From 7b50bc243f215c8b9085c769c21c24ad572d0051 Mon Sep 17 00:00:00 2001
From: Redmar van den Berg <RedmarvandenBerg@lumc.nl>
Date: Mon, 2 Dec 2019 12:59:10 +0100
Subject: [PATCH] Make sure the parent output folder exists
Also update the argparse help text for the --discordant-vcf flag to
refer to a regular VCF file, instead of a gzipped VCF file.
---
vtools/cli.py | 7 ++++++-
1 file changed, 6 insertions(+), 1 deletion(-)
diff --git a/vtools/cli.py b/vtools/cli.py
index 97ee6df..ebddab0 100644
--- a/vtools/cli.py
+++ b/vtools/cli.py
@@ -6,6 +6,7 @@ vtools.cli
:copyright: (c) Leiden University Medical Center
:license: MIT
"""
+import os
import json
import click
from cyvcf2 import VCF, Writer
@@ -35,7 +36,7 @@ from .gcoverage import RefRecord, region_coverages
@click.option("-s", "--stats", type=click.Path(writable=True),
help="Path to output stats json file")
@click.option("-dvcf", "--discordant-vcf", type=click.Path(writable=True),
- help="Path to output gzipped discordant vcf file",
+ help="Path to output the discordant vcf file",
required=False)
@click.option("-mq", "--min-qual", type=float,
help="Minimum quality of variants to consider", default=30)
@@ -56,6 +57,10 @@ def evaluate_cli(call_vcf, positive_vcf, call_samples, positive_samples,
# If there were discordand records, and a discordant-vcf should be written
if len(disc) > 0 and discordant_vcf:
+ # make sure the parent folder exists
+ parent_folder = os.path.dirname(discordant_vcf)
+ os.makedirs(parent_folder, exist_ok=True)
+
with click.open_file(discordant_vcf, 'w') as fout:
# First, we write the vcf header
with gzip.open(call_vcf, 'rt') as fin:
--
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