Linux while read only reads first line of file - linux

Question

I'm trying to subtitute headers in a file that looks like this:
NC_037638.1 Apis mellifera strain DH4 linkage group LG1, Amel_HAv3.1, whole genome shotgun sequence
GAGAGAATTAACTACCTTAACCTGAACCTAAACCTACCGATAACCTAACTCTAAACTATACCTTTAACCCCTAAACCCTA
CACCTAAGTCCTAAACCAATAACCTTAACCCTAACAACTATATAAAACACTAACCTATAACCTAATCCCCTAACTACTAA
ActactaacctaacctaaaactatatacctaacctaaaccttaCCCTAACCATAACCTATTACTCTAACCCTACCAAGAG
CCTAAACCTAGAAACTTAACCCCTACAACCCTTAACCTTAACCTACACCTAACTACCTAATCCTACCTAACCtataccta
The file (Bee.fasta) has several headers (one for each sequence), the headers look like this:
NC_037638.1 Apis mellifera strain DH4 linkage group LG1, Amel_HAv3.1, whole genome shotgun sequence
I want to change them into this:
LG1
*LG1 is just an example, depending on the line of the file it can be LG1, LG2, LG3, ...
The above code changes only the first header per iteration, leaving the latter headers unchanged.
Thanks in advance :)
I'm trying to subtitute headers in a file with the following code:
#!/bin/bash
grep 'LG' Be.fasta > old_headers.txt
while read header
do
new_header=$(echo $header | awk -F ' ' '{print $8}')
sed "s/$header/$new_header/g" Bee.fasta >> somefile.txt
done < old_headers.txt
The above code changes only the first header per iteration, leaving the latter headers unchanged.

Answer 1

You're overthinking this. Plus looping over lines of text using bash is pretty much always a bad idea, performance-wise. Tools like sed, awk & perl were born to this job (text processing).
Since we know that the word group can only appear in headers and never in the gene-sequence Jason's sed in the comments should do all you ask for.
$ cat Bee.fasta
NC_037638.1 Apis mellifera strain DH4 linkage group LG1, Amel_HAv3.1, whole genome shotgun sequence
GAGAGAATTAACTACCTTAACCTGAACCTAAACCTACCGATAACCTAACTCTAAACTATACCTTTAACCCCTAAACCCTA CACCTAAGTCCTAAACCAATAACCTTAACCCTAACAACTATATAAAACACTAACCTATAACCTAATCCCCTAACTACTAA ActactaacctaacctaaaactatatacctaacctaaaccttaCCCTAACCATAACCTATTACTCTAACCCTACCAAGAG CCTAAACCTAGAAACTTAACCCCTACAACCCTTAACCTTAACCTACACCTAACTACCTAATCCTACCTAACCtataccta
$ sed -E 's/^.*group *([^,]+).*$/\1/g' Bee.fasta > somefile.txt
$ cat somefile.txt
LG1
GAGAGAATTAACTACCTTAACCTGAACCTAAACCTACCGATAACCTAACTCTAAACTATACCTTTAACCCCTAAACCCTA CACCTAAGTCCTAAACCAATAACCTTAACCCTAACAACTATATAAAACACTAACCTATAACCTAATCCCCTAACTACTAA ActactaacctaacctaaaactatatacctaacctaaaccttaCCCTAACCATAACCTATTACTCTAACCCTACCAAGAG CCTAAACCTAGAAACTTAACCCCTACAACCCTTAACCTTAACCTACACCTAACTACCTAATCCTACCTAACCtataccta
$