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Improved exception handling
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@Char-Al
Char-Al committed Feb 28, 2023
1 parent 8840056 commit 5d96e6a
Showing 1 changed file with 155 additions and 116 deletions.
271 changes: 155 additions & 116 deletions seal/schedulers.py
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Original file line number Diff line number Diff line change
Expand Up @@ -8,8 +8,10 @@
from datetime import datetime

from seal import app, scheduler, db
from seal.models import Sample, Variant, Family, Var2Sample, Run, Transcript, Team, Bed, Filter, History
from seal.models import (Sample, Variant, Family, Var2Sample, Run, Transcript,
Team, Bed, Filter, History, Comment_sample)

from sqlalchemy import exc

CONSEQUENCES_DICT = {
"stop_gained": 20,
Expand Down Expand Up @@ -253,7 +255,7 @@ def create_sample(data):
filter = get_filter(id, name)
if filter:
sample.filter = filter

db.session.add(sample)
db.session.commit()
return sample

Expand Down Expand Up @@ -402,7 +404,9 @@ def importvcf():
return

sample = create_sample(data)
current_date = datetime.now().isoformat()
history = History(sample_ID=sample.id, user_ID=user_id, date=date_import, action=f"Import Sample")
db.session.add(history)
db.session.commit()

vcf_vep = path_inout.joinpath(f'{vcf_path.stem}.vep.vcf')
stats_vep = path_inout.joinpath(f'{vcf_path.stem}.vep.html')
Expand All @@ -413,124 +417,159 @@ def importvcf():
"stats_vep": stats_vep
}

current_date = datetime.now().isoformat()
try:
app.logger.info("------ Variant Annotation with VEP ------")
create_and_execute_shell_command(Path(app.root_path).joinpath('static/vep.config.json'), values)
app.logger.info("------ END VEP ------")
with annotVcf.AnnotVCFIO(vcf_vep) as vcf_io:
for v in vcf_io:
if v.alt[0] == "*":
continue
variant = Variant.query.get(f"{v.chrom}-{v.pos}-{v.ref}-{v.alt[0]}")
if not variant:
annotations = [{
"date": current_date,
"ANN": list()
}]

for annot in v.info["ANN"]:
# Split annotations
for splitAnn in ANNOT_TO_SPLIT:
if splitAnn == 'VAR_SYNONYMS':
try:
var_synonyms = dict()
for vs in annot[splitAnn].split("--"):
key, values = vs.split("::")
values_array = values.split("&")
var_synonyms[key] = values_array

annot[splitAnn] = var_synonyms
except AttributeError:
annot[splitAnn] = dict()
else:
try:
annot[splitAnn] = annot[splitAnn].split("&")
except AttributeError:
annot[splitAnn] = []

# transcript
transcript = Transcript.query.get(annot["Feature"])
if not transcript and annot["Feature"] is not None:
transcript = Transcript(
feature=annot["Feature"],
biotype=annot["BIOTYPE"],
feature_type=annot["Feature_type"],
symbol=annot["SYMBOL"],
symbol_source=annot["SYMBOL_SOURCE"],
gene=annot["Gene"],
source=annot["SOURCE"],
protein=annot["ENSP"],
canonical=annot["CANONICAL"],
hgnc=annot["HGNC_ID"]
)
db.session.add(transcript)

# Get consequence score
consequence_score = 0
for consequence in annot["Consequence"]:
consequence_score += CONSEQUENCES_DICT[consequence]
annot["consequenceScore"] = consequence_score

# Get Exon/Intron
annot["EI"] = None
if annot["EXON"] is not None:
annot["EI"] = f"Exon {annot['EXON']}"
if annot["INTRON"] is not None:
annot["EI"] = f"Intron {annot['INTRON']}"

# Get Exon/Intron
annot["canonical"] = True if annot['CANONICAL'] == 'YES' else False

# missense
missenses = list()
for value in MISSENSES:
missenses.append(annot[value])
missenses = numpy.array(missenses, dtype=numpy.float64)
mean = numpy.nanmean(missenses)
annot["missensesMean"] = None if numpy.isnan(mean) else mean

# max spliceAI
spliceAI = list()
for value in SPLICEAI:
spliceAI.append(annot[value])
spliceAI = numpy.array(spliceAI, dtype=numpy.float64)
max = numpy.nanmax(spliceAI)
annot["spliceAI"] = None if numpy.isnan(max) else max

# max MaxEntScan
annot["MES_var"] = None
if annot["MaxEntScan_alt"] is not None and annot["MaxEntScan_ref"] is not None:
annot["MES_var"] = -100 + (float(annot["MaxEntScan_alt"]) * 100) / float(annot["MaxEntScan_ref"])

annotations[-1]["ANN"].append(annot)

# app.logger.debug(f" - Create Variant : {sample}")
variant = Variant(id=f"{v.chrom}-{v.pos}-{v.ref}-{v.alt[0]}", chr=v.chrom, pos=v.pos, ref=v.ref, alt=v.alt[0], annotations=annotations)
db.session.add(variant)

