From: Charilaos Skiadas cskiadas@uchicago.edu
Any insight greatly appreciated (and apologies if this is an inappropriate post for the forum)
I'd say it's very appropriate for the forum. The problem is I think that TextMate does not do multiline matching in the syntax, so none of these is going to work I'm afraid. Can't see a way out of this, unless of course you have the luxury of placing an empty line before the next >, and then matching that in foldingStopMarker.
Haris
From: Timothy Bates timothy.c.bates@gmail.com I had exactly this problem without output from our matrix package.
My solution was to pre-process the output with a find-replace macro.
The macro finds the taglines, and replaces them with "end\n($1)"
That way, each block is wrapped in <tagline>...<end>
Then the folding is trivial.
Thanks to both Haris and Timothy for replying so quickly to this....I guess not having multiline matching in the syntax explains it...thought I was going nuts!
The workaround as suggested by both was to preprocess the sequence files (iterating over the entries using simple BioPerl - I'm pulling the data on the fly from a RDMS anyway) and add a tab to the end of each FASTA record...this tab is both invisible and unique to the end of each entry and everything collapses as I want...
BTW, not only is TextMate amazing for programming/markup etc, it is also awesome for bioinformatics analysis...I use v. large genome datasets (flat file and RDMS) with scripting the primary mechanism of retrieving/analyzing the data...I used to use NEdit but have ported everything over to TextMate...using column selection, I can push fields (like sets of gene names) as input to perl/shell scripts that query the db and return the data formatted and highlighted...am finding new stuff to do with it every day...