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Merge pull request #134 from c-BIG/develop
Release/0.13.0
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,64 @@ | ||
| #!/usr/bin/env python3 | ||
|
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| import argparse | ||
| import json | ||
| import pprint as pp | ||
| import subprocess | ||
| import numpy as np | ||
| import sys | ||
| import os | ||
| from pathlib import Path | ||
|
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| def parse_args(): | ||
| parser = argparse.ArgumentParser() | ||
| parser.add_argument("--sample_id", dest="sample_id", required=True, | ||
| default=None, | ||
| help="Sample ID") | ||
| parser.add_argument("--input_aln_metrics", dest="input_aln_metrics", required=True, | ||
| default=None, | ||
| help="Path to input aln metrics list") | ||
| parser.add_argument("--input_variants_metrics", dest="input_variants_metrics", required=True, | ||
| default=None, | ||
| help="Path to input variants metrics list") | ||
| parser.add_argument("--output_json", dest="output_json", required=False, | ||
| default="./metrics.json", | ||
| help="Path to output file for variant metrics. Default: ./variant_counts.json") | ||
| parser.add_argument("--scratch_dir", dest="scratch_dir", required=False, | ||
| default="./", | ||
| help="Path to scratch dir. Default: ./") | ||
| args = parser.parse_args() | ||
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| # create scratch dir if it doesn't exist | ||
| Path(args.scratch_dir).mkdir(parents=True, exist_ok=True) | ||
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| return args | ||
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| def data1(input_aln_metrics): | ||
| aln_input = {} | ||
| with open(input_aln_metrics, 'r') as f1: | ||
| aln_input = json.load(f1) | ||
| return aln_input | ||
|
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| def data2(input_variants_metrics): | ||
| variants_input = {} | ||
| with open(input_variants_metrics, 'r') as f2: | ||
| variants_input = json.load(f2) | ||
| return variants_input | ||
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| def save_output(data1, data2, outfile): | ||
| with open(outfile, "w") as f: | ||
| data1['wgs_qc_metrics']['variant_metrics'].update(data2['wgs_qc_metrics']['variant_metrics']) | ||
| #data1['wgs_qc_metrics']['variant_metrics'] = data2['wgs_qc_metrics']['variant_metrics'] | ||
| print(data1) | ||
| json.dump(data1, f, sort_keys=True, indent=4) | ||
| #json.dump({"biosample": data1["biosample"], "wgs_qc_metrics": {**data1["wgs_qc_metrics"], **data2["wgs_qc_metrics"]}}, f, sort_keys=True, indent=4) | ||
| f.write("\n") | ||
|
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| if __name__ == "__main__": | ||
| args = parse_args() | ||
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| aln = data1(args.input_aln_metrics) | ||
| variants = data2(args.input_variants_metrics) | ||
| save_output(aln, variants, args.output_json) |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,65 @@ | ||
| #!/usr/bin/env python3 | ||
|
|
||
| import argparse | ||
| import json | ||
| import pprint as pp | ||
| import subprocess | ||
| import numpy as np | ||
| import sys | ||
| import os | ||
| from pathlib import Path | ||
|
|
||
|
|
||
| def parse_args(): | ||
| parser = argparse.ArgumentParser() | ||
| parser.add_argument("--sample_id", dest="sample_id", required=True, | ||
| default=None, | ||
| help="Sample ID") | ||
| parser.add_argument("--input_metrics", dest="input_metrics", required=True, | ||
| default=None, | ||
| help="Path to input aln metrics list") | ||
| parser.add_argument("--output_json", dest="output_json", required=False, | ||
| default="./variant_counts.json", | ||
| help="Path to output file for variant metrics. Default: ./variant_counts.json") | ||
| parser.add_argument("--scratch_dir", dest="scratch_dir", required=False, | ||
| default="./", | ||
| help="Path to scratch dir. Default: ./") | ||
| args = parser.parse_args() | ||
|
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| # create scratch dir if it doesn't exist | ||
| Path(args.scratch_dir).mkdir(parents=True, exist_ok=True) | ||
|
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| return args | ||
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| def raw_data(input_metrics): | ||
| d = {} | ||
| with open(input_metrics) as f: | ||
| for line in f: | ||
| if not line.strip(): | ||
| continue | ||
| row = line.split('\t') | ||
| key = row[0] | ||
| value_str = row[1] | ||
| #d[key] = value_str.replace("\n", "") | ||
| try: | ||
| #value = float(value_str.strip()) | ||
| value = int(value_str) | ||
| except ValueError: | ||
| #value = value_str.strip() | ||
| value = float(value_str.strip()) | ||
| d[key] = value | ||
| return d | ||
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| def save_output(data_metrics, outfile): | ||
| with open(outfile, "w") as f: | ||
| # data_metrics = {"biosample" : {"id" : args.sample_id}, "wgs_qc_metrics" : data_metrics} | ||
| data_metrics = {"biosample" : {"id" : args.sample_id}, "wgs_qc_metrics" : {"aln_metrics" : data_metrics, "variant_metrics" : {}}} | ||
| json.dump(data_metrics, f, sort_keys=True, indent=4) | ||
| f.write("\n") | ||
|
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| if __name__ == "__main__": | ||
| args = parse_args() | ||
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| data_metrics = raw_data(args.input_metrics) | ||
| save_output(data_metrics, args.output_json) |
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