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Cellranger VDJ: handle missing vdj_annotation and vdj_enrichment sect…
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…ions (#2579)
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@vladsavelyev
vladsavelyev committed May 17, 2024
1 parent bc61f51 commit b0ebfbb
Showing 1 changed file with 46 additions and 53 deletions.
99 changes: 46 additions & 53 deletions multiqc/modules/cellranger/vdj.py
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
""" MultiQC module to parse output from Cell Ranger count """
"""MultiQC module to parse output from Cell Ranger count"""

import json
import logging
Expand Down Expand Up @@ -164,13 +164,20 @@ def parse_vdj_html(self):
def parse_vdj_report(self, f):
"""Go through the html report of cell ranger and extract the data in a dicts"""

mydict = None
for line in f["f"]:
line = line.strip()
if line.startswith("const data"):
line = line.replace("const data = ", "")
mydict = json.loads(line)
mydict = mydict["summary"]
break
if mydict is None:
log.debug(f"Could not find VDJ data in {f['fn']}")
return
if "vdj_sequencing" not in mydict["summary_tab"] or "cells" not in mydict["summary_tab"]:
log.debug(f"Could not find VDJ sections in {f['fn']}")
return

s_name = self.clean_s_name(mydict["sample"]["id"], f)

Expand Down Expand Up @@ -206,6 +213,7 @@ def parse_vdj_report(self, f):
"VDJ",
)

# Store sequencing results data from vdj report
col_dict = {
"Number of Reads": "reads",
"Valid Barcodes": "valid bc",
Expand All @@ -223,12 +231,11 @@ def parse_vdj_report(self, f):
"VDJ",
)

# Store sequencing results data from vdj report
data_rows = (
mydict["summary_tab"]["vdj_sequencing"]["table"]["rows"]
+ mydict["summary_tab"]["cells"]["table"]["rows"]
+ mydict["summary_tab"]["vdj_enrichment"]["table"]["rows"]
)
data_rows = mydict["summary_tab"]["vdj_sequencing"]["table"]["rows"]
if "cells" in mydict["summary_tab"]:
data_rows += mydict["summary_tab"]["cells"]["table"]["rows"]
if "vdj_enrichment" in mydict["summary_tab"]:
data_rows += mydict["summary_tab"]["vdj_enrichment"]["table"]["rows"]
col_dict = {
"Number of Reads": "reads",
"Valid Barcodes": "valid bc",
Expand All @@ -254,51 +261,36 @@ def parse_vdj_report(self, f):
"VDJ",
)

# Store VDJ annotation and expression data from vdj report
col_dict = {
"Cells With Productive V-J Spanning Pair": "cells VJ span",
"Cells With Productive V-J Spanning (IGK, IGH) Pair": "cells IGK-IGH span",
"Cells With Productive V-J Spanning (IGL, IGH) Pair": "cells IGL-IGH span",
"Paired Clonotype Diversity": "clonotype diversity",
"Cells With IGH Contig": "cells IGH contig",
"Cells With IGK Contig": "cells IGK contig",
"Cells With IGL Contig": "cells IGL contig",
"Cells With CDR3-annotated IGH Contig": "cells IGH CDR3",
"Cells With CDR3-annotated IGK Contig": "cells IGK CDR3",
"Cells With CDR3-annotated IGL Contig": "cells IGL CDR3",
"Cells With V-J Spanning IGH Contig": "cells IGH VJ span",
"Cells With V-J Spanning IGK Contig": "cells IGK VJ span",
"Cells With V-J Spanning IGL Contig": "cells IGL VJ span",
"Cells With Productive IGH Contig": "cells IGH productive",
"Cells With Productive IGK Contig": "cells IGK productive",
"Cells With Productive IGL Contig": "cells IGL productive",
}
colours = {
# "cells VJ span": "",
# "cells IGK-IGH span": "",
# "cells IGL-IGH span": "",
# "clonotype diversity": "",
# "cells IGH contig": "",
# "cells IGK contig": "",
# "cells IGL contig": "",
# "cells IGH CDR3": "",
# "cells IGK CDR3": "",
# "cells IGL CDR3": "",
# "cells IGH VJ span": "",
# "cells IGK VJ span": "",
# "cells IGL VJ span": "",
# "cells IGH productive": "",
# "cells IGK productive": "",
# "cells IGL productive": "",
}
data_annotations, self.vdj_annotations_headers = update_dict(
data_general_stats,
self.vdj_annotations_headers,
mydict["summary_tab"]["vdj_annotation"]["table"]["rows"],
col_dict,
colours,
"VDJ",
)
if "vdj_annotation" in mydict["summary_tab"]:
# Store VDJ annotation and expression data from vdj report
col_dict = {
"Cells With Productive V-J Spanning Pair": "cells VJ span",
"Cells With Productive V-J Spanning (IGK, IGH) Pair": "cells IGK-IGH span",
"Cells With Productive V-J Spanning (IGL, IGH) Pair": "cells IGL-IGH span",
"Paired Clonotype Diversity": "clonotype diversity",
"Cells With IGH Contig": "cells IGH contig",
"Cells With IGK Contig": "cells IGK contig",
"Cells With IGL Contig": "cells IGL contig",
"Cells With CDR3-annotated IGH Contig": "cells IGH CDR3",
"Cells With CDR3-annotated IGK Contig": "cells IGK CDR3",
"Cells With CDR3-annotated IGL Contig": "cells IGL CDR3",
"Cells With V-J Spanning IGH Contig": "cells IGH VJ span",
"Cells With V-J Spanning IGK Contig": "cells IGK VJ span",
"Cells With V-J Spanning IGL Contig": "cells IGL VJ span",
"Cells With Productive IGH Contig": "cells IGH productive",
"Cells With Productive IGK Contig": "cells IGK productive",
"Cells With Productive IGL Contig": "cells IGL productive",
}
data_annotations, self.vdj_annotations_headers = update_dict(
data_general_stats,
self.vdj_annotations_headers,
mydict["summary_tab"]["vdj_annotation"]["table"]["rows"],
col_dict,
{},
"VDJ",
)
else:
data_annotations = None

# Extract warnings if any
warnings = dict()
Expand Down Expand Up @@ -335,7 +327,8 @@ def parse_vdj_report(self, f):
self.add_data_source(f, s_name, module="cellranger", section="count")
self.cellrangervdj_mapping[s_name] = data
self.cellrangervdj_general_data[s_name] = data_general_stats
self.cellrangervdj_annotations[s_name] = data_annotations
if data_annotations:
self.cellrangervdj_annotations[s_name] = data_annotations
if len(warnings) > 0:
self.cellrangervdj_warnings[s_name] = warnings
self.cellrangervdj_plots_conf = plots
Expand Down

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