input fasta file case sensitivity

[GoogleCodeExporter]

What steps will reproduce the problem?
1. fasta input file in lower case
2.
3.

What is the expected output? What do you see instead?
when the input file is in lower case the primer.tdt output file is empty but 
the microsatellites.tdt file is ok which means that the program is able to 
locate the microsatellites but is not able to design primers.I also dont get 
any error message for this. 
when i changed the case of the input file the problem was fixed. 

What version of the product are you using? On what operating system?
msatcommander-1.0.8 beta with Primer3-2.2.3
Operating system: linux (ubuntu 11.04)

Please provide any additional information below.

Original issue reported on code.google.com by stefanos...@gmail.com on 6 Sep 2011 at 9:12

[GoogleCodeExporter]

I'll take a look at this when i've got a few moments.  For now, I'm going to 
leave this posted as-is, in case anyone runs into the same problem.

If you have a patch, fire that to me and i'll apply... I'm pretty sure I know 
where the issue lies, just need some time to track it down.

thx for the report,
b

Original comment by brant.fa...@gmail.com on 14 Sep 2011 at 9:56

• Added labels: OpSys-Linux, Priority-High, Type-Defect

[GoogleCodeExporter]

I am having a difficult time inputting files--the .txt, .fsa or .fasta files 
are not recognized by msatcommander...what to do to input files? There do not 
seem to be directions; perhaps this post is also my problem?

Original comment by klglen...@gmail.com on 19 Sep 2011 at 1:23

[GoogleCodeExporter]

It seems that msatcommander can recognize only files with the extensions
.fasta and .fsa (at least in my case!).
What version of msatcommander are you using and what operating system?
Did you try using the testSequence.fsa file included?

Original comment by stefanos...@gmail.com on 19 Sep 2011 at 3:50

[GoogleCodeExporter]

yes, msatcommander will only recognize *.fa, *.fasta. and *.fsa (although, as 
of revision 224 the list of accepted file names includes: *.fna).

additional details (operating system, version of msatcommander, if linux, other 
setup details like which python, Qt, and QtPython, etc.) would be helpful as 
mentioned above (sorry - i would just use names, but you can't see them on 
here...).

-b

Original comment by brant.fa...@gmail.com on 19 Sep 2011 at 3:56