def set_meta( self, dataset, **kwd ):
"""
for lped/pbed eg
"""
Html.set_meta( self, dataset, **kwd )
if kwd.get('overwrite') == False:
return True
try:
efp = dataset.extra_files_path
except:
return False
try:
flist = os.listdir(efp)
except:
return False
if len(flist) == 0:
return False
self.regenerate_primary_file(dataset)
if not dataset.info:
dataset.info = 'Galaxy Impute2 datatype object'
if not dataset.blurb:
dataset.blurb = 'Composite file - Otago Impute2 Galaxy toolkit'
return True
def set_meta( self, dataset, **kwd ):
"""
for lped/pbed eg
"""
Html.set_meta( self, dataset, **kwd )
if kwd.get('overwrite') == False:
if verbose:
gal_Log.debug('@@@ rgenetics set_meta called with overwrite = False')
return True
try:
efp = dataset.extra_files_path
except:
if verbose:
gal_Log.debug('@@@rgenetics 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('@@@rgenetics 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('@@@rgenetics 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 genotype datatype object'
if not dataset.blurb:
dataset.blurb = 'Composite file - Rgenetics Galaxy toolkit'
return True
def set_meta( self, dataset, **kwd ):
"""
for lped/pbed eg
"""
Html.set_meta( self, dataset, **kwd )
if kwd.get('overwrite') == False:
if verbose:
gal_Log.debug('@@@ rgenetics set_meta called with overwrite = False')
return True
try:
efp = dataset.extra_files_path
except:
if verbose:
gal_Log.debug('@@@rgenetics 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('@@@rgenetics 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('@@@rgenetics 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 genotype datatype object'
if not dataset.blurb:
dataset.blurb = 'Composite file - Rgenetics Galaxy toolkit'
return True
def set_meta(self, dataset, **kwd):
Html.set_meta(self, dataset, **kwd)
efp = dataset.extra_files_path
flist = os.listdir(efp)
for i, fname in enumerate(flist):
if fname.endswith('.grp'):
dataset.metadata.reference_name = fname[:-4]
break
self.regenerate_primary_file(dataset)
def __init__(self, **kwd):
Html.__init__(self, **kwd)
self.add_composite_file('%s.ped',
description='Pedigree File',
substitute_name_with_metadata='base_name',
is_binary=False)
self.add_composite_file('%s.map',
description='Map File',
substitute_name_with_metadata='base_name',
is_binary=False)
def __init__(self, **kwd):
Html.__init__( self, **kwd )
#self.add_composite_file('tagInfo.txt', description = 'basic configuration information', mimetype = 'text/html') # Contains basic configuration information
self.add_composite_file('tagLengthDistribution.txt', description = 'histogram of read lengths used for alignment', mimetype = 'text/html') # File contains a histogram of read lengths used for alignment.
self.add_composite_file('tagCountDistribution.txt', description = 'histogram of clonal read depth, showing the number of reads per unique position', mimetype = 'text/html') # File contains a histogram of clonal read depth, showing the number of reads per unique position.
self.add_composite_file('tagAutocorrelation.txt', description = 'distribution of distances between adjacent reads in the genome', mimetype = 'text/html') # The autocorrelation routine creates a distribution of distances between adjacent reads in the genome.
self.add_composite_file('tagFreq.txt', description = "nucleotide and dinucleotide frequencies as a function of distance from the 5' end of all reads", mimetype = 'text/html', optional=True) # Calculates the nucleotide and dinucleotide frequencies as a function of distance from the 5' end of all reads.
self.add_composite_file('tagFreqUniq.txt', description = "nucleotide and dinucleotide frequencies as a function of distance from the 5' end of all reads (counted only once)", mimetype = 'text/html', optional=True) # Same as tagFreq.txt, however individual genomic positions are only counted once.
self.add_composite_file('tagGCcontent.txt', description = 'Distribution of fragment GC%-content', mimetype = 'text/html', optional=True) # Distribution of fragment GC%-content.
self.add_composite_file('genomeGCcontent.txt', description = 'Distribution of fragment GC%-content at each location in the genome', mimetype = 'text/html', optional=True) # Distribution of fragment GC%-content at each location in the genome.
