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: <[email protected]>
To: "Stefanie Lück" <[email protected]>
Cc: <[email protected]>
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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