problem with wildcard in emboss applications.

Ted Chiang tchiang at
Tue Jan 8 15:52:11 UTC 2002


Thanks for the patch.  We've installed and tested the 'wildcard' function
for seqret and a number of other emboss applications and it seems to work

We've conducted some further tests of emboss2.1.0 after our recent
installation, and I noticed some bugs that might be of interest.

1. I noticed that emboss2.1.0 has a few new applications not present in
earlier version (1.13), however 'wossname' does not seem to be able to
pick them up. ie.

	%wossname -alphabet

fails to list the following programs which are in the
/blah/emboss2.1.0/bin directory:

> acdc
> contacts
> extractfeat
> infoalign
> listor
> mwfilter
  (prima (1.13)--> primer3(2.1) -->this is a program replacement, I guess)
> runJemboss.csh
> seqretallfeat
> swissparse
> trimest

2. In executing some of the above programs, I've encountered some of the
following errors:


   EMBOSS An error in acdc.c at line 36:
Error - must specify an application to compile

   EMBOSS An error in ajacd.c at line 1207:
acdfile '/tools/emboss2.1.0/share/EMBOSS/acd/contacts.acd' not opened
Warning: Efeatures.embl: tag note (feature 3'clip) not in Etags file
Warning: Efeatures.embl: tag partial (feature 3'clip) not in Etags file
Warning: Efeatures.embl: tag standard_name (feature 3'clip) not in Etags
Picks PCR primers and hybridization oligos
Input sequence(s): AF104304
Output file [af104304.primer3]: 

   EMBOSS An error in primer3.c at line 316:
The program 'primer3_core' must be on the path.
It is part of the 'primer3' package,
available from the Whitehead Institute.
Broken pipe

   EMBOSS An error in ajacd.c at line 1207:
acdfile '/tools/emboss2.1.0/share/EMBOSS/acd/swissparse.acd' not opened

---->If you could please help us in solving some of these problems, we
would really appreciate it.  I presume some of them may be due to
installation nuances on our side...



Ted Chiang
Bioinformatics Supercomputing Centre
Hospital for Sick Children, Toronto
ext. 7028
tchiang at

On Mon, 7 Jan 2002 ableasby at wrote:

> Ted,
> Ah, its a GenBank thing. Specifically the horrible header information
> at the start of each distribution file. I've put a replacement
> ajseqread.c file in:
> Put that in the ajax directory and "make install" again and you
> should be OK. Being good Europeans we can tend to forget about some
> genbank nuances. Apologies.
> Alan
> PS: This probably means a new distribution soon incorporating the
>     patch and the srs patch.

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