From b7c628aa1df65e577f9f33c5a001fc26f1322293 Mon Sep 17 00:00:00 2001
From: Blaise Li <blaise.li__git@nsup.org>
Date: Tue, 6 Oct 2020 09:07:05 +0200
Subject: [PATCH] Wrong percentage escape attempt.

---
 smwrappers/explore_mapping_parameters/wrapper.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/smwrappers/explore_mapping_parameters/wrapper.py b/smwrappers/explore_mapping_parameters/wrapper.py
index 7f94718..0cebcfc 100644
--- a/smwrappers/explore_mapping_parameters/wrapper.py
+++ b/smwrappers/explore_mapping_parameters/wrapper.py
@@ -27,7 +27,7 @@ def mapping_command(aligner):
 cmd="niceload --noswap -q hisat2 -p {snakemake.threads} --dta --seed 123 -t {snakemake.params.these_settings} --mm -x {snakemake.params.index} -U {snakemake.params.fastq} --no-unal -S /dev/null"
 echo ${{cmd}} 1> {snakemake.log.log}
 eval ${{cmd}} 1>> {snakemake.log.log} 2> {snakemake.log.err}
-rate=$(grep 'overall alignment rate' {snakemake.log.err} | tail -1 | tee -a {snakemake.log.log} | cut -d"%%" -f1)
+rate=$(grep 'overall alignment rate' {snakemake.log.err} | tail -1 | tee -a {snakemake.log.log} | cut -d"%" -f1)
 echo -e "${{rate}}\\t{snakemake.params.these_settings}" >> {snakemake.params.rates_record}
 """
     elif aligner == "bowtie2":
@@ -36,7 +36,7 @@ echo -e "${{rate}}\\t{snakemake.params.these_settings}" >> {snakemake.params.rat
 cmd="niceload --noswap -q bowtie2 -p {snakemake.threads} --seed 123 -t {snakemake.params.these_settings} --mm -x {snakemake.params.index} -U {snakemake.params.fastq} --no-unal -S /dev/null"
 echo ${{cmd}} > {snakemake.log.log}
 eval ${{cmd}} 1>> {snakemake.log.log} 2> {snakemake.log.err}
-rate=$(grep 'overall alignment rate' {snakemake.log.err} | tail -1 | tee -a {snakemake.log.log} | cut -d"%%" -f1)
+rate=$(grep 'overall alignment rate' {snakemake.log.err} | tail -1 | tee -a {snakemake.log.log} | cut -d"%" -f1)
 echo -e "${{rate}}\\t{snakemake.params.these_settings}" >> {snakemake.params.rates_record}
 """
 #    elif aligner == "crac":
-- 
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