Work 072412

2015-01-13

azim58 - Work 072412

Started working on Glam2Scan_Handler class

I need to figure out just how to use glam2 first.
The system command for using glam2_scan appears to be
glam2scan p my_motif.glam2 my_seqs.fa

What does a glam2 file look like?
It just looks like the output of glam2 in the txt file. However, most of
the output is not needed. A fake glam2 file can be made that looks
something like this

minimal glam2 motif file example found here
"C:\home_DR\9-6-12\Motif Peptide Analysis\minimal_glam2_motif_file.glam2"

More information about glam2scan and file formats can be found here
http://meme.nbcr.net/meme/doc/glam2scan_man.html

The higher the score, the better the match. It looks like a score of
higher than about 6 could be reasonable threshold.

===========================================================================
Note that much of the code in the Glam2Scan_Handler class was copied from
the Glam2_Handler class, and it needs to be changed.

===========================================================================
9-6-12 Completed Glam2Scan_Handler class

azim58wiki: