Entering edit mode
2.9 years ago
Begonia_pavonina
▴
150
Hello everyone,
I wish to change the name of the contigs in a SAM file.
For this, I have to change each line of the RNAME field in the SAM file, based on a reference list.txt file with the format:
head -2 list.txt
>former_contig_name_1 new_contig_name_1
>former_contig_name_2 new_contig_name_2
I have tried different command to replace the former_name by the new_name, but it is a bit tricky.
The AWK command is printing the entire BAM file for one substitution, and I have failed to make a loop with it.
The SED command seems not to consider different fields, and I don't know how to target the RNAME field (3rd field).
cat list.txt | while read f ;
do
echo $f > temp_file ;
former_name=$(cut -f1 temp_file) ;
new_name=$(cut -f2 temp_file) ;
sed -i 's/$former_name/$new_name/g' file.sam ;
done
Would anyone know a more simple way to do it? Or just know how to target the 3rd column of the file.sam with sed? Thanks for the help!