def __init__(self, **kwd):
Html.__init__(self, **kwd)
log.debug("######### FUSION INSPECTOR DATA ############\n\n\n")
#sys.exit(1)
self.add_composite_file('FInspector.fusion_predictions.txt',
description='fusion predictions',
is_binary=False)
self.add_composite_file('FInspector.fa',
description='fusion contigs',
mimetype='text/html',
is_binary=False)
self.add_composite_file('FInspector.fa.fai',
description='fusion contigs index',
is_binary=False)
self.add_composite_file("FInspector.fusion_predictions.txt",
description="fusion predictions summary",
is_binary=False)
self.add_composite_file("FInspector.igv.FusionJuncSpan",
description="fusion support for IGV viewing",
is_binary=False)
self.add_composite_file("FInspector.consolidated.cSorted.bam",
description="all fusion-supporting reads",
is_binary=True)
self.add_composite_file("FInspector.consolidated.cSorted.bam.bai",
description="bam index",
is_binary=True)
self.add_composite_file(
"FInspector.junction_reads.bam.bed.sorted.bed.gz",
description="junction reads in bed.gz format",
is_binary=True)
self.add_composite_file(
"FInspector.junction_reads.bam.bed.sorted.bed.gz.tbi",
description="tabix index for junction reads bed.gz",
is_binary=True)
self.add_composite_file(
"FInspector.spanning_reads.bam.bed.sorted.bed.gz",
description="spanning reads in bed.gz format",
is_binary=True)
self.add_composite_file(
"FInspector.spanning_reads.bam.bed.sorted.bed.gz.tbi",
description="tabix index for spanning reads bed.gz",
is_binary=True)
self.add_composite_file(
"FInspector.gmap_trinity_GG.fusions.gff3.bed.sorted.bed.gz",
description="Trinity fusion transcript structures",
is_binary=True)
self.add_composite_file(
"FInspector.gmap_trinity_GG.fusions.gff3.bed.sorted.bed.gz.tbi",
description=
"tabix index for trinity fusion transcript structures in bed.gz",
is_binary=True)
def set_meta(self, dataset, **kwd):
"""
NOTE we apply the tabular machinary to the phenodata extracted
from a BioC eSet or affybatch.
"""
Html.set_meta(self, dataset, **kwd)
try:
flist = os.listdir(dataset.extra_files_path)
except:
if verbose:
gal_Log.debug('@@@rexpression set_meta failed - no dataset?')
return False
bn = dataset.metadata.base_name
if not bn:
for f in flist:
n = os.path.splitext(f)[0]
bn = n
dataset.metadata.base_name = bn
if not bn:
bn = '?'
dataset.metadata.base_name = bn
pn = '%s.pheno' % (bn)
pp = os.path.join(dataset.extra_files_path, pn)
dataset.metadata.pheno_path = pp
try:
pf = file(pp, 'r').readlines(
) # read the basename.phenodata in the extra_files_path
except:
pf = None
if pf:
h = pf[0].strip()
h = h.split('\t') # hope is header
h = [escape(x) for x in h]
dataset.metadata.column_names = h
dataset.metadata.columns = len(h)
dataset.peek = ''.join(pf[:5])
else:
dataset.metadata.column_names = []
dataset.metadata.columns = 0
dataset.peek = 'No pheno file found'
if pf and len(pf) > 1:
dataset.metadata.pheCols = self.get_phecols(phenolist=pf)
else:
dataset.metadata.pheCols = [
('', 'No useable phenotypes found', False),
]
#self.regenerate_primary_file(dataset)
if not dataset.info:
dataset.info = 'Galaxy Expression datatype object'
if not dataset.blurb:
dataset.blurb = 'R loadable BioC expression object for the Rexpression Galaxy toolkit'
return True
def set_meta( self, dataset, **kwd ):
"""
NOTE we apply the tabular machinary to the phenodata extracted
from a BioC eSet or affybatch.
"""
Html.set_meta(self, dataset, **kwd)
try:
flist = os.listdir(dataset.extra_files_path)
except:
if verbose:
gal_Log.debug('@@@rexpression set_meta failed - no dataset?')
return False
bn = dataset.metadata.base_name
if not bn:
for f in flist:
n = os.path.splitext(f)[0]
bn = n
dataset.metadata.base_name = bn
if not bn:
bn = '?'
