def __init__(self):
"""Handle command line argument parsing"""
desc = "Extract unmapped subreads from a fasta file."
PBToolRunner.__init__(self, desc)
self.set_parser(self.parser)
self.fastaFN = None
self.cmpH5FNs = []
def __init__(self):
desc = __doc__
PBToolRunner.__init__(self, desc)
add_ice_daligner_arguments(self.parser)
def __init__(self):
desc = "Filter gmap sam alignments which have bad cigar strings."
PBToolRunner.__init__(self, desc)
self.parser.add_argument("in_sam", type=str, help="Input sam file.")
self.parser.add_argument("out_sam", type=str, help="Output sam file.")
def __init__(self):
desc = "Call quiver to polish consensus isoforms with " + \
"non-full-length reads."
PBToolRunner.__init__(self, desc)
set_parser(self.parser)
def __init__(self):
desc = "Post-quiver processing, selecting high QV consensus isoforms."
PBToolRunner.__init__(self, desc)
set_parser(self.parser)
def __init__(self):
desc = "Assign all non-full-length reads to unpolished isoform clusters"
PBToolRunner.__init__(self, desc)
set_parser(self.parser)
def __init__(self):
desc = "Call quiver to polish consensus isoforms with " + \
"non-full-length reads."
PBToolRunner.__init__(self, desc)
set_parser(self.parser)
def __init__(self):
desc = "Post-quiver processing, selecting high QV consensus isoforms."
PBToolRunner.__init__(self, desc)
set_parser(self.parser)
def __init__(self):
desc = "Assign all non-full-length reads to unpolished isoform clusters"
PBToolRunner.__init__(self, desc)
set_parser(self.parser)
def __init__(self):
desc = "Call quiver to polish consensus isoforms."
PBToolRunner.__init__(self, desc)
set_parser(self.parser)
def __init__(self):
PBToolRunner.__init__(self, IceQuiverMerge.desc)
add_ice_quiver_merge_arguments(self.parser)
def __init__(self):
desc = "Call quiver to polish consensus isoforms."
PBToolRunner.__init__(self, desc)
set_parser(self.parser)
def __init__(self):
desc = __doc__
PBToolRunner.__init__(self, desc)
add_ice_combine_cluster_bins_arguments(self.parser)
def __init__(self):
desc = "Assign non-full-length reads in a splitted fasta file " + \
"to unpolished isoform clusters"
PBToolRunner.__init__(self, desc)
set_parser(self.parser)
def __init__(self):
desc = "Converting bas/bax.h5 files within a fofn to fasta " + \
"files and create a fasta fofn."
PBToolRunner.__init__(self, desc)
set_parser(self.parser)
def __init__(self):
desc = "Call quiver to polish consensus isoforms with " + \
"non-full-length reads."
PBToolRunner.__init__(self, desc)
add_ice_polish_arguments(self.parser)
def __init__(self):
desc = "Converting bas/bax.h5 files within a fofn to fasta " + \
"files and create a fasta fofn."
PBToolRunner.__init__(self, desc)
set_parser(self.parser)
def __init__(self):
desc = __doc__
PBToolRunner.__init__(self, desc)
add_ice_daligner_arguments(self.parser)
def __init__(self):
PBToolRunner.__init__(self, IceQuiverMerge.desc)
add_ice_quiver_merge_arguments(self.parser)
def __init__(self):
desc = "Filter gmap sam alignments which have bad cigar strings."
PBToolRunner.__init__(self, desc)
self.parser.add_argument("in_sam", type=str, help="Input sam file.")
self.parser.add_argument("out_sam", type=str, help="Output sam file.")
def __init__(self):
desc = "Assign non-full-length reads in a splitted fasta file " + "to unpolished isoform clusters"
PBToolRunner.__init__(self, desc)
set_parser(self.parser)