[Bioclusters] [OT] help on EMBOSS EMBASSY mse

hardies bioclusters@bioinformatics.org
Thu, 13 Mar 2003 15:31:28 -0600

This isn't a cluster computing problem, but I'm hoping someone in the group is 
familiar with the program MSE.

I am checking out program installation for our bioinformatics center looking 
for  missing environment variables, missing data files, missing documentation, 
etc.  MSE installed with the EMBOSS package under linux is failing basic I/O 
operations.  I'm seeking clarification as to whether this is likely due to an 
installation problem, or if I just don't understand the command syntax or have 
false expectations of the program.

A specific test failed is to run mse with an msf alignment file from the 
command line as mse <file.msf>, edit a character, and then try to save the 
edited alignment with the exit command. Whether or not a filename is given 
with "exit", the program quits with nothing written and the original file is 
not changed.  I am unaware of an alternative syntax for outputting the edited 
alignment file.

A second specific test failed is to issue the edit command from within mse.  
Even though the internal help menu describes edit as a means of inputting a 
new alignment; giving edit, EDIT, or EDI produces the message that edit is not 
a mse command.

The write command and hardcopy commands produce output files consistent with 
the documentation.

Can anyone advise me or point me to someone more familiar with this program?

Stephen C. Hardies
Assoc. Prof. of Biochemistry
Univ. of Texas Health Science Center at San Antonio