def __init__(self):
opts = (_mapseq_lims_opt, (
"-f", "--fasta_path",
"Path to a directory containing a fasta file for each chromosome",
{
'default': None
}
), ("--mincov", "Minimum coverage to call the SNP.", {
'default': 5
}), (
"--minsnp",
"Minimum percentage of reads per allele to call the SNP.", {
'default': 40
}
), ("-b", "--make_bigwigs",
"Create genome-wide coverage, heterozygosity and quality bigwigs.",
{
'action': "store_true"
}))
usage = "[-m mapseq_minilims] [--mincov --minsnp]"
desc = """Compares sequencing data to a reference assembly to detect SNPs."""
Workflow.__init__(self,
module="snp",
opts=opts,
usage=usage,
desc=desc)
def check_options(self):
Workflow.check_options(self)
self.main_args = {"job": self.job,
"assembly": self.job.assembly,
"logfile": self.logfile,
"via": self.opts.via}
return True
def __init__(self):
opts = (
_mapseq_lims_opt,
("-p", "--pileup_level",
"Target features, inside of quotes, separated by commas. E.g. 'genes,exons,transcripts'.",
{
'default': "genes,exons,transcripts"
}),
("-j", "--junctions",
"Whether or not to search for splice junctions using soapsplice.",
{
'action': "store_true",
'default': False
}),
("--stranded",
"To indicate that the protocol was strand-specific.", {
'action': "store_true",
'default': False
}),
)
usage = "[-m mapseq_minilims] [-p -j --stranded]"
desc = """A High-throughput RNA-seq analysis workflow. It returns text files containing
read counts for exons, genes and transcripts for each given BAM file, and the result
of a DESeq run (differential expression analysis) for every pair of groups. """
Workflow.__init__(self,
module="rnaseq",
opts=opts,
usage=usage,
desc=desc)
def check_options(self):
Workflow.check_options(self)
self.main_args = {"job": self.job,
"gl": self.globals,
"via": self.opts.via,
"debugfile": self.debugfile,
"logfile": self.logfile}
return True
def check_options(self):
Workflow.check_options(self)
self.main_args = {"job_or_dict": self.job,
"assembly": self.job.assembly,
"script_path": self.globals.get('script_path',''),
"logfile": self.logfile,
"via": self.opts.via}
return True
def __init__(self):
opts = (_mapseq_lims_opt, )
usage = "[-m mapseq_minilims]"
desc = """A High-throughput ChIP-seq peak analysis workflow."""
Workflow.__init__(self,
module="chipseq",
opts=opts,
usage=usage,
desc=desc)
def __init__(self):
opts = (("--noqc", "Skip fastqc step", {'action': "store_true"}), )
usage = "[--noqc]"
desc = "A High-throughput sequencing data mapping workflow."
Workflow.__init__(self,
module="mapseq",
opts=opts,
usage=usage,
desc=desc)
def check_options(self):
Workflow.check_options(self)
self.main_args = {
"job": self.job,
"assembly": self.job.assembly,
"logfile": self.logfile,
"via": self.opts.via
}
return True
def check_options(self):
Workflow.check_options(self)
self.main_args = {
"job": self.job,
"gl": self.globals,
"via": self.opts.via,
"debugfile": self.debugfile,
"logfile": self.logfile
}
return True
def __init__(self):
opts = (_mapseq_lims_opt, )
usage = "[-m mapseq_minilims]"
desc = """A High-throughput DNAseI-seq analysis workflow."""
Workflow.__init__(self,
module="dnaseseq",
name="dnaseseq",
opts=opts,
usage=usage,
desc=desc)
def __init__(self):
opts = (_mapseq_lims_opt, )
usage = "[-m mapseq_minilims]"
desc = """A High-throughput microbiome analysis workflow. Will return counts per level for the selected microbiome database."""
