adjustments to the server

[wge11]

• skip N's while reading in sequences;
• adjust occur2bed.py so that it automatically converts occurrence file to bed file when header information in input FASTA file is provided;
• read in multiple BaMM files at the same time;
• look into the problem where it takes longer time for EM optimization as given BaMM than MEME as seeds;
• look into the problem where log odds distribution of positives is shifted to the left of that of negatives;
• investigate on why TGACTCA motif is everywhere;
• write out the hyper-parameters to the BaMM model file: e.g. k, alpha
• check if the bed file positions are correct.
• how to treat the short sequences fairly.
• v[k] does not sum up to Y[k+1]
• ignore the usual end-of-line char in the input files.
• write Uni_test for tracing the changes.