dataset.metadata.base_name = bn
pn = '%s.pheno' % (bn)
pp = os.path.join(dataset.extra_files_path,pn)
dataset.metadata.pheno_path=pp
try:
pf = file(pp,'r').readlines() # read the basename.phenodata in the extra_files_path
except:
pf = None
if pf:
h = pf[0].strip()
h = h.split('\t') # hope is header
h = [escape(x) for x in h]
dataset.metadata.column_names = h
dataset.metadata.columns = len(h)
dataset.peek = ''.join(pf[:5])
else:
dataset.metadata.column_names = []
dataset.metadata.columns = 0
dataset.peek = 'No pheno file found'
if pf and len(pf) > 1:
dataset.metadata.pheCols = self.get_phecols(phenolist=pf)
else:
dataset.metadata.pheCols = [('','No useable phenotypes found',False),]
#self.regenerate_primary_file(dataset)
if not dataset.info:
dataset.info = 'Galaxy Expression datatype object'
if not dataset.blurb:
dataset.blurb = 'R loadable BioC expression object for the Rexpression Galaxy toolkit'
return True
def __init__(self, **kwd):
Html.__init__(self, **kwd)
self.add_composite_file('Sequences',
mimetype='text/html',
description='Sequences',
substitute_name_with_metadata=None,
is_binary=False)
self.add_composite_file('Roadmaps',
mimetype='text/html',
description='Roadmaps',
substitute_name_with_metadata=None,
is_binary=False)
self.add_composite_file('Log',
mimetype='text/html',
description='Log',
optional='True',
substitute_name_with_metadata=None,
is_binary=False)
def __init__( self, **kwd ):
Html.__init__( self, **kwd )
log.debug("######### FUSION INSPECTOR DATA ############\n\n\n")
#sys.exit(1)
self.add_composite_file('FInspector.fusion_predictions.txt', description = 'fusion predictions', is_binary = False )
self.add_composite_file('FInspector.fa', description = 'fusion contigs', mimetype = 'text/html', is_binary = False )
self.add_composite_file('FInspector.fa.fai', description = 'fusion contigs index', is_binary = False )
self.add_composite_file("FInspector.fusion_predictions.txt", description="fusion predictions summary", is_binary=False)
self.add_composite_file("FInspector.igv.FusionJuncSpan", description="fusion support for IGV viewing", is_binary=False)
self.add_composite_file("FInspector.consolidated.cSorted.bam", description="all fusion-supporting reads", is_binary=True)
self.add_composite_file("FInspector.consolidated.cSorted.bam.bai", description="bam index", is_binary=True)
self.add_composite_file("FInspector.junction_reads.bam.bed.sorted.bed.gz", description="junction reads in bed.gz format", is_binary=True)
self.add_composite_file("FInspector.junction_reads.bam.bed.sorted.bed.gz.tbi", description="tabix index for junction reads bed.gz", is_binary=True)
self.add_composite_file("FInspector.spanning_reads.bam.bed.sorted.bed.gz", description="spanning reads in bed.gz format", is_binary=True)
self.add_composite_file("FInspector.spanning_reads.bam.bed.sorted.bed.gz.tbi", description="tabix index for spanning reads bed.gz", is_binary=True)
self.add_composite_file("FInspector.gmap_trinity_GG.fusions.gff3.bed.sorted.bed.gz", description="Trinity fusion transcript structures", is_binary=True)
self.add_composite_file("FInspector.gmap_trinity_GG.fusions.gff3.bed.sorted.bed.gz.tbi", description="tabix index for trinity fusion transcript structures in bed.gz", is_binary=True)
def __init__( self, **kwd ):
Html.__init__( self, **kwd )
self.add_composite_file('run.info', description = 'run.info', mimetype = 'text/html', optional = True, is_binary = False )
self.add_composite_file('read_groups.info', description = 'read_groups.info', mimetype = 'text/html', optional = True, is_binary = False )
self.add_composite_file('cds.count_tracking', description = 'cds.count_tracking', mimetype = 'text/html', optional = True, is_binary = False )
self.add_composite_file('cds.diff', description = 'cds.diff', mimetype = 'text/html', optional = True, is_binary = False )
self.add_composite_file('cds.fpkm_tracking', description = 'cds.fpkm_tracking', mimetype = 'text/html', optional = True, is_binary = False )
self.add_composite_file('cds.read_group_tracking', description = 'cds.read_group_tracking', mimetype = 'text/html', optional = True, is_binary = False )
self.add_composite_file('cds_exp.diff', description = 'cds_exp.diff', mimetype = 'text/html', optional = True, is_binary = False )
self.add_composite_file('gene_exp.diff', description = 'gene_exp.diff', mimetype = 'text/html', optional = True, is_binary = False )
self.add_composite_file('genes.count_tracking', description = 'genes.count_tracking', mimetype = 'text/html', optional = True, is_binary = False )
