awk error, retrieving stuff from primer3 output file

Question

[sp]

I would like to make primer file in fasta format by "greping" some information (Primer template, Primer ID, and left & right primers sequence) from primer3 output as below. Goutham Atla graciously gave me a command (grep -E "PRIMER_RIGHT_0_SEQUENCE|PRIMER_LEFT_0_SEQUENCE|SEQUENCE_ID" test.fasta | paste - - - | awk '{ gsub("\047|,","",$0); print ">"$6"-left\n"$2"\n" ">"$6"-right\n"$4}'​) , and used it well. This time I would like to design 3 pairs of candidate for each target, and modified his command line like this (grep -E "PRIMER_RIGHT_\d_SEQUENCE|PRIMER_LEFT_\d_SEQUENCE|SEQUENCE_ID|SEQUENCE_TEMPLATE" x.out | paste - - - - - - - - | awk '{ gsub("\047|,","",$0); print ">"$14"\n"$16"\n" ">"$14"-L0"\n"$2"\n" ">"$14"-L1"\n"$4"\n" ">"$14"-L2"\n"$6"\n" ">"$14"-R0"\n"$8"\n" ">"$14"-R1"\n"$10"\n" ">"$14"-R2"\n"$12}' > xgrep_3primers.out). Of course, it's not working with errors, and I have no clue. Please help me out.

Below is the example of source primer3 output...

{'PRIMER_INTERNAL_NUM_RETURNED': 0L,

...

'PRIMER_LEFT_0_SEQUENCE': 'ATGGCAAATACACAGAGGAAGC',

...

'PRIMER_LEFT_1_SEQUENCE': 'GCAAATACACAGAGGAAGCCTT',

...

'PRIMER_LEFT_2_SEQUENCE': 'TGATGGCAAATACACAGAGGAAG',

...

'PRIMER_RIGHT_0_SEQUENCE': 'AGATGGTGAAACCTGTTTGTTG',

...

'PRIMER_RIGHT_1_SEQUENCE': 'AGATGGTGAAACCTGTTTGTTG',

...

'PRIMER_RIGHT_2_SEQUENCE': 'AGATGGTGAAACCTGTTTGTTG',

...

'SEQUENCE_ID': 'chr1:114713809-114714010',

...

'SEQUENCE_TEMPLATE': 'TAATATCCGCAAATGACTTGCTATTATTGATGGCAAATACACAGAGGAAGCCTTCGCCTGTCCTCATGTATTGGTCTCTCATGGCACTGTACTCTTCTTGTCCAGCTGTATCCAGTATGTCCAACAAACAGGTTTCACCATCTATAACCACTTGTTTTCTGTAAGAATCCTGGGGGTGTggagggtaagggggcagggagg'}

None

Desired output format is:

>chr1:114713809-114714010

TAATATCCGCAAATGACTTGCTATTATTGATGGCAAATACACAGAGGAAGCCTTCGCCTGTCCTCATGTATTGGTCTCTCATGGCACTGTACTCTTCTTGTCCAGCTGTATCCAGTATGTCCAACAAACAGGTTTCACCATCTATAACCACTTGTTTTCTGTAAGAATCCTGGGGGTGTggagggtaagggggcagggagg

>chr1:114713809-114714010-L0

ATGGCAAATACACAGAGGAAGC

>chr1:114713809-114714010-L1

GCAAATACACAGAGGAAGCCTT

>chr1:114713809-114714010-L2

TGATGGCAAATACACAGAGGAAG

>chr1:114713809-114714010-R0

AGATGGTGAAACCTGTTTGTTG

>chr1:114713809-114714010-R1

AGATGGTGAAACCTGTTTGTTG

>chr1:114713809-114714010-R2

AGATGGTGAAACCTGTTTGTTG

[gangireddy]

First my doubt is why are using \d instead of 0.

[sp]

I would like to use regular expression to cover all (Left0, Left1, Left2 etc) the primers. Tried with individual numbers and ends up same error as below:

sp@sp-ThinkPad-X220:~/multiplex_primer_design/2016_03_18_DC_Hot$ grep -E "PRIMER_LEFT_0_SEQUENCE|PRIMER_LEFT_1_SEQUENCE|PRIMER_LEFT_2_SEQUENCE|PRIMER_RIGHT_0_SEQUENCE|PRIMER_RIGHT_1_SEQUENCE|PRIMER_RIGHT_2_SEQUENCE|SEQUENCE_ID|SEQUENCE_TEMPLATE" x.out | paste - - - - - - - - | awk '{ gsub("\047|,","",$0); print ">"$14"\n"$16"\n" ">"$14"-L0"\n"$2"\n" ">"$14"-L1"\n"$4"\n" ">"$14"-L2"\n"$6"\n" ">"$14"-R0"\n"$8"\n" ">"$14"-R1"\n"$10"\n" ">"$14"-R2"\n"$12}' > xgrep_3primers.out awk: cmd. line:1: { gsub("\047|,","",$0); print ">"$14"\n"$16"\n" ">"$14"-L0"\n"$2"\n" ">"$14"-L1"\n"$4"\n" ">"$14"-L2"\n"$6"\n" ">"$14"-R0"\n"$8"\n" ">"$14"-R1"\n"$10"\n" ">"$14"-R2"\n"$12} awk: cmd. line:1: ^ backslash not last character on line awk: cmd. line:1: { gsub("\047|,","",$0); print ">"$14"\n"$16"\n" ">"$14"-L0"\n"$2"\n" ">"$14"-L1"\n"$4"\n" ">"$14"-L2"\n"$6"\n" ">"$14"-R0"\n"$8"\n" ">"$14"-R1"\n"$10"\n" ">"$14"-R2"\n"$12} awk: cmd. line:1: ^ syntax error

Answer 1

[gangireddy]

Found it

$14"-R2"\n"$

quote missing and this mistake is at many places.

change to

$14"-R2""\n"

I am sure it will work

suggestion:

the following would be better

$14"-R2\n"

do not place two qoutes side by side u can place them in single quote.

The cmd worked is

grep -E PRIMER_LEFT_0_SEQUENCE|PRIMER_LEFT_1_SEQUENCE|PRIMER_LEFT_2_SEQUENCE|PRIMER_RIGHT_0_SEQUENCE|PRIMER_RIGHT_1_SEQUENCE|PRIMER_RIGHT_2_SEQUENCE|SEQUENCE_ID|SEQUENCE_TEMPLATE" x.out | paste - - - - - - - - | awk '{ gsub("\047|,","",$0); print ">"$14"\n"substr($16,0,length($16)-1)"\n>"$14"-L0\n"$2"\n>"$14"-L1\n"$4"\n>"$14"-L2\n"$6"\n>"$14"-R0\n"$8"\n>"$14"-R1\n"$10"\n>"$14"-R2\n"$12}' > xgrep_3primers.out

[sp]

That's right! It works now. Thanks!