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Check External gene annot #546

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Check External gene annot #546

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ac3f2fd
set GENE_ANNOTATION to null for non-external samples
AtaJadidAhari May 3, 2024
49ddb21
remove redundant prints
AtaJadidAhari May 27, 2024
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10 changes: 10 additions & 0 deletions drop/config/ExportCounts.py
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Original file line number Diff line number Diff line change
@@ -1,5 +1,6 @@
from snakemake.io import expand
from drop import utils
from snakemake.logging import logger


class ExportCounts:
Expand Down Expand Up @@ -37,6 +38,8 @@ def __init__(

self.pattern = self.outputRoot / "{dataset}--{genomeAssembly}--{annotation}"

self.checkNonExternalGeneAnnotation()

def setDefaults(self, config_dict, gene_annotations):
utils.setKey(config_dict, None, "geneAnnotations", gene_annotations)
utils.setKey(config_dict, None, "excludeGroups", list())
Expand Down Expand Up @@ -107,3 +110,10 @@ def getExportCountFiles(self, count_type, suffix="tsv.gz", expandPattern=None, *
datasets = self.getExportGroups([self.COUNT_TYPE_MAP[count_type]])
expandPattern = count_type if expandPattern is None else expandPattern
return self.getFiles(f"{expandPattern}.{suffix}", datasets, **kwargs)

def checkNonExternalGeneAnnotation(self):
excluded_groups = self.config_dict['excludeGroups']
non_excluded_samples = self.sampleAnnotation.annotationTable[self.sampleAnnotation.annotationTable['DROP_GROUP'].isin(excluded_groups) == False]
if sum(non_excluded_samples['GENE_ANNOTATION'].isna() == False) > 0:
logger.info("WARNING: Found %d samples that had `GENE_ANNOTATION` provided in sample annotation table but are not external counts. The provided `GENE_ANNOTATIONs` are ignored.\n" % (sum(non_excluded_samples['GENE_ANNOTATION'].isna() == False)))
self.sampleAnnotation.annotationTable.loc[self.sampleAnnotation.annotationTable['DROP_GROUP'].isin(excluded_groups) == False, "GENE_ANNOTATION"] = ""
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