[EMBOSS] EMBOSS eprimer3 and latest primer3_core

[Tom Keller]

Hi,
I've just installed the beta version of primer3-2.2.2 also. The boulder_io format has been changed. For example, instead of 
SEQUENCE=ACGT....
the new tag is
SEQUENCE_TEMPLATE=ACGT...
also, notice the underscores (they are hard to see in the html manual, cause of the link markup)

I tested primer3_core. It works with this example:
SEQUENCE_ID=PT203_A02
SEQUENCE_TEMPLATE=GTGCCGTGCTCGGCTTCTCTGGTCACAGTCTTTTGTCTCTAGGGCTAAGACAGTGCCTGTCCCTGAAAAGTGGACCACTCCTCAAGAGATAAAACAAAAGATCCAACTCCTCCACCAGAAGTCAGAGTTTGTGGAGAAGAGCACAAAGTACTTCTCAGGTAGATGGGCTTGGGAGAAGATTGGAGGTGCATGCTCACTTCCTCCCTAAGATCCACATAGCCCAGAGCCCCTCACTTCCCTCCTCTTCCCCTGGTCTTGCTGACCTGCCTTCAACCTCTCCTCCATCTGTCCCTGGCTGAGGGACCTAACTCCAGCTTCTCTCTGCTCCCTTTCCCACATTTTAGAAACCCTGCGTTCAGAAATGGAAATGTTCAATGGTGAGTCCAGCGGTAATGGTGTGTGCTGGCCTGGGGTTGTTGCAGTGTTCCCTTGTGCTGTTGACTTGAGGGGCCCTATTTAGAAGACAAAAAAAAAACCAAACACCTGGGGGCAAAAGTAAAA
SEQUENCE_TARGET=395,12
PRIMER_TASK=pick_detection_primers
PRIMER_PICK_LEFT=1
PRIMER_PICK_INTERNAL=1
PRIMER_PICK_RIGHT=1
PRIMER_OPT_SIZE=20
PRIMER_MIN_SIZE=17
PRIMER_MAX_SIZE=23
PRIMER_MAX_NS_ACCEPTED=1
PRIMER_PRODUCT_SIZE_RANGE=75-300
P3_FILE_FLAG=1
PRIMER_EXPLAIN_FLAG=1
=

But eprimer3 dies:
Error: Unable to read sequence './boulderio_template.txt'
Died: eprimer3 terminated: Bad value for '-sequence' and no prompt

Is it that the new format has not yet been accommodated?


thanks,
Tom

Thomas (Tom) Keller, PhD
kellert at ohsu.edu
503.494.2442
6339b R Jones Hall (BSc/CROET)
www.ohsu.edu/xd/research/research-cores/dna-analysis/

On Apr 13, 2010, at 4:43 AM, Peter wrote:

> Hello EMBOSS team,
> 
> I'm using EMBOSS 6.2.0 on Mac OS X 10.6.3 Snow Leopard:
> 
> $ embossversion
> Reports the current EMBOSS version number
> 6.2.0
> 
> I need to design some primers so I wanted to try the EMBOSS tool
> eprimer3, which as your documentation clearly explains requires me to
> install the 'primer3' program from the Whitehead Institute
> (specifically the primer3_core tool).
> 
> I downloaded and compiled the latest version of primer3, version 2.2.2
> beta (using the default, i.e. just "make", which seems to be fine -
> the Snow Leopard specific Makefile failed). It seems that EMBOSS
> eprimer3 does not like this:
> 
> $ export EMBOSS_PRIMER3_CORE="/Users/xxx/Downloads/Software/primer3-2.2.2-beta/src/primer3_core"
> $ eprimer3 fasta::lupine.nu lupine.eprimer3
> Picks PCR primers and hybridization oligos
> Error: Missing SEQUENCE tag
> 
> Instead, I downloaded and compiled primer3 version 1.1.4 (using the
> defaults, i.e. just "make", there is no Snow Leopard specific Makefile
> included) and that seems to work:
> 
> $ export EMBOSS_PRIMER3_CORE="/Users/xxx/Downloads/Software/primer3-1.1.4/src/primer3_core"
> $ eprimer3 fasta::lupine.nu lupine.eprimer3Picks PCR primers and
> hybridization oligos
> Picks PCR primers and hybridization oligos
> 
> The eprimer3 output looks sensible too.
> 
> My guess is that something in the recent primer3 alpha and beta
> releases of 2.x.x has changed since version 1.x.x and that EMBOSS
> needs to be updated to cope. Is this a known issue?
> 
> Thanks,
> 
> Peter C.
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