Workflow.__init__(self,
module="microbiome",
name="microbiome",
opts=opts,
usage=usage,
desc=desc)
def check_options(self):
Workflow.check_options(self)
self.main_args = {
"job_or_dict": self.job,
"assembly": self.job.assembly,
"script_path": self.globals.get('script_path', ''),
"logfile": self.logfile,
"via": self.opts.via
}
return True
def check_options(self):
Workflow.check_options(self)
self.suffix = ['merged']
primers_dict = self.sysmod.loadPrimers(os.path.join(self.opts.wdir,'primers.fa'))
self.main_args = {"job": self.job,
"primers_dict": primers_dict,
"assembly": self.job.assembly,
"script_path": self.globals.get('script_path',''),
"logfile": self.logfile,
"via": self.opts.via}
return True
def __init__(self):
opts = (_mapseq_lims_opt,
("-f", "--fasta_path", "Path to a directory containing a fasta file for each chromosome",
{'default':None}),
("--mincov", "Minimum coverage to call the SNP.",
{'default':5}),
("--minsnp", "Minimum percentage of reads per allele to call the SNP.",
{'default':40}),
("-b","--make_bigwigs", "Create genome-wide coverage, heterozygosity and quality bigwigs.",
{'action':"store_true"}))
usage = "[-m mapseq_minilims] [--mincov --minsnp]"
desc = """Compares sequencing data to a reference assembly to detect SNPs."""
Workflow.__init__(self,module="snp",opts=opts,usage=usage,desc=desc)
def check_options(self):
more_defs = {'discard_pcr_duplicates': (False,),
'find_junctions': (False,),
'stranded': (False,)}
Workflow.check_options(self, more_defs)
self.main_args = {"job": self.job,
"pileup_level": self.opts.pileup_level.split(','),
"via": self.opts.via,
"junctions": self.job.options['find_junctions'] or self.opts.junctions,
"stranded": self.job.options['stranded'] and not self.opts.stranded,
"logfile": self.logfile,
"debugfile": self.debugfile}
return True
def check_options(self):
Workflow.check_options(self)
self.suffix = ['merged']
primers_dict = self.sysmod.loadPrimers(
os.path.join(self.opts.wdir, 'primers.fa'))
self.main_args = {
"job": self.job,
"primers_dict": primers_dict,
"assembly": self.job.assembly,
"script_path": self.globals.get('script_path', ''),
"logfile": self.logfile,
"via": self.opts.via
}
return True
def check_options(self):
Workflow.check_options(self,{'bowtie2': (True,)})
map_args = self.job.options.get('map_args',{})
self.job.options['create_gdv_project'] &= self.job.options['compute_densities']
self.main_args = {"job": self.job,
"assembly": self.job.assembly,
"map_args": map_args,
"gl": self.globals,
"bowtie2": self.job.options['bowtie2'],
"via": self.opts.via,
"debugfile": self.debugfile,
"logfile": self.logfile}
return True
def check_options(self):
_mbw = str(self.job.options.get('compute_densities_snp','1')).lower()
more_defs = {'bowtie2': (True,),
'make_bigwigs': (True,_mbw in ['1','true','t'])}
Workflow.check_options(self, more_defs)
mincov = int(self.job.options.get('mincov') or self.opts.mincov)
minsnp = int(self.job.options.get('minsnp') or self.opts.minsnp)
self.main_args = {"job": self.job,
"assembly": self.job.assembly,
"mincov": mincov,
"minsnp": minsnp,
"path_to_ref": self.opts.fasta_path,
"via": self.opts.via}
return True
def __init__(self):
opts = (_mapseq_lims_opt,
("-p", "--pileup_level",
"Target features, inside of quotes, separated by commas. E.g. 'genes,exons,transcripts'.",
{'default':"genes,exons,transcripts"}),
("-j", "--junctions", "Whether or not to search for splice junctions using soapsplice.",
{'action':"store_true", 'default':False}),
("--stranded", "To indicate that the protocol was strand-specific.",
{'action':"store_true", 'default':False}),
)
usage = "[-m mapseq_minilims] [-p -j --stranded]"
desc = """A High-throughput RNA-seq analysis workflow. It returns text files containing
read counts for exons, genes and transcripts for each given BAM file, and the result
of a DESeq run (differential expression analysis) for every pair of groups. """
Workflow.__init__(self,module="rnaseq",opts=opts,usage=usage,desc=desc)
