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get_metadata.py
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get_metadata.py
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#!/usr/bin/env python
from __future__ import print_function
import xmltodict
from collections import OrderedDict
import re
import argparse
import os
import json
from pathlib import Path
import yaml
class RunfolderInfo:
def __init__(self, runfolder, bcl2fastq_outdir):
self.runfolder = runfolder
self.run_parameters = self.read_run_parameters()
self.stats_json = self.read_stats_json(bcl2fastq_outdir)
self.description_and_identifier = OrderedDict()
self.run_parameters_tags = {
"RunId": "Run ID",
"RunID": "Run ID",
"InstrumentType": "Instrument type",
"ApplicationName": "Control software",
"Application": "Control software",
"ApplicationVersion": "Control software version",
"SystemSuiteVersion": "Control software version",
"Flowcell": "Flowcell type",
"FlowCellMode": "Flowcell type",
"ReagentKitVersion": "Reagent kit version",
"RTAVersion": "RTA Version",
"RtaVersion": "RTA Version",
}
def find(self, d, tag):
if isinstance(d, dict):
if tag in d:
yield d[tag]
for k, v in d.items():
if isinstance(v, dict):
yield from self.find(v, tag)
if isinstance(v, list):
for i in v:
yield from self.find(i, tag)
def read_run_parameters(self):
alt_1 = os.path.join(self.runfolder, "runParameters.xml")
alt_2 = os.path.join(self.runfolder, "RunParameters.xml")
if os.path.exists(alt_1):
with open(alt_1) as f:
return xmltodict.parse(f.read())
elif os.path.exists(alt_2):
with open(alt_2) as f:
return xmltodict.parse(f.read())
else:
return None
def find_flowcell_type_novaseqx(self):
try:
consumables = self.run_parameters["RunParameters"]["ConsumableInfo"][
"ConsumableInfo"
]
flowcell = next(
consumable
for consumable in consumables
if consumable["Type"] == "FlowCell"
)
flowcell_type = flowcell.get("Name", flowcell.get("Mode"))
except (KeyError, StopIteration):
return None
return {"Flowcell type": flowcell_type}
def read_stats_json(self, bcl2fastq_outdir):
stats_json_path = os.path.join(
self.runfolder, bcl2fastq_outdir, "Stats/Stats.json"
)
if os.path.exists(stats_json_path):
with open(stats_json_path) as f:
return json.load(f)
else:
return None
def get_bcl2fastq_version(self, runfolder):
with open(os.path.join(runfolder, "bcl2fastq_version")) as f:
bcl2fastq_str = f.read()
return bcl2fastq_str.split("v")[1].strip()
def get_software_version(self, runfolder):
with open(Path(runfolder) / "pipeline_info" / "software_versions.yml") as f:
return {
software: version
for software_dict in yaml.safe_load(f).values()
for software, version in software_dict.items()
}
def get_run_parameters(self):
results = OrderedDict()
for key, value in self.run_parameters_tags.items():
info = list(self.find(self.run_parameters, key))
if info:
results[value] = info[0]
return results
def get_read_cycles(self):
read_and_cycles = OrderedDict()
read_counter = 1
index_counter = 1
try:
for read_info in self.stats_json["ReadInfosForLanes"][0]["ReadInfos"]:
if read_info["IsIndexedRead"]:
read_and_cycles[f"Index {index_counter} (bp)"] = read_info[
"NumCycles"
]
index_counter += 1
else:
read_and_cycles[f"Read {read_counter} (bp)"] = read_info[
"NumCycles"
]
read_counter += 1
return read_and_cycles
except TypeError:
return read_and_cycles
def get_info(self):
results = self.get_read_cycles()
results.update(self.get_run_parameters())
flowcell_type = self.find_flowcell_type_novaseqx()
if flowcell_type:
results.update(flowcell_type)
return results
def get_demultiplexing_info(self):
try:
return {
"Demultiplexing": {
"bcl2fastq": self.get_bcl2fastq_version(self.runfolder)
}
}
except FileNotFoundError:
pass
try:
return {"Demultiplexing": self.get_software_version(self.runfolder)}
except FileNotFoundError:
pass
return {}
if __name__ == "__main__":
parser = argparse.ArgumentParser(description="Dumps a metadata yaml for MultiQC")
parser.add_argument(
"--runfolder", type=str, required=True, help="Path to runfolder"
)
parser.add_argument(
"--bcl2fastq-outdir",
type=str,
default="Data/Intensities/BaseCalls",
help="Path to bcl2fastq output folder relative to the runfolder",
)
args = parser.parse_args()
runfolder = args.runfolder
bcl2fastq_outdir = args.bcl2fastq_outdir
runfolder_info = RunfolderInfo(runfolder, bcl2fastq_outdir)
info = runfolder_info.get_info()
print(
"""
id: 'sequencing_metadata'
section_name: 'Sequencing Metadata'
plot_type: 'html'
description: 'regarding the sequencing run'
data: |
<dl class="dl-horizontal">
"""
)
for k, v in info.items():
print(f" <dt>{k}</dt><dd><samp>{v}</samp></dd>")
print(" <dt>Demultiplexing</dt>")
for software, version in runfolder_info.get_demultiplexing_info().items():
print(f" <dd>{software}: <samp>{version}</samp></dd>")
print(" </dl>")