Some of the file names and locations were different because I was at the office then at home and that was a problem leading to typos. I apologize for that and am back in the office. The details below are the exact files in the directory.
There are always 3 vcf.gz files in the following format below in each directory:
The numeric prefix of each is always 7 characters xx-xxxx and unique. The portion of code in the previous post uses each vcf.gz file to create a corresponding .txt file with only the unique numeric prefix followed by _header.
Files in /home/cmccabe/Desktop/NGS/test (if code works as expected)
I am trying to match the 16-0000.vcf.gz with the 16-0000.txt and read 16-0000.vcf.gz into $file1 and 16-0000.txt into $file2.
These two variables $file1 and $file2 would be passed to the reheader command, in bold,below which is part of a loop.
After the $file1 and $file2 are processed for 16-0000, the process is repeated for the remaining two files, 16-0002 and 16-0005.
reheader command
Code:
logfile=/home/cmccabe/Desktop/NGS/test/process.log
for f in /home/cmccabe/Desktop/NGS/test/*.vcf.gz ; do
echo "Start vcf edit header creation: $(date) - file: $f"
bname=`basename $f`
pref=${bname%%.vcf.gz}
bcftools reheader -h $file1 $file2 > ${pref}_fixed.vcf.gz
echo "End edit header creation: $(date) - file: $f"
done >> "$logfile"
There is only one directory that contains the files and that is /home/cmccabe/Desktop/NGS/test. The numerical prefixes are not being stripped off and used to perform the match between files nor are the variables being passed to reheader. Thank you .
Code:
ls -l /home/cmccabe/Desktop/NGS/test
total 6116
-rw-rw-r-- 1 cmccabe cmccabe 9350 Feb 3 07:08 16-0000_File-A_variant_strandbias_readcount_header.txt
-rw-rw-r-- 1 cmccabe cmccabe 2031861 Jan 31 11:07 16-0000_File-A_variant_strandbias_readcount.vcf.gz
-rw-rw-r-- 1 cmccabe cmccabe 9353 Feb 3 07:08 16-0002_File-B_variant_strandbias_readcount_header.txt
-rw-rw-r-- 1 cmccabe cmccabe 2361911 Jan 31 11:07 16-0002_File-B_variant_strandbias_readcount.vcf.gz
-rw-rw-r-- 1 cmccabe cmccabe 9351 Feb 3 07:08 16-0005_File-C_variant_strandbias_readcount_header.txt
-rw-rw-r-- 1 cmccabe cmccabe 1816700 Jan 31 11:07 16-0005_File-C_variant_strandbias_readcount.vcf.gz
-rw-rw-r-- 1 cmccabe cmccabe 2622 Feb 3 07:08 process.log
-rw-rw-r-- 1 cmccabe cmccabe 1278 Feb 2 13:17 process.log~
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