def get_contract_parser():
p = get_base_contract_parser(Constants, default_level="DEBUG")
tcp = p.tool_contract_parser
add_fofn_arguments(p.arg_parser.parser,
bas_fofn=True,
tool_contract_parser=tcp)
tcp.add_input_file_type(FileTypes.DS_CONTIG,
"consensus_fa",
name="Consensus isoforms",
description="ContigSet of consensus isoforms")
tcp.add_input_file_type(FileTypes.PICKLE,
"cluster_pickle",
name="Clusters",
description="Cluster pickle file")
tcp.add_input_file_type(
FileTypes.PICKLE,
"map_nofl_pickle",
name="Pickle file",
description="Pickle file for non-full-length read mapping")
tcp.add_input_file_type(FileTypes.JSON,
"json_in",
name="JSON file",
description="Sentinel file from ice_quiver task")
add_cluster_summary_report_arguments(p)
add_ice_post_quiver_hq_lq_arguments(p)
return p
def get_contract_parser():
""" Return resolved tool contract.
input files:
idx 0 - ChunkTasksPickle of ClusterChunkTask objects
idx 1 - sentinel txt
output files:
idx 0 - consensus_isoforms.fa
idx 1 - summary.json
idx 2 - cluster_report.csv
idx 3 - hq_isoforms.contigset.xml
idx 4 - hq_isoforms.fq
idx 5 - lq_isoforms.contigset.xml
idx 6 - lq_isoforms.fq
idx 7 - hq_lq_prefix_dict.pickle
"""
p = get_base_contract_parser(Constants, default_level="DEBUG")
p.add_input_file_type(FileTypes.PICKLE, "cluster_chunks_pickle",
"Pickle In", "Cluster chunks pickle file") # input 0
p.add_input_file_type(FileTypes.TXT, "cluster_sentinel_in", "Sentinel In",
"Setinel file") # input idx 1
# output idx 0, consensus_isoforms.contigset,
p.add_output_file_type(FileTypes.DS_CONTIG,
"consensus_isoforms",
name="Unpolished Consensus Isoforms",
description="Output unpolished consensus isoforms",
default_name="consensus_isoforms")
# output idx 1, summary.json,
# output idx 2, cluster_report.csv
add_cluster_summary_report_arguments(p)
# output idx 3, hq_isoforms_fa, idx 4, hq_isoforms_fq,
# idx 5 lq_isoforms_fa, idx 6 lq_isoforms_fq
add_ice_post_quiver_hq_lq_arguments(p)
# output idx 7, hq_lq_prefix_dict.pickle
p.add_output_file_type(
FileTypes.PICKLE,
"hq_lq_prefix_dict",
name="HQ LQ Sample Prefix Dict",
description="Pickle mapping HQ (LQ) sample prefixes to ICE dir",
default_name="hq_lq_prefix_dict")
# user specified sample name.
p.add_str(option_id=Constants.SAMPLE_NAME_ID,
option_str="sample_name",
default=Constants.SAMPLE_NAME_DEFAULT,
name="sample Name",
description="Sample Name")
return p
def get_contract_parser():
""" Return resolved tool contract.
input files:
idx 0 - ChunkTasksPickle of ClusterChunkTask objects
idx 1 - sentinel txt
output files:
idx 0 - consensus_isoforms.fa
idx 1 - summary.json
idx 2 - cluster_report.csv
idx 3 - hq_isoforms.contigset.xml
idx 4 - hq_isoforms.fq
idx 5 - lq_isoforms.contigset.xml
idx 6 - lq_isoforms.fq
idx 7 - hq_lq_prefix_dict.pickle
"""
p = get_base_contract_parser(Constants, default_level="DEBUG")
p.add_input_file_type(FileTypes.PICKLE, "cluster_chunks_pickle", "Pickle In",
"Cluster chunks pickle file") # input 0
p.add_input_file_type(FileTypes.TXT, "cluster_sentinel_in", "Sentinel In",
"Setinel file") # input idx 1
# output idx 0, consensus_isoforms.contigset,
p.add_output_file_type(FileTypes.DS_CONTIG, "consensus_isoforms",
name="Unpolished Consensus Isoforms",
description="Output unpolished consensus isoforms",
default_name="consensus_isoforms")
# output idx 1, summary.json,
# output idx 2, cluster_report.csv
add_cluster_summary_report_arguments(p)
# output idx 3, hq_isoforms_fa, idx 4, hq_isoforms_fq,
# idx 5 lq_isoforms_fa, idx 6 lq_isoforms_fq
add_ice_post_quiver_hq_lq_arguments(p)
# output idx 7, hq_lq_prefix_dict.pickle
p.add_output_file_type(FileTypes.PICKLE, "hq_lq_prefix_dict",
name="HQ LQ Sample Prefix Dict",
description="Pickle mapping HQ (LQ) sample prefixes to ICE dir",
default_name="hq_lq_prefix_dict")
# user specified sample name.
p.add_str(option_id=Constants.SAMPLE_NAME_ID, option_str="sample_name",
default=Constants.SAMPLE_NAME_DEFAULT, name="sample Name",
description="Sample Name")
return p
def add_ice_polish_arguments(parser):
"""Set up argument parser."""
