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Ingest qc score fix 2 #318

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Ingest qc score fix 2 #318

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4d7dd15
Update run_scanpyQC_rna.py
wlason Nov 6, 2024
a8fadc3
Update ingest pipeline.yml QC defaults
wlason Nov 6, 2024
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2 changes: 1 addition & 1 deletion panpipes/panpipes/pipeline_ingest/pipeline.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -86,7 +86,7 @@ custom_genes_file: resources/qc_genelist_1.0.csv

# (for pipeline_ingest.py)
calc_proportions: hb,mt,rp
score_genes:
score_genes: MarkersNeutro

# cell cycle action
ccgenes: default
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14 changes: 7 additions & 7 deletions panpipes/python_scripts/run_scanpyQC_rna.py
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good catch @wlason setting None in the python script will kick in if nothing is specified in the pipeline.yml. (current default in the pipeline.yml is MarkersNeutro but the change you have introduced ensures that None is the intended parameter)

Original file line number Diff line number Diff line change
Expand Up @@ -54,7 +54,7 @@
default=None,
help="path to file containing list of genes to quantify")
parser.add_argument("--calc_proportions",
default="mitochondrial,ribosomal",
default=None,
help="which list of genes to use to calc proportion of mapped reads over total,per cell?")
parser.add_argument("--score_genes",
default=None,
Expand Down Expand Up @@ -125,11 +125,12 @@
L.error("You have not provided a list of custom genes to use for QC purposes")
sys.exit("You have not provided a list of custom genes to use for QC purposes")

for kk in calc_proportions:
xname= kk
gene_list = cat_dic[kk]
rna.var[xname] = [x in gene_list for x in rna.var_names] # annotate the group of hb genes as 'hb'
qc_vars.append(xname)
if args.calc_proportions is not None and args.calc_proportions != 'None':
for kk in calc_proportions:
xname = kk
gene_list = cat_dic[kk]
rna.var[xname] = [x in gene_list for x in rna.var_names] # annotate the group of hb genes as 'hb'
qc_vars.append(xname)

qc_info = ""
if qc_vars != []:
Expand Down Expand Up @@ -173,4 +174,3 @@
mdata.write(args.outfile)

L.info("Done")

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