# sample.variants.append(variant)
v2s = Var2Sample(variant_ID=variant.id, sample_ID=sample.id, depth=v.getPopDP(), allelic_depth=v.getPopAltAD()[0], filter=v.filter)
db.session.add(v2s)

except CommandFailedError as e:
app.logger.info(f"{type(e).__name__} : {e}")
sample.status = -1
except Exception as e:
db.session.remove()
app.logger.info(f"{type(e).__name__} : {e}")
sample.status = -1
else:
sample.status = 1
current_file.unlink()
vcf_vep.unlink()
stats_vep.unlink()
if interface:
vcf_path.unlink()
history = History(sample_ID=sample.id, user_ID=user_id, date=date_import, action=f"Import Sample")
db.session.add(history)
history = History(sample_ID=sample.id, user_ID=user_id, date=datetime.now(), action=f"Sample Imported")
db.session.add(history)
finally:
db.session.commit()
app.logger.info(f"---- Variants Added for Sample : {sample} - {sample.id} ----")
path_locker.unlink()
db.session.commit()
error_file = current_file.with_suffix('.error')
current_file.rename(error_file)
return

with annotVcf.AnnotVCFIO(vcf_vep) as vcf_io:
for v in vcf_io:
if v.alt[0] == "*":
continue
variant = Variant.query.get(f"{v.chrom}-{v.pos}-{v.ref}-{v.alt[0]}")
if not variant:
annotations = [{
"date": current_date,
"ANN": list()
}]

for annot in v.info["ANN"]:
# Split annotations
for splitAnn in ANNOT_TO_SPLIT:
if splitAnn == 'VAR_SYNONYMS':
try:
var_synonyms = dict()
for vs in annot[splitAnn].split("--"):
key, values = vs.split("::")
values_array = values.split("&")
var_synonyms[key] = values_array

annot[splitAnn] = var_synonyms
except AttributeError:
annot[splitAnn] = dict()
else:
try:
annot[splitAnn] = annot[splitAnn].split("&")
except AttributeError:
annot[splitAnn] = []

# transcript
transcript = Transcript.query.get(annot["Feature"])
if not transcript and annot["Feature"] is not None:
transcript = Transcript(
feature=annot["Feature"],
biotype=annot["BIOTYPE"],
feature_type=annot["Feature_type"],
symbol=annot["SYMBOL"],
symbol_source=annot["SYMBOL_SOURCE"],
gene=annot["Gene"],
source=annot["SOURCE"],
protein=annot["ENSP"],
canonical=annot["CANONICAL"],
hgnc=annot["HGNC_ID"]
)
db.session.add(transcript)

# Get consequence score
consequence_score = 0
for consequence in annot["Consequence"]:
consequence_score += CONSEQUENCES_DICT[consequence]
annot["consequenceScore"] = consequence_score

# Get Exon/Intron
annot["EI"] = None
if annot["EXON"] is not None:
annot["EI"] = f"Exon {annot['EXON']}"
if annot["INTRON"] is not None:
annot["EI"] = f"Intron {annot['INTRON']}"

# Get Exon/Intron
annot["canonical"] = True if annot['CANONICAL'] == 'YES' else False

# missense
missenses = list()
for value in MISSENSES:
missenses.append(annot[value])
missenses = numpy.array(missenses, dtype=numpy.float64)
mean = numpy.nanmean(missenses)
annot["missensesMean"] = None if numpy.isnan(mean) else mean

# max spliceAI
spliceAI = list()
for value in SPLICEAI:
spliceAI.append(annot[value])
spliceAI = numpy.array(spliceAI, dtype=numpy.float64)
max = numpy.nanmax(spliceAI)
annot["spliceAI"] = None if numpy.isnan(max) else max

# max MaxEntScan
annot["MES_var"] = None
if (annot["MaxEntScan_alt"] is not None
and annot["MaxEntScan_ref"] is not None):
annot["MES_var"] = -100 + (float(annot["MaxEntScan_alt"]) * 100) / float(annot["MaxEntScan_ref"])

annotations[-1]["ANN"].append(annot)

# app.logger.debug(f" - Create Variant : {sample}")
variant = Variant(
id=f"{v.chrom}-{v.pos}-{v.ref}-{v.alt[0]}",
chr=v.chrom,
pos=v.pos,
ref=v.ref,
alt=v.alt[0],
annotations=annotations)
db.session.add(variant)

# If duplicate variant for sample :
# - catch exception
# - add to history & comments
try:
v2s = Var2Sample(
variant_ID=variant.id,
sample_ID=sample.id,
depth=v.getPopDP(),
allelic_depth=v.getPopAltAD()[0],
filter=v.filter)
db.session.add(v2s)
db.session.commit()
except exc.IntegrityError as e:
db.session.rollback()
app.logger.info(f"{type(e).__name__} : {e}")
history = History(
sample_ID=sample.id,
user_ID=user_id,
date=datetime.now(),
action=f"{type(e).__name__}")
db.session.add(history)
comment = Comment_sample(
comment=f"{type(e).__name__} : {e}",
sampleid=sample.id,
date=datetime.now(),
userid=user_id)
db.session.add(comment)
db.session.commit

path_locker.unlink()
db.session.commit()
current_file.unlink()
vcf_vep.unlink()
stats_vep.unlink()
if interface:
vcf_path.unlink()
history = History(
sample_ID=sample.id,
user_ID=user_id,
date=datetime.now(),
action=f"Sample Imported")
db.session.add(history)
sample.status = 1
db.session.commit()

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