def check_options(self):
Workflow.check_options(self,{'bowtie2': (True,), 'local_align': (False,)})
map_args = self.job.options.get('map_args',{})
if self.job.options['local_align']:
map_args.setdefault("bwt_args",[])
map_args["bwt_args"] += ["--local"]
self.job.options['create_gdv_project'] &= self.job.options['compute_densities']
self.main_args = {"job": self.job,
"assembly": self.job.assembly,
"map_args": map_args,
"gl": self.globals,
"bowtie2": self.job.options['bowtie2'],
"via": self.opts.via,
"debugfile": self.debugfile,
"logfile": self.logfile}
return True
def check_options(self):
Workflow.check_options(self, {'bowtie2': (True, )})
map_args = self.job.options.get('map_args', {})
self.job.options['create_gdv_project'] &= self.job.options[
'compute_densities']
self.main_args = {
"job": self.job,
"assembly": self.job.assembly,
"map_args": map_args,
"gl": self.globals,
"bowtie2": self.job.options['bowtie2'],
"via": self.opts.via,
"debugfile": self.debugfile,
"logfile": self.logfile
}
return True
def check_options(self):
_mbw = str(self.job.options.get('compute_densities_snp', '1')).lower()
more_defs = {
'bowtie2': (True, ),
'make_bigwigs': (True, _mbw in ['1', 'true', 't'])
}
Workflow.check_options(self, more_defs)
mincov = int(self.job.options.get('mincov') or self.opts.mincov)
minsnp = int(self.job.options.get('minsnp') or self.opts.minsnp)
self.main_args = {
"job": self.job,
"assembly": self.job.assembly,
"mincov": mincov,
"minsnp": minsnp,
"path_to_ref": self.opts.fasta_path,
"via": self.opts.via
}
return True
def check_options(self):
more_defs = {
'discard_pcr_duplicates': (False, ),
'find_junctions': (False, ),
'stranded': (False, )
}
Workflow.check_options(self, more_defs)
self.main_args = {
"job": self.job,
"pileup_level": self.opts.pileup_level.split(','),
"via": self.opts.via,
"junctions": self.job.options['find_junctions']
or self.opts.junctions,
"stranded": self.job.options['stranded']
and not self.opts.stranded,
"logfile": self.logfile,
"debugfile": self.debugfile
}
return True
def check_options(self):
Workflow.check_options(self, {
'bowtie2': (True, ),
'local_align': (False, )
})
map_args = self.job.options.get('map_args', {})
if self.job.options['local_align']:
map_args.setdefault("bwt_args", [])
map_args["bwt_args"] += ["--local"]
self.job.options['create_gdv_project'] &= self.job.options[
'compute_densities']
self.main_args = {
"job": self.job,
"assembly": self.job.assembly,
"map_args": map_args,
"gl": self.globals,
"bowtie2": self.job.options['bowtie2'],
"via": self.opts.via,
"debugfile": self.debugfile,
"logfile": self.logfile
}
return True
def __init__(self):
opts = (_mapseq_lims_opt,)
usage = "[-m mapseq_minilims]"
desc = """A High-throughput ChIP-seq peak analysis workflow."""
Workflow.__init__(self,module="chipseq",opts=opts,usage=usage,desc=desc)
def __init__(self):
opts = (("--noqc","Skip fastqc step",{'action':"store_true"}),
("--local_align","Perform local alignment",{'action':"store_true"}),)
usage = "[--noqc] [--local_align]"
desc = "A High-throughput sequencing data mapping workflow."
Workflow.__init__(self,module="mapseq",opts=opts,usage=usage,desc=desc)
def __init__(self):
desc = "Demultiplexing routine for 4C-seq data."
Workflow.__init__(self,
module="demultiplex",
name="demultiplexing",
desc=desc)
def __init__(self):
opts = (_mapseq_lims_opt,)
usage = "[-m mapseq_minilims]"
desc = """A High-throughput DNAseI-seq analysis workflow."""
Workflow.__init__(self,module="dnaseseq",name="dnaseseq",opts=opts,usage=usage,desc=desc)
def __init__(self):
opts = (_mapseq_lims_opt,)
usage = "[-m mapseq_minilims]"
desc = """A High-throughput microbiome analysis workflow. Will return counts per level for the selected microbiome database."""
Workflow.__init__(self,module="microbiome",name="microbiome",opts=opts,usage=usage,desc=desc)
def __init__(self):
desc = "Demultiplexing routine for 4C-seq data."
Workflow.__init__(self,module="demultiplex",name="demultiplexing",desc=desc)