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Merge pull request #1006 from fls-bioinformatics-core/report-fix-10x-…
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…multiplexed-samples

'report' command: fix reporting of 10x multiplexed samples
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@pjbriggs
pjbriggs authored Nov 4, 2024
2 parents 7a84172 + 15d58d5 commit 41edd99
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Showing 2 changed files with 549 additions and 56 deletions.
126 changes: 70 additions & 56 deletions auto_process_ngs/commands/report_cmd.py
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Original file line number Diff line number Diff line change
Expand Up @@ -164,24 +164,23 @@ def report_info(ap):
(bcf_utils.pretty_print_names(
info.multiplexed_samples.split(',')),
project.prettyPrintSamples())
elif project.info.library_type in ("CellPlex",
"Flex"):
# Fetch implicit multiplexed sample info from config
try:
multi_config = CellrangerMultiConfigCsv(
os.path.join(project.dirn,"10x_multi_config.csv"))
number_of_samples = "%s multiplexed (%s physical)" % \
(len(multi_config.sample_names),
len(project.samples))
sample_names = "%s (%s)" % \
(multi_config.pretty_print_samples(),
project.prettyPrintSamples())
except FileNotFoundError:
number_of_samples = "%s (physical)" % len(project.samples)
sample_names = project.prettyPrintSamples()
else:
number_of_samples = len(project.samples)
sample_names = project.prettyPrintSamples()
multiplexed_samples = get_multiplexed_samples(project)
if multiplexed_samples is not None:
if multiplexed_samples:
number_of_samples = "%s multiplexed (%s physical)" % \
(len(multiplexed_samples),
len(project.samples))
sample_names = "%s (%s)" % \
(bcf_utils.pretty_print_names(
multiplexed_samples),
project.prettyPrintSamples())
else:
number_of_samples = "%s (physical)" % len(project.samples)
sample_names = project.prettyPrintSamples()
else:
number_of_samples = len(project.samples)
sample_names = project.prettyPrintSamples()
report.append("\n- %s" % project.name)
report.append(" %s" % ('-'*len(project.name),))
report.append(" User : %s" % info.user)
Expand Down Expand Up @@ -232,20 +231,15 @@ def report_concise(ap):
number_of_samples = len(p.info.multiplexed_samples.\
split(','))
has_multiplexed_samples = True
elif p.info.library_type in ("CellPlex",
"Flex"):
# Fetch implicit multiplexed sample info from config
try:
multi_config = CellrangerMultiConfigCsv(
os.path.join(p.dirn,
"10x_multi_config.csv"))
number_of_samples = len(multi_config.sample_names)
else:
multiplexed_samples = get_multiplexed_samples(p)
if multiplexed_samples:
# Implicit multiplexed sample info from config
number_of_samples = len(multiplexed_samples)
has_multiplexed_samples = True
except FileNotFoundError:
else:
# Fall back to physical samples
number_of_samples = len(p.samples)
else:
# Physical samples
number_of_samples = len(p.samples)
if has_multiplexed_samples:
samples = "%s multiplexed sample%s" % \
('?' if number_of_samples == 0
Expand Down Expand Up @@ -464,20 +458,15 @@ def report_summary(ap):
number_of_samples = len(project.info.multiplexed_samples.\
split(','))
has_multiplexed_samples = True
elif project.info.library_type in ("CellPlex",
"Flex"):
# Fetch implicit multiplexed sample info from config
try:
multi_config = CellrangerMultiConfigCsv(
os.path.join(project.dirn,
"10x_multi_config.csv"))
number_of_samples = len(multi_config.sample_names)
else:
multiplexed_samples = get_multiplexed_samples(project)
if multiplexed_samples:
# Implicit multiplexed sample info from config
number_of_samples = len(multiplexed_samples)
has_multiplexed_samples = True
except FileNotFoundError:
else:
# Physical samples
number_of_samples = len(project.samples)
else:
# Physical samples
number_of_samples = len(project.samples)
if has_multiplexed_samples:
samples = "%s multiplexed sample%s" % \
('?' if number_of_samples == 0
Expand Down Expand Up @@ -646,15 +635,8 @@ def fetch_value(ap,project,field):
info = project.info
except AttributeError:
info = None
# 10x CellPlex and Flex data
multi_config = None
if project.info.library_type in ("CellPlex",
"Flex"):
try:
multi_config = CellrangerMultiConfigCsv(
os.path.join(project.dirn,"10x_multi_config.csv"))
except FileNotFoundError:
pass
# Implicit multiplexed samples
multiplexed_samples = get_multiplexed_samples(project)
# Generate value for supplied field name
if field == 'datestamp':
return IlluminaData.split_run_name(ap.run_name)[0]
Expand Down Expand Up @@ -703,9 +685,9 @@ def fetch_value(ap,project,field):
return '?'
else:
return str(len(info.multiplexed_samples.split(',')))
elif multi_config:
# Number of multiplexed samples from 10x multi config
return str(len(multi_config.sample_names))
elif multiplexed_samples:
# Implicit number of multiplexed samples
return str(len(multiplexed_samples))
else:
# Number of "physical" samples
return str(len(project.samples))
Expand All @@ -722,9 +704,9 @@ def fetch_value(ap,project,field):
else:
return bcf_utils.pretty_print_names(
info.multiplexed_samples.split(','))
elif multi_config:
# Names of multiplexed samples from 10x multi config
return multi_config.pretty_print_samples()
elif multiplexed_samples:
# Names of implicit multiplexed samples
return bcf_utils.pretty_print_names(multiplexed_samples)
else:
# Names of "physical" samples
return project.prettyPrintSamples()
Expand All @@ -741,3 +723,35 @@ def default_value(s,default=""):
if s is None:
return default
return s

def get_multiplexed_samples(project):
"""
Return the names of implicit multiplexed samples in a project
Arguments:
project (AnalysisProject): project to get implicit multiplexed
samples for
Returns:
List: list of multiplexed sample names, or empty list if
project should have multiplexed samples but the cannot be
identified. Returns None if project is not of a type to
have multiplexed samples.
"""
if project.info.library_type in ("CellPlex",
"CellPlex scRNA-seq",
"Flex"):
# Fetch implicit multiplexed sample info from configs
multiplexed_samples = []
for f in os.listdir(project.dirn):
if f.startswith("10x_multi_config.") and \
f.endswith(".csv"):
multi_config = CellrangerMultiConfigCsv(
os.path.join(project.dirn, f))
multiplexed_samples.extend(multi_config.sample_names)
# Return multiplexed sample names
return sorted(multiplexed_samples)
else:
# No multiplexed samples expected
# Return None
return None
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