[EMBOSS] New and confusing problem with infoseq!

[michael watson (IAH-C)]

Thanks for the reply!

I did indeed set my ACD root, and I seem to recall I did that because my
EMBOSS applications were trying to access acd files in the unpack
directory I installed from rather than the install directory I installed
to.  This seemed to work.  

However, you are right, my EMBOSS_ACDROOT variable has been hijacked by
a 3rd party app - grrr!!

-----Original Message-----
From: ajb at ebi.ac.uk [mailto:ajb at ebi.ac.uk] 
Sent: 23 September 2008 13:29
To: michael watson (IAH-C)
Cc: emboss at lists.open-bio.org
Subject: Re: [EMBOSS] New and confusing problem with infoseq!

Hello Mick,

The -database qualifier was added to infoseq in EMBOSS-5.0.0.
The error you're getting would, for example, happen if your
EMBOSS 5.0.0 infoseq executable was reading an EMBOSS 4.x.x
infoseq.acd file. That could happen if you
had set the EMBOSS_ACDROOT environment variable to point to
an old ACD directory or, similarly, set an emboss_acdroot in your
.embossrc or emboss.default file.

For most simple EMBOSS installations you shouldn't need to set
EMBOSS_ACDROOT (or equivalent) at all.

HTH

Alan



> Confusing because this didn't happen before and I haven't changed
> anything!
>
> EMBOSS 5.0.0 on RHEL 4.
>
> Why is infoseq complaining about a database?  Has my environment
changed
> because this used to work exactly how I wanted it to!
>
> Mick
>
> -bash-3.00$ infoseq
> Displays some simple information about sequences
> Input (gapped) sequence(s):  Contig0.1399.fasta
> Died: Qualifier '-database' not found
>
> -bash-3.00$ more Contig0.1399.fasta
>>lcl|Contig0.1399 No definition line found
>
AGAGGAGAGGAGAGGACAAAATATGTTATTCCTTGGCAAGTGTTCCCTTGAGAAGGTGTCTGTTAGGGCACA
> GTCCATTG
>
GTGCCTGTGAGGAAAAAGAAGCTGAAGGACTTACTGGGCCACACAGTTGCGACCATCAGAGCTGCCAGCAGC
> AGCATGTT
>
TGCTGCTCCAGCTCAGCTGCTGCTGAGACTCAGAGATGTGTGAGTGAGGCCCCAGATGGGGACATACTGAGT
> AGGAGGAG
>
CTGTCCCCAGCAGTGTTTTTTTTTCTGTGCATAACACCATGGGGCTGTGCTTGTCAAGACGTTACAGCAACC
> CGGGAAAT
>
AAGCAAGACCAGAGAATGCTGAGGTTGTTTTGAAGGAGGTGGTCCTGTCTGCTTTCCTGAGAAATGCAAAGA
> ACCGTTGC
>
TCAGTCCAAGGACTGAAAGGCATGAAGGCTCTTCCAACACAAGCTGTGTTCAGAGCCTCGCAAAACCAGCAC
> TATGGAAA
>
>
>
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