Pattern lists and fuzz(nuc|pro|tran) and [pd]reg

[Henrikki Almusa]

Hello,

There might be a need for doing sequences with a list of patterns. Now at the 
moment there is only tfscan and patmatmotifs that uses list of patterns to 
search in seqeunces. The problem is that tfscan uses only fixed sequences and 
patmatmotifs uses a directory of files.

I propose to modify reg and fuzz pattern searches to read a "fasta format of 
pattern" file. Example file using dreg might be

>pat1
[ac]{2}gg
>pat2
[gc]{3}att

Pattern could span multiple lines.

I would be willing to try out some changes in fuzz group as start. Should the 
code that reads the pattern file reading be coded somewhere else (eg not in 
fuzznuc.c)?

Any feedback or suggestions etc would be welcome
-- 
Henrikki Almusa