Primer3_core

Question

[Mohamed]

How to make fasta file as input to primer3_core using bash command line

Answer 1

[Pierre Lindenbaum]

awk '/^>/ {printf("%s%s\t",(N>0?"\n":""),$0);N++;next;} {printf("%s",$0);} END {printf("\n");}' < input.fa  |\
awk '{printf("SEQUENCE_ID=%s\nSEQUENCE_TEMPLATE=%s\n=\n",substr($1,2),$2);}' |\
primer3_core 

[Mohamed]

Thank you so much, this command works perfectly,

awk '/^>/ {printf("%s%s\t",(N>0?"\n":""),$0);N++;next;} {printf("%s",$0);} END {printf("\n");}' < M_gen_seq.fa  |awk '{printf("SEQUENCE_TEMPLATE=%s\nSSEQUENCE_ID=%s\n=\n",substr($1,2),$2);}' | primer3_core