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PacBio_feature_parse_specs.yaml
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# Description:
# YAML file that specifies how .parse_alignment method parses the alignments
# for each feature of the amplicon. Filters will be applied in the order the
# features appear in the feature_parse_specs.
# Name of amplicon
PacBio_amplicon:
# keys ‘query_clip5’ and ‘query_clip3’ give the max amount that
# can be clipped from each end of the query prior to the alignment
query_clip5: 12
query_clip3: 12
# Feature of amplicon
termini5:
# filter: dict keyed by ‘clip5’, ‘clip3’, ‘mutation_nt_count’, and ‘mutation_op_count’
# If ‘filter’ itself or any of the keys are missing, the value is set to zero.
# If the value is None (‘null’ in YAML notation), then no filter is applied
filter:
# clip5 and clip3 give max clipping at each end
clip5: 12
# mutation_nt_count give number of nucleotide mutations allowed for feature
mutation_nt_count: 1
# mutation_op_count give number of cs tag mutation operations allowed for feature
mutation_op_count: null
# Feature of amplicon
gene:
# filter: dict keyed by ‘clip5’, ‘clip3’, ‘mutation_nt_count’, and ‘mutation_op_count’
# If ‘filter’ itself or any of the keys are missing, the value is set to zero.
# If the value is None (‘null’ in YAML notation), then no filter is applied
filter:
# mutation_nt_count give number of nucleotide mutations allowed for feature
mutation_nt_count: 45
# mutation_op_count give number of cs tag mutation operations allowed for feature
mutation_op_count: null
# ’return’: str or list of strings indicating what to return for this feature.
# If ‘returns’ is absent or the value is None (‘null’ in YAML notation), nothing is returned for this feature.
# Otherwise list one or more of ‘sequence’, ‘mutations’, ‘accuracy’, ‘cs’, ‘clip5’, and ‘clip3’ to get
# the sequence, mutation string, cs tag, or number of clipped nucleotides from each end.
return: [mutations, accuracy]
# # Feature of amplicon
# spacer:
# # filter: dict keyed by ‘clip5’, ‘clip3’, ‘mutation_nt_count’, and ‘mutation_op_count’
# # If ‘filter’ itself or any of the keys are missing, the value is set to zero.
# # If the value is None (‘null’ in YAML notation), then no filter is applied
# filter:
# # mutation_nt_count give number of nucleotide mutations allowed for feature
# mutation_nt_count: 1
# # mutation_op_count give number of cs tag mutation operations allowed for feature
# mutation_op_count: null
# Feature of amplicon
barcode:
# filter: dict keyed by ‘clip5’, ‘clip3’, ‘mutation_nt_count’, and ‘mutation_op_count’
# If ‘filter’ itself or any of the keys are missing, the value is set to zero.
# If the value is None (‘null’ in YAML notation), then no filter is applied
filter:
# mutation_nt_count give number of nucleotide mutations allowed for feature
mutation_nt_count: 0
# mutation_op_count give number of cs tag mutation operations allowed for feature
mutation_op_count: null
# ’return’: str or list of strings indicating what to return for this feature.
# If ‘returns’ is absent or the value is None (‘null’ in YAML notation), nothing is returned for this feature.
# Otherwise list one or more of ‘sequence’, ‘mutations’, ‘accuracy’, ‘cs’, ‘clip5’, and ‘clip3’ to get
# the sequence, mutation string, cs tag, or number of clipped nucleotides from each end.
return: [sequence, accuracy]
# Feature of amplicon
termini3:
# filter: dict keyed by ‘clip5’, ‘clip3’, ‘mutation_nt_count’, and ‘mutation_op_count’
# If ‘filter’ itself or any of the keys are missing, the value is set to zero.
# If the value is None (‘null’ in YAML notation), then no filter is applied
filter:
# clip5 and clip3 give max clipping at each end
clip3: 12
# mutation_nt_count give number of nucleotide mutations allowed for feature
mutation_nt_count: 1
# mutation_op_count give number of cs tag mutation operations allowed for feature
mutation_op_count: null
# Feature of amplicon
variant_tag5:
# filter: dict keyed by ‘clip5’, ‘clip3’, ‘mutation_nt_count’, and ‘mutation_op_count’
# If ‘filter’ itself or any of the keys are missing, the value is set to zero.
# If the value is None (‘null’ in YAML notation), then no filter is applied
# ’return’: str or list of strings indicating what to return for this feature.
# If ‘returns’ is absent or the value is None (‘null’ in YAML notation), nothing is returned for this feature.
# Otherwise list one or more of ‘sequence’, ‘mutations’, ‘accuracy’, ‘cs’, ‘clip5’, and ‘clip3’ to get
# the sequence, mutation string, cs tag, or number of clipped nucleotides from each end.
return: sequence
# Feature of amplicon
variant_tag3:
# filter: dict keyed by ‘clip5’, ‘clip3’, ‘mutation_nt_count’, and ‘mutation_op_count’
# If ‘filter’ itself or any of the keys are missing, the value is set to zero.
# If the value is None (‘null’ in YAML notation), then no filter is applied
# ’return’: str or list of strings indicating what to return for this feature.
# If ‘returns’ is absent or the value is None (‘null’ in YAML notation), nothing is returned for this feature.
# Otherwise list one or more of ‘sequence’, ‘mutations’, ‘accuracy’, ‘cs’, ‘clip5’, and ‘clip3’ to get
# the sequence, mutation string, cs tag, or number of clipped nucleotides from each end.
return: sequence
# Feature of amplicon
# illuminaprimer:
# # filter: dict keyed by ‘clip5’, ‘clip3’, ‘mutation_nt_count’, and ‘mutation_op_count’
# # If ‘filter’ itself or any of the keys are missing, the value is set to zero.
# # If the value is None (‘null’ in YAML notation), then no filter is applied
# filter:
# # mutation_nt_count give number of nucleotide mutations allowed for feature
# mutation_nt_count: 0
# # mutation_op_count give number of cs tag mutation operations allowed for feature
# mutation_op_count: null
# # ’return’: str or list of strings indicating what to return for this feature.
# # If ‘returns’ is absent or the value is None (‘null’ in YAML notation), nothing is returned for this feature.
# # Otherwise list one or more of ‘sequence’, ‘mutations’, ‘accuracy’, ‘cs’, ‘clip5’, and ‘clip3’ to get
# # the sequence, mutation string, cs tag, or number of clipped nucleotides from each end.
# return: [sequence, accuracy]