Primer3_core
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7 weeks ago
Mohamed • 0

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

line command Primer3_core • 243 views
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7 weeks ago
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 
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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
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