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Dysgu dev #116

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merged 2 commits into from
Nov 21, 2024
Merged

Dysgu dev #116

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636883d
Merge branch 'master' into dysgu_dev
kcleal Nov 20, 2024
9266790
Fixed merge None type error. Added wb3 as default compression level f…
kcleal Nov 21, 2024
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1 change: 1 addition & 0 deletions dysgu/call_component.pyx
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Original file line number Diff line number Diff line change
Expand Up @@ -833,6 +833,7 @@ def linear_scan_clustering(spanning, informative):
# return result



def process_spanning(paired_end, spanning_alignments, divergence, length_extend, informative,
generic_insertions, insert_ppf, to_assemble):
# echo("PROCESS SPANNING")
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22 changes: 12 additions & 10 deletions dysgu/main.py
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Original file line number Diff line number Diff line change
Expand Up @@ -60,7 +60,8 @@
"trust_ins_len": "False",
"sd": 0.6,
"symbolic_sv_size": 50000,
"divergence": "auto"
"divergence": "auto",
"compression": "wb3",
},
"nanopore-r10": {"mq": 1,
"min_support": "auto",
Expand All @@ -72,7 +73,8 @@
"trust_ins_len": "False",
"sd": 0.35,
"thresholds": "0.35,0.35,0.35,0.35,0.35",
"symbolic_sv_size": 50000
"symbolic_sv_size": 50000,
"compression": "wb3",
},
"pacbio-sequel2": {"mq": 1,
"min_support": "auto",
Expand All @@ -83,7 +85,8 @@
"clip_length": -1,
"trust_ins_len": "True",
"sd": 0.45,
"symbolic_sv_size": 50000
"symbolic_sv_size": 50000,
"compression": "wb3",
},
"pacbio-revio": {"mq": 1,
"min_support": "auto",
Expand All @@ -95,7 +98,8 @@
"trust_ins_len": "True",
"sd": 0.4,
"thresholds": "0.25,0.25,0.25,0.25,0.25",
"symbolic_sv_size": 50000
"symbolic_sv_size": 50000,
"compression": "wb3",
},
"pe": {"mq": defaults["mq"],
"min_support": defaults["min_support"],
Expand Down Expand Up @@ -211,12 +215,11 @@ def cli():
@click.option("-p", "--procs", help="Number of cpu cores to use", type=cpu_range, default=1,
show_default=True)
@click.option('--mode', help=f"Type of input reads. Multiple options are set, overrides other options. "
f"pacbio-sequel2: --mq {presets['pacbio-sequel2']['mq']} --paired False --min-support '{presets['pacbio-sequel2']['min_support']}' --max-cov {presets['pacbio-sequel2']['max_cov']} --dist-norm {presets['pacbio-sequel2']['dist_norm']} --trust-ins-len True --symbolic-sv-size {presets['pacbio-sequel2']['symbolic_sv_size']} --sd {presets['pacbio-sequel2']['sd']}."
f"pacbio-revio: --mq {presets['pacbio-revio']['mq']} --paired False --min-support '{presets['pacbio-revio']['min_support']}' --max-cov {presets['pacbio-revio']['max_cov']} --dist-norm {presets['pacbio-revio']['dist_norm']} --trust-ins-len True --thresholds {presets['pacbio-revio']['thresholds']} --symbolic-sv-size {presets['pacbio-revio']['symbolic_sv_size']} --sd {presets['pacbio-revio']['sd']}."
f"nanopore-r9: --mq {presets['nanopore-r9']['mq']} --paired False --min-support '{presets['nanopore-r9']['min_support']}' --max-cov {presets['nanopore-r9']['max_cov']} --dist-norm {presets['nanopore-r9']['dist_norm']} --trust-ins-len False --symbolic-sv-size {presets['nanopore-r9']['symbolic_sv_size']} --sd {presets['nanopore-r9']['sd']} --divergence {presets['nanopore-r9']['divergence']}."
f"nanopore-r10: --mq {presets['nanopore-r10']['mq']} --paired False --min-support '{presets['nanopore-r10']['min_support']}' --max-cov {presets['nanopore-r10']['max_cov']} --dist-norm {presets['nanopore-r10']['dist_norm']} --trust-ins-len False --thresholds {presets['nanopore-r10']['thresholds']} --symbolic-sv-size {presets['nanopore-r10']['symbolic_sv_size']} --sd {presets['nanopore-r10']['sd']}",
f"pacbio-sequel2: --mq {presets['pacbio-sequel2']['mq']} --paired False --min-support '{presets['pacbio-sequel2']['min_support']}' --max-cov {presets['pacbio-sequel2']['max_cov']} --dist-norm {presets['pacbio-sequel2']['dist_norm']} --trust-ins-len True --symbolic-sv-size {presets['pacbio-sequel2']['symbolic_sv_size']} --sd {presets['pacbio-sequel2']['sd']} --compression wb3. "
f"pacbio-revio: --mq {presets['pacbio-revio']['mq']} --paired False --min-support '{presets['pacbio-revio']['min_support']}' --max-cov {presets['pacbio-revio']['max_cov']} --dist-norm {presets['pacbio-revio']['dist_norm']} --trust-ins-len True --thresholds {presets['pacbio-revio']['thresholds']} --symbolic-sv-size {presets['pacbio-revio']['symbolic_sv_size']} --sd {presets['pacbio-revio']['sd']} --compression wb3. "
f"nanopore-r9: --mq {presets['nanopore-r9']['mq']} --paired False --min-support '{presets['nanopore-r9']['min_support']}' --max-cov {presets['nanopore-r9']['max_cov']} --dist-norm {presets['nanopore-r9']['dist_norm']} --trust-ins-len False --symbolic-sv-size {presets['nanopore-r9']['symbolic_sv_size']} --sd {presets['nanopore-r9']['sd']} --divergence {presets['nanopore-r9']['divergence']} --compression wb3. "
f"nanopore-r10: --mq {presets['nanopore-r10']['mq']} --paired False --min-support '{presets['nanopore-r10']['min_support']}' --max-cov {presets['nanopore-r10']['max_cov']} --dist-norm {presets['nanopore-r10']['dist_norm']} --trust-ins-len False --thresholds {presets['nanopore-r10']['thresholds']} --symbolic-sv-size {presets['nanopore-r10']['symbolic_sv_size']} --sd {presets['nanopore-r10']['sd']} --compression wb3",
default="pe", type=click.Choice(["pe", "pacbio-sequel2", "pacbio-revio", "nanopore-r9", "nanopore-r10", "pacbio", "nanopore"]), show_default=True)

