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)
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)
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('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('%s.pheno',
description='Phenodata tab text file',
substitute_name_with_metadata='base_name',
is_binary=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)
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)
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('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)