self.add_composite_file('genes.fpkm_tracking', description = 'genes.fpkm_tracking', mimetype = 'text/html', optional = True, is_binary = False )
self.add_composite_file('genes.read_group_tracking', description = 'genes.read_group_tracking', mimetype = 'text/html', optional = True, is_binary = False )
self.add_composite_file('isoform_exp.diff', description = 'isoform_exp.diff', mimetype = 'text/html', optional = True, is_binary = False )
self.add_composite_file('isoforms.count_tracking', description = 'isoforms.count_tracking', mimetype = 'text/html', optional = True, is_binary = False )
self.add_composite_file('isoforms.fpkm_tracking', description = 'isoforms.fpkm_tracking', mimetype = 'text/html', optional = True, is_binary = False )
self.add_composite_file('isoforms.read_group_tracking', description = 'isoforms.read_group_tracking', mimetype = 'text/html', optional = True, is_binary = False )
self.add_composite_file('promoters.diff', description = 'promoters.diff', mimetype = 'text/html', optional = True, is_binary = False )
self.add_composite_file('splicing.diff', description = 'splicing.diff', mimetype = 'text/html', optional = True, is_binary = False )
self.add_composite_file('tss_group_exp.diff', description = 'tss_group_exp.diff', mimetype = 'text/html', optional = True, is_binary = False )
self.add_composite_file('tss_groups.count_tracking', description = 'tss_groups.count_tracking', mimetype = 'text/html', optional = True, is_binary = False )
self.add_composite_file('tss_groups.fpkm_tracking', description = 'tss_groups.fpkm_tracking', mimetype = 'text/html', optional = True, is_binary = False )
self.add_composite_file('tss_groups.read_group_tracking', description = 'tss_groups.read_group_tracking', mimetype = 'text/html', optional = True, is_binary = False )
def __init__(self, **kwd):
Html.__init__(self, **kwd)
self.add_composite_file(
"Sequences",
mimetype="text/html",
description="Sequences",
substitute_name_with_metadata=None,
is_binary=False,
)
self.add_composite_file(
"Roadmaps",
mimetype="text/html",
description="Roadmaps",
substitute_name_with_metadata=None,
is_binary=False,
)
self.add_composite_file(
"Log",
mimetype="text/html",
description="Log",
optional="True",
substitute_name_with_metadata=None,
is_binary=False,
)
def __init__( self, **kwd ):
Html.__init__( self, **kwd )
self.add_composite_file( 'Sequences', mimetype='text/html', description='Sequences', substitute_name_with_metadata=None, is_binary=False )
self.add_composite_file( 'Roadmaps', mimetype='text/html', description='Roadmaps', substitute_name_with_metadata=None, is_binary=False )
self.add_composite_file( 'Log', mimetype='text/html', description='Log', optional='True', substitute_name_with_metadata=None, is_binary=False )
def __init__( self, **kwd ):
Html.__init__(self,**kwd)
self.add_composite_file( '%s.pheno', description = 'Phenodata tab text file',
substitute_name_with_metadata = 'base_name', is_binary=False)
def __init__(self, **kwd):
Html.__init__(self, **kwd)
self.add_composite_file('run.info',
description='run.info',
mimetype='text/html',
optional=True,
is_binary=False)
self.add_composite_file('read_groups.info',
description='read_groups.info',
mimetype='text/html',
optional=True,
is_binary=False)
self.add_composite_file('cds.count_tracking',
description='cds.count_tracking',
mimetype='text/html',
optional=True,
is_binary=False)
self.add_composite_file('cds.diff',
description='cds.diff',
mimetype='text/html',
optional=True,
is_binary=False)
self.add_composite_file('cds.fpkm_tracking',
description='cds.fpkm_tracking',
mimetype='text/html',
optional=True,
is_binary=False)
self.add_composite_file('cds.read_group_tracking',
description='cds.read_group_tracking',
mimetype='text/html',
optional=True,
is_binary=False)
self.add_composite_file('cds_exp.diff',
description='cds_exp.diff',
mimetype='text/html',
optional=True,
is_binary=False)
self.add_composite_file('gene_exp.diff',
description='gene_exp.diff',
mimetype='text/html',
optional=True,
is_binary=False)
self.add_composite_file('genes.count_tracking',
description='genes.count_tracking',
mimetype='text/html',
optional=True,
is_binary=False)
self.add_composite_file('genes.fpkm_tracking',
description='genes.fpkm_tracking',
mimetype='text/html',
optional=True,
is_binary=False)
self.add_composite_file('genes.read_group_tracking',
description='genes.read_group_tracking',
mimetype='text/html',
optional=True,
is_binary=False)
self.add_composite_file('isoform_exp.diff',
