bash script to run clustalw and fetching sequences
Hello,
I'm trying to run a bash script. I need to execute on all the files in the folder.
Here I'm posting the script
#!/bin/bash
module bash load clustalw pal2nal exonerate
file_path="/dirname/"
source=`pwd`
dir=`mktemp -d` && cd $dir
for file in file_path;do
echo "processsing "$file" file";
ln -fs "$file" pep
clustalw -INFILE=pep -PWGAPOPEN=10 PWGAPEXT=1 > pep.out
extract_value.py pep.out
fastaindex pep pep.idx
fastafetch -f pep -i pep.idx -q sequence_lst -F > $source/$1pep.fa
rm -r $dir
done
When I run this I get
processsing file_path file
Error: unknown option -wgapext.
My understanding is that it is not reading the files one by one at all.Any input will be appreciated. Thanks in advance
• 3,841 views
•
link
updated
by
Ram
•
written
by
Biocode_user •
•
written
by
Biocode_user •
1 answer
You've missed a hyphen near PWGAPEXT:
#!/bin/bash
module bash load clustalw pal2nal exonerate
file_path="/dirname/"
source=`pwd`
dir=`mktemp -d` && cd $dir
for file in file_path;do
echo "processsing "$file" file";
ln -fs "$file" pep
clustalw -INFILE=pep -PWGAPOPEN=10 -PWGAPEXT=1 > pep.out
# ---------------------------here--^
extract_value.py pep.out
fastaindex pep pep.idx
fastafetch -f pep -i pep.idx -q sequence_lst -F > $source/$1pep.fa
rm -r $dir
done
Log in to answer this question.
More posts like this
