I am in a class on Biocomputing and we have a project due VERY soon. In part of it, we have to write a script and this is what we have to do:
It can execute in the shell, python, or perl. The script should do the following on an input file.
1. When the script is executed, it should as for the input file name.
2. perform a sanity check to ensure that the input file exists; otherwise, prints an error message and aborts
3. after a good sanity check, it passes the data from the input file to clustalw for sequence alignment
4. pass the alignment to collapse1.5
5. use seqret from EMBOSS to convert to file from PHYLIP to Nexus non-interleaved
6. clean up any intermediate files
I have done some of this, but I keep getting errors. Can anyone help me???