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 = []
Exemplo n.º 2
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 def __init__(self):
     desc = __doc__
     PBToolRunner.__init__(self, desc)
     add_ice_daligner_arguments(self.parser)
Exemplo n.º 3
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 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.")
Exemplo n.º 4
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 def __init__(self):
     desc = "Call quiver to polish consensus isoforms with " + \
            "non-full-length reads."
     PBToolRunner.__init__(self, desc)
     set_parser(self.parser)
Exemplo n.º 5
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 def __init__(self):
     desc = "Post-quiver processing, selecting high QV consensus isoforms."
     PBToolRunner.__init__(self, desc)
     set_parser(self.parser)
Exemplo n.º 6
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 def __init__(self):
     desc = "Assign all non-full-length reads to unpolished isoform clusters"
     PBToolRunner.__init__(self, desc)
     set_parser(self.parser)
Exemplo n.º 7
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 def __init__(self):
     desc = "Call quiver to polish consensus isoforms with " + \
            "non-full-length reads."
     PBToolRunner.__init__(self, desc)
     set_parser(self.parser)
Exemplo n.º 8
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 def __init__(self):
     desc = "Post-quiver processing, selecting high QV consensus isoforms."
     PBToolRunner.__init__(self, desc)
     set_parser(self.parser)
Exemplo n.º 9
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 def __init__(self):
     desc = "Assign all non-full-length reads to unpolished isoform clusters"
     PBToolRunner.__init__(self, desc)
     set_parser(self.parser)
Exemplo n.º 10
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 def __init__(self):
     desc = "Call quiver to polish consensus isoforms."
     PBToolRunner.__init__(self, desc)
     set_parser(self.parser)
Exemplo n.º 11
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 def __init__(self):
     PBToolRunner.__init__(self, IceQuiverMerge.desc)
     add_ice_quiver_merge_arguments(self.parser)
Exemplo n.º 12
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 def __init__(self):
     desc = "Call quiver to polish consensus isoforms."
     PBToolRunner.__init__(self, desc)
     set_parser(self.parser)
Exemplo n.º 13
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 def __init__(self):
     desc = __doc__
     PBToolRunner.__init__(self, desc)
     add_ice_combine_cluster_bins_arguments(self.parser)
Exemplo n.º 14
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 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)
Exemplo n.º 15
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 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)
Exemplo n.º 16
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 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)
Exemplo n.º 17
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 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)
Exemplo n.º 18
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 def __init__(self):
     desc = __doc__
     PBToolRunner.__init__(self, desc)
     add_ice_daligner_arguments(self.parser)
Exemplo n.º 19
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 def __init__(self):
     PBToolRunner.__init__(self, IceQuiverMerge.desc)
     add_ice_quiver_merge_arguments(self.parser)
Exemplo n.º 20
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 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.")
Exemplo n.º 21
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 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)