description='isoform_exp.diff',
mimetype='text/html',
optional=True,
is_binary=False)
self.add_composite_file('isoforms.count_tracking',
description='isoforms.count_tracking',
mimetype='text/html',
optional=True,
is_binary=False)
self.add_composite_file('isoforms.fpkm_tracking',
description='isoforms.fpkm_tracking',
mimetype='text/html',
optional=True,
is_binary=False)
self.add_composite_file('isoforms.read_group_tracking',
description='isoforms.read_group_tracking',
mimetype='text/html',
optional=True,
is_binary=False)
self.add_composite_file('promoters.diff',
description='promoters.diff',
mimetype='text/html',
optional=True,
is_binary=False)
self.add_composite_file('splicing.diff',
description='splicing.diff',
mimetype='text/html',
optional=True,
is_binary=False)
self.add_composite_file('tss_group_exp.diff',
description='tss_group_exp.diff',
mimetype='text/html',
optional=True,
is_binary=False)
self.add_composite_file('tss_groups.count_tracking',
description='tss_groups.count_tracking',
mimetype='text/html',
optional=True,
is_binary=False)
self.add_composite_file('tss_groups.fpkm_tracking',
description='tss_groups.fpkm_tracking',
mimetype='text/html',
optional=True,
is_binary=False)
self.add_composite_file('tss_groups.read_group_tracking',
description='tss_groups.read_group_tracking',
mimetype='text/html',
optional=True,
is_binary=False)
def set_meta( self, dataset, **kwd ):
log.debug("## set_meta for FusionInspector ")
Html.set_meta( self, dataset, **kwd )
self.regenerate_primary_file(dataset)
def set_meta( self, dataset, **kwd ):
Html.set_meta( self, dataset, **kwd )
self.regenerate_primary_file(dataset)
def __init__(self, **kwd):
Html.__init__(self, **kwd)
def __init__( self, **kwd ):
Html.__init__( self, **kwd )
self.add_composite_file( '%s.ped', description = 'Pedigree File', substitute_name_with_metadata = 'base_name', is_binary = False )
self.add_composite_file( '%s.map', description = 'Map File', substitute_name_with_metadata = 'base_name', is_binary = False )
def __init__(self, **kwd):
Html.__init__(self, **kwd)
"""
Expecting files:
extra_files_path/<reference_name>.grp
extra_files_path/<reference_name>.ti
extra_files_path/<reference_name>.seq
extra_files_path/<reference_name>.transcripts.fa
Optionally includes files:
extra_files_path/<reference_name>.chrlist
extra_files_path/<reference_name>.idx.fa
extra_files_path/<reference_name>.1.ebwt
extra_files_path/<reference_name>.2.ebwt
extra_files_path/<reference_name>.3.ebwt
extra_files_path/<reference_name>.4.ebwt
extra_files_path/<reference_name>.rev.1.ebwt
extra_files_path/<reference_name>.rev.2.ebwt
"""
self.add_composite_file('%s.grp',
description='Group File',
substitute_name_with_metadata='reference_name',
is_binary=False)
self.add_composite_file('%s.ti',
description='',
substitute_name_with_metadata='reference_name',
is_binary=False)
self.add_composite_file('%s.seq',
description='',
substitute_name_with_metadata='reference_name',
is_binary=False)
self.add_composite_file('%s.transcripts.fa',
description='',
substitute_name_with_metadata='reference_name',
is_binary=False)
self.add_composite_file('%s.chrlist',
description='',
substitute_name_with_metadata='reference_name',
is_binary=False,
optional=True)
self.add_composite_file('%s.idx.fa',
description='',
substitute_name_with_metadata='reference_name',
is_binary=False,
optional=True)
self.add_composite_file('%s.1.ebwt',
description='',
substitute_name_with_metadata='reference_name',
is_binary=True,
optional=True)
self.add_composite_file('%s.2.ebwt',
description='',
substitute_name_with_metadata='reference_name',
is_binary=True,
optional=True)
self.add_composite_file('%s.3.ebwt',
description='',
substitute_name_with_metadata='reference_name',
is_binary=True,
optional=True)
self.add_composite_file('%s.4.ebwt',
description='',
substitute_name_with_metadata='reference_name',
is_binary=True,
optional=True)
self.add_composite_file('%s.rev.1.ebwt',
description='',
substitute_name_with_metadata='reference_name',
is_binary=True,
optional=True)
self.add_composite_file('%s.rev.2.ebwt',
description='',
substitute_name_with_metadata='reference_name',
is_binary=True,
optional=True)
def __init__(self, **kwd):
Html.__init__(self, **kwd)
self.add_composite_file('%s.pheno',
description='Phenodata tab text file',
substitute_name_with_metadata='base_name',
is_binary=True)
def set_meta(self, dataset, **kwd):
log.debug("## set_meta for FusionInspector ")
Html.set_meta(self, dataset, **kwd)
self.regenerate_primary_file(dataset)
