rename mutiple fasta header for mutiple fasta files

[shashankgupta]

Hi,

I have mutiple fasta file and I want to change the header, for this I am using -

awk '/^>/{print ">C1_" ++i; next}{print}' C1_pandaseq.fasta > C1_pandaseq_new.fasta

input fasta-
>M03419:60:656544:1:1101:25150:3877:1
CCTACGGGTGGCTGCAGTGGGGAATTTTGGACAA
>M03419:60:656544:1:1101:8498:4267:1
ACTACGGGAGGCAGCAGGGGGGAATTTTGGACAATGGAAACCAGGG
>M03419:60:656544:1:1101:7884:4445:1
CCTACGGGTGGCAGCAGTGGGGAATATTGGACAATGCAACCCTGATCCAGC

output fasta-
>C1_1
CCTACGGGTGGCTGCAGTGGGGAATTTTGGACAAAAAAAAAAAAAAAA
>C1_2
ACTACGGGAGGCAGCAGGGGGGAATTTTGGACAATGGAAACCAGGG
>C1_3
CCTACGGGTGGCAGCAGTGGGGAATATTGGACAATGCAACCCTGATCCAGC


Similarly i have mutiple fasta file, which looks like-
C2_pandaseq.fasta
C4_pandaseq.fasta
C5_pandaseq.fasta
C8_pandaseq.fasta
T2_pandaseq.fasta
T7_pandaseq.fasta

So I need to rename all the fasta file header, e.g.,

for fasta file C2_pandaseq.fasta
>C2_1
AAAAAAAAAAAAAAAAAAAAAAA
>C2_2
ATTTTGGGGGGGGCCCCCCCGGGGGGGA


for fasta file C4_pandaseq.fasta
>C4_1
AAAAAAAAAAAAAAAAAAAAAAA
>C4_2
ATTTTGGGGGGGGCCCCCCCGGGGGGGA


and so on...

For each fasta file, i need to rename fasta header according to the file name only. Therefore, I need to write a for loop for this, but i dont know how can i do that.

Any help.
Thanks

[wdecoster]

I would try something like:

for file in *_pandaseq.fasta
do
newname=$(echo $file |  sed s/_pandaseq.fasta//)
awk '/^>/{print $newname ++i; next}{print}' $file > ${newname}_pandaseq_new.fasta
done

[shashankgupta]

I would try something like:

for file in *_pandaseq.fasta
do
newname=$(echo $file |  sed s/_pandaseq.fasta//)
awk '/^>/{print $newname ++i; next}{print}' $file > ${newname}_pandaseq_new.fasta
done

I have tried above for loop, but its not working.


The output I got looks like -

0
CCTACGGGTGGCTGCAGTGGGGAATTTTGG
0
ACTACGGGAGGCAGCAGGGGGGAATTTTGGACA