[EMBOSS] Eprimer3 alternative output formats

[Stefanie Lück]

Hi Alan!

Thanks a lot for the patch!

I design hundrets of primers in a batch mode and want to parse it in a bit 
more convenient way to look at /oder the primers. In addition it's good to 
know all informations about the designed primers for documentation purposes.

I need something like this:

Thanks again and have a nice day!
Stefanie
----- Original Message ----- 
From: <ajb at ebi.ac.uk>
To: "Stefanie Lück" <lueck at ipk-gatersleben.de>
Cc: <emboss at lists.open-bio.org>
Sent: Wednesday, March 25, 2009 6:28 PM
Subject: Re: [EMBOSS] Eprimer3 alternative output formats


> 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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>>
>