Hi
I have the following headers for my fasta files downloaded from IMG/JGI
2648318750 Ga0098755_14192 DNA gyrase subunit B [Microbacterium sp. GCS4 : Ga0098755_14]
I would like this:
Microbacterium sp. GCS4 : Ga0098755_14
The strings/characters are all different for each header. I found this to try:
sed 's/.[([^]])].*/\1/g'
Its works, but I need to keep the '>' at the start to obviously denote each sequence in the fasta file. Is there some parenthesis I can add to keep this character alongside my current command?
Cheers in advance!
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Micro_Warwick •
Using awk ?
awk '/^>/ {i=index($0,"[");j=index($0,"]");print ">" substr($0,i+1,(j-i)-1); next;} {print;}' in.fa > out.fa
Sorry, that just ended up with a blank file? The file contains 20, 000 sequences, not just one if that means something else needs to be added
there is something wrong in the way you run my awk script:
$ echo -e '>2648318750 Ga0098755_14192 DNA gyrase subunit B [Microbacterium sp. GCS4 : Ga0098755_14]\nATACGACGATCGT\n>2648318750 Ga0098755_14192 DNA gyrase subunit B [Microbacterium sp. GCS4 : Ga0098755_14]\nATACGACGATCGT' | awk '/^>/ {i=index($0,"[");j=index($0,"]");print ">" substr($0,i+1,(j-i)-1); next;} {print;}'
>Microbacterium sp. GCS4 : Ga0098755_14
ATACGACGATCGT
>Microbacterium sp. GCS4 : Ga0098755_14
ATACGACGATCGT
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Yes, you may use another pair of parenthesis to catch the '>' at the beginning of the line. On a Debian system I also have to use option '-r' to allow referencing of subpatterns.