Hi everyone,
I made a short script to count the number of raw reads (fastq.gz) in my folder. The results will save in a text file (.txt).
echo "We count the number of reads for each file (fastq.gz)."
echo "file\traw_reads\ttrimmed_reads" > count_read_evolution_trim_test.txt
for f1 in *paired.fq.gz
do
echo $f1
RAW_READS=`gunzip -c $f1 | echo $((`wc -l`/4))`
echo -e "$f1\t$RAW_READS" >> count_read_evolution_trim_test.txt
done
But I obtained this error message:
./test_count_raw_reads.sh: command substitution: line 9: syntax error near unexpected token `)'
./test_count_raw_reads.sh: command substitution: line 9: `/4))'
./test_count_raw_reads.sh: command substitution: line 9: unexpected EOF while looking for matching `)'
./test_count_raw_reads.sh: command substitution: line 10: syntax error: unexpected end of file
./test_count_raw_reads.sh: line 9: -l: command not found code here
How I can fix this problem?
Thank you.
•
written
by
wanaga3166 •
Yep, exactly. The second ` stops the expression at:
`gunzip -c $f1 | echo $((`
If you want to keep this line you can maybe use awk to divide by 4:
RAW_READS=`gunzip -c $f1 | wc -l | awk '{print($1/4)}'`
edit: this is probably more efficient:
RAW_READS=`gunzip -c $f1 | awk 'END{print(NR/4)}'`
Thank you Martombo. Your solution works. I will be more careful with the backquotes.
you want:
find . -name "*q.gz" | while read F; do echo -n "$F " && echo $(( $(gunzip -c $F | wc -l) / 4 )) ; done
When I did this command line:
gunzip -c $f1 | echo $((wc -l/4))
It works, I obtained the number of raw reads. I just want to put the number of raw reads in a table, like in this example.
file | raw_read_number my_file_1 | 130000 my_file_2 | 160000 my_file_3 | 200000 I don't understand where I did a mistake.
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When I did this command line:
It works, I obtained the number of raw reads. I just want to put the number of raw reads in a table, like in this example.
file | raw_read_number
my_file_1 | 130000
my_file_2 | 160000
my_file_3 | 200000
I don't understand where I did a mistake.
you're piping a stream in echo : wrong
your use of ` is messing up this line:
If you watch my initial code (in the top) of this post, I put the back quote as you wrote. And I can't save the number of raw reads in my text table (count_read_evolution_trim_test.txt).
The problem in my code, that a I have two backquote in this line:
And it doesn't count the raw reads number.