From acff4bd9fffbd5a6326b96144f2fe47c2b548a36 Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Tue, 11 Jan 2022 12:28:28 +0100
Subject: [PATCH] Also create directories
---
umi.wdl | 6 ++++--
1 file changed, 4 insertions(+), 2 deletions(-)
diff --git a/umi.wdl b/umi.wdl
index 7c43565..360405f 100644
--- a/umi.wdl
+++ b/umi.wdl
@@ -37,8 +37,9 @@ task BamReadNameToUmiTag {
String bamIndexPath = sub(select_first([outputPath]), "\.bam$", ".bai")
command <<<
python <<CODE
- import pysam
+ import pysam
import sys
+ import os
from typing import Tuple
@@ -56,8 +57,9 @@ task BamReadNameToUmiTag {
return " ".join([new_id, other_parts]), umi
return new_id, umi
- def annotate_umis(in_file, out_file, bam_tag = "RX"):
+ def annotate_umis(in_file, out_file, bam_tag="RX"):
in_bam = pysam.AlignmentFile(in_file, "rb")
+ os.makedirs(os.path.dirname(out_file), exist_ok=True)
out_bam = pysam.AlignmentFile(out_file, "wb", template=in_bam)
for segment in in_bam: # type: pysam.AlignedSegment
new_name, umi = split_umi_from_name(segment.query_name)
--
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