: 0 diff changeset	173 dataset.metadata.replicate_names = get_contents(os.path.join(tmp_dir,fname)).split(',')
137aab1d9ac1 Add metadata to datatype: CuffDataDB Jim Johnson <jj@umn.edu> parents: 0 diff changeset	174 elif sfname == 'out.gene_ids':
137aab1d9ac1 Add metadata to datatype: CuffDataDB Jim Johnson <jj@umn.edu> parents: 0 diff changeset	175 dataset.metadata.gene_ids = get_contents(os.path.join(tmp_dir,fname)).split(',')
137aab1d9ac1 Add metadata to datatype: CuffDataDB Jim Johnson <jj@umn.edu> parents: 0 diff changeset	176 except Exception, e:
137aab1d9ac1 Add metadata to datatype: CuffDataDB Jim Johnson <jj@umn.edu> parents: 0 diff changeset	177 log.error('Error setting cummeRbund CuffDataDB metadata : %s' % str(e))
137aab1d9ac1 Add metadata to datatype: CuffDataDB Jim Johnson <jj@umn.edu> parents: 0 diff changeset	178

Mercurial > repos > jjohnson > cummerbund

annotate cuffdata.py @ 6:137aab1d9ac1