@click.option('--pl', help=f"Type of input reads [default: {defaults['pl']}]",
type=click.Choice(["pe", "pacbio", "nanopore"]), callback=add_option_set)
@click.option('--clip-length', help="Minimum soft-clip length, >= threshold are kept. Set to -1 to ignore [default: {deafults['clip_length']}]", type=int, callback=add_option_set)
Expand Down Expand Up @@ -376,7 +379,6 @@ def get_reads(ctx, **kwargs):
f"nanopore-r9: --mq {presets['nanopore-r9']['mq']} --paired False --min-support '{presets['nanopore-r9']['min_support']}' --max-cov {presets['nanopore-r9']['max_cov']} --dist-norm {presets['nanopore-r9']['dist_norm']} --trust-ins-len False --symbolic-sv-size {presets['nanopore-r9']['symbolic_sv_size']} --sd {presets['nanopore-r9']['sd']} --divergence {presets['nanopore-r9']['divergence']}."
f"nanopore-r10: --mq {presets['nanopore-r10']['mq']} --paired False --min-support '{presets['nanopore-r10']['min_support']}' --max-cov {presets['nanopore-r10']['max_cov']} --dist-norm {presets['nanopore-r10']['dist_norm']} --trust-ins-len False --thresholds {presets['nanopore-r10']['thresholds']} --symbolic-sv-size {presets['nanopore-r10']['symbolic_sv_size']} --sd {presets['nanopore-r10']['sd']}",
default="pe", type=click.Choice(["pe", "pacbio-sequel2", "pacbio-revio", "nanopore-r9", "nanopore-r10", "pacbio", "nanopore"]), show_default=True)

@click.option('--pl', help=f"Type of input reads [default: {defaults['pl']}]",
type=click.Choice(["pe", "pacbio", "nanopore"]), callback=add_option_set)
@click.option('--clip-length', help="Minimum soft-clip length, >= threshold are kept. Set to -1 to ignore [default: {deafults['clip_length']}]", type=int, callback=add_option_set)
Expand Down
5 changes: 4 additions & 1 deletion dysgu/merge_svs.pyx
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Expand Up @@ -159,6 +159,8 @@ def consistent_alignment_and_cigars(ei, ej, l_ratio):


def jaccard_similarity(set1, set2):
if not set1 or not set2:
return 0
intersection = len(set1.intersection(set2))
union = len(set1.union(set2))
return intersection / union if union != 0 else 0
Expand Down Expand Up @@ -648,7 +650,8 @@ def merge_events(potential, max_dist, tree, paired_end=False, try_rev=False, pic
best_var_seq = w0.variant_seq
for k in range(1, len(best)):
item = best[k]
w0.qnames |= item.qnames
if w0.qnames is not None and item.qnames is not None:
w0.qnames |= item.qnames
w0.pe += item.pe
w0.supp += item.supp
w0.sc += item.sc
Expand Down