[EMBOSS] Eprimer3 alternative output formats

[ajb at ebi.ac.uk]

Hello Stefanie,

There is currently no such argument but it is a trivial thing to hack
in to the source code - the attached patch against EMBOSS-6.0.1 would do it
by adding a '-originalformat' switch.

As it stands, the output is provided in what was deemed a more
easily digestible format.

Out of interest, is there a specific reason why you need the original
output format e.g. do you use a subsequent application that requires it?
We try to be flexible if there's reasonable demand for something.

HTH

Alan


> Hi!
>
> Is there an argument in the eprimer 3 to get an alternative output format?
>
> Something like this, which I got once from primer3 running on a server:
>
> PRIMER_SEQUENCE_ID=HF15E08r
> SEQUENCE=GCATGTAATAATGCCAAAGCTCACAGCTGCAGTTGAATCTTGGGACCCGCGGAGCGAGAATGTACCAATCCATGTATGGGTACACCCATGGCTGCCAACTCTAGGGCAAAGGATAGATACACTGTGCCACTCTATCCGGTACAAGCTGAGTAGTGTCCTCCAATTATGGCAAGCTCACGATTCATCAGCTTATGCTGTGCTATCTCCATGGAAGGGTGTATTTGATCCAGCAAGTTGGGAAGACTTGATAGTGCGTTATATCATTCCTAAACTGAAAATGGCACTCCAGGAGTTCCAGATTAACCCAGCAAGCCAAAAGTTTGACCAGTTTAACTGGGTTATGATCTGGGCTTCTGCTGTCCCGGTACACCATATGGTCCATATGTTGGAAGTTGATTTCTTTAGCAAGTGGCAGCTGGTTTTGTACCATTGGCTGAGCTCACCAAATCCTGATTTCAATGAGATAATGAATTGGTAT
> PRIMER_PRODUCT_SIZE_RANGE=500-1000 450-500 400-450 350-400 300-350 250-300
> 200-250 150-200
> PRIMER_OPT_TM=60.0
> PRIMER_MIN_TM=58.0
> PRIMER_MAX_TM=65.0
> PRIMER_MAX_DIFF_TM=3.0
> PRIMER_DNA_CONC=420
> PRIMER_NUM_RETURN=1
> PRIMER_PAIR_PENALTY=0.8691
> PRIMER_LEFT_PENALTY=0.708329
> PRIMER_RIGHT_PENALTY=0.160746
> PRIMER_LEFT_SEQUENCE=GCATGTAATAATGCCAAAGC
> PRIMER_RIGHT_SEQUENCE=TTGAAATCAGGATTTGGTGA
> PRIMER_LEFT=0,20
> PRIMER_RIGHT=458,20
> PRIMER_LEFT_TM=59.292
> PRIMER_RIGHT_TM=60.161
> PRIMER_LEFT_GC_PERCENT=40.000
> PRIMER_RIGHT_GC_PERCENT=35.000
> PRIMER_LEFT_SELF_ANY=7.00
> PRIMER_RIGHT_SELF_ANY=8.00
> PRIMER_LEFT_SELF_END=2.00
> PRIMER_RIGHT_SELF_END=2.00
> PRIMER_LEFT_END_STABILITY=8.5000
> PRIMER_RIGHT_END_STABILITY=7.9000
> PRIMER_PAIR_COMPL_ANY=5.00
> PRIMER_PAIR_COMPL_END=3.00
> PRIMER_PRODUCT_SIZE=459
>
> Thanks in advance!
> Stefanie
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