So I have a textfile with headers for genes and there are different gene sequences under the same species. So I have extracted the headers (headers.txt) and copied it into another file (uniqueheaders.txt). I removed all the duplicates in uniqueheaders.txt.
I am trying to loop read a line of uniqueheaders.txt then loop read headers.txt to check for duplicates. The if statement detects the duplicate and increments a counter to append it to the header. This will number all the headers in headers.txt so I insert them back into my FASTA file. my code is here:
while IFS= read -r uniqueline do counter=0 while IFS= read headline do if [ "$uniqueline" == "$headline" ] then let "counter++" #append counter to the headline variable to number it. sed "$headline s/$/$counter/" -i headers if done < headers.txt done < uniqueheaders.txt The issue is that the terminal keeps spitting out the error
sed: -e expression #1, char 1: unknown command: 'M' and
sed: -e expression #1, char 2: extra characters after command Both files contain unique header names:
Mus musculus Homo sapiens Rattus norvegicus How do I modify the sed command to prevent this error? Is there a better way of doing this in bash?
Example of inputs (note that gene sequence don't really have a pattern in terms of how many lines it takes up) **** Gene sequences are all in one file
Mus musculus MDFJSGHDFSBGKJBDFSGKJBDFS NGBJDFSBGKJDFSHNGKJDFSGHG Rattus norvegicus SNOFBDSFNLSFSFSFSJFJSDFSD Mus musculus NJALDJASJDLAJSJAPOJPOASDJG DSFHBDSFHSDFHDFSHJDFSJKSSF Desired output:
Mus musculus1 MDFJSGHDFSBGKJBDFSGKJBDFS NGBJDFSBGKJDFSHNGKJDFSGHG Rattus norvegicus SNOFBDSFNLSFSFSFSJFJSDFSD Mus musculus2 NJALDJASJDLAJSJAPOJPOASDJG DSFHBDSFHSDFHDFSHJDFSJKSSF 
