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Primer3_core

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2.3 years ago

Mohamed • 0

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

line command Primer3_core • 742 views

ADD COMMENT • link updated 2.3 years ago by GenoMax 147k • written 2.3 years ago by Mohamed • 0

GenoMax · Answer 1 · 2022-08-10

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2.3 years ago

Pierre Lindenbaum 164k

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

ADD COMMENT • link 2.3 years ago by Pierre Lindenbaum 164k

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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

ADD REPLY • link updated 2.3 years ago by GenoMax 147k • written 2.3 years ago by Mohamed • 0