parser = add_cluster_root_dir_as_positional_argument(parser)
parser = add_nfl_fa_argument(parser, positional=True)
parser = add_fofn_arguments(parser, ccs_fofn=True, bas_fofn=True)
parser = add_ice_post_quiver_hq_lq_arguments(parser)
parser = add_sge_arguments(parser, quiver_nproc=True, blasr_nproc=True)
parser = add_tmp_dir_argument(parser)
return parser
def add_ice_polish_arguments(parser):
"""Set up argument parser."""
parser = add_cluster_root_dir_as_positional_argument(parser)
parser = add_nfl_fa_argument(parser, positional=True)
parser = add_fofn_arguments(parser, ccs_fofn=True, bas_fofn=True)
parser = add_ice_post_quiver_hq_lq_arguments(parser)
parser = add_sge_arguments(parser, quiver_nproc=True, blasr_nproc=True)
parser = add_tmp_dir_argument(parser)
return parser
def get_contract_parser():
p = get_base_contract_parser(Constants, default_level="DEBUG")
tcp = p.tool_contract_parser
add_fofn_arguments(p.arg_parser.parser, bas_fofn=True,
tool_contract_parser=tcp)
tcp.add_input_file_type(FileTypes.DS_CONTIG, "consensus_fa",
name="Consensus isoforms",
description="ContigSet of consensus isoforms")
tcp.add_input_file_type(FileTypes.PICKLE, "cluster_pickle",
name="Clusters",
description="Cluster pickle file")
tcp.add_input_file_type(FileTypes.PICKLE, "map_nofl_pickle",
name="Pickle file",
description="Pickle file for non-full-length read mapping")
tcp.add_input_file_type(FileTypes.JSON, "json_in", name="JSON file",
description="Sentinel file from ice_quiver task")
add_cluster_summary_report_arguments(p)
add_ice_post_quiver_hq_lq_arguments(p)
return p
def add_ice_quiver_all_arguments(parser):
"""Add arguments for IceQuiverAll, including arguments for IceQuiver and
IceQuiverPostprocess."""
arg_parser = parser.arg_parser.parser
tcp = parser.tool_contract_parser
arg_parser = add_cluster_root_dir_as_positional_argument(arg_parser)
arg_parser = add_fofn_arguments(arg_parser, bas_fofn=True,
tool_contract_parser=parser.tool_contract_parser)
tcp_parser = add_cluster_summary_report_arguments(_wrap_parser(arg_parser))
arg_parser = add_ice_post_quiver_hq_lq_arguments(arg_parser)
arg_parser = add_sge_arguments(arg_parser, quiver_nproc=True,
blasr_nproc=True)
arg_parser = add_tmp_dir_argument(arg_parser)
return parser
def add_ice_quiver_all_arguments(parser):
"""Add arguments for IceQuiverAll, including arguments for IceQuiver and
IceQuiverPostprocess."""
arg_parser = parser.arg_parser.parser
tcp = parser.tool_contract_parser
arg_parser = add_cluster_root_dir_as_positional_argument(arg_parser)
arg_parser = add_fofn_arguments(
arg_parser,
bas_fofn=True,
tool_contract_parser=parser.tool_contract_parser)
tcp_parser = add_cluster_summary_report_arguments(_wrap_parser(arg_parser))
arg_parser = add_ice_post_quiver_hq_lq_arguments(arg_parser)
arg_parser = add_sge_arguments(arg_parser,
quiver_nproc=True,
blasr_nproc=True)
arg_parser = add_tmp_dir_argument(arg_parser)
return parser
def add_ice_quiver_postprocess_arguments(arg_parser):
"""Add arugments for IceQuiverPostprocess ($ICE_QUIVER_PY postprocess)."""
arg_parser = add_cluster_root_dir_as_positional_argument(arg_parser)
arg_parser = add_ice_post_quiver_hq_lq_arguments(arg_parser)
tcp_parser = add_cluster_summary_report_arguments(_wrap_parser(arg_parser))
arg_parser.add_argument("--use_sge",
default=False,
dest="use_sge",
action="store_true",
help="quiver jobs have been submitted to sge."
"Check qstat")
arg_parser.add_argument("--quit_if_not_done",
default=False,
dest="quit_if_not_done",
action="store_true",
help="Quit if quiver jobs haven't been completed.")
return arg_parser
def add_ice_quiver_postprocess_arguments(arg_parser):
"""Add arugments for IceQuiverPostprocess ($ICE_QUIVER_PY postprocess)."""
arg_parser = add_cluster_root_dir_as_positional_argument(arg_parser)
arg_parser = add_ice_post_quiver_hq_lq_arguments(arg_parser)
tcp_parser = add_cluster_summary_report_arguments(_wrap_parser(arg_parser))
arg_parser.add_argument("--use_sge",
default=False,
dest="use_sge",
action="store_true",
help="quiver jobs have been submitted to sge."
"Check qstat")
arg_parser.add_argument("--quit_if_not_done",
default=False,
dest="quit_if_not_done",
action="store_true",
help="Quit if quiver jobs haven't been completed.")
return arg_parser