[TxMt] Re: problems with regex

tandemrepeat tandemrepeat at gmail.com
Tue Feb 28 00:14:53 UTC 2006

>From: Charilaos Skiadas <cskiadas at 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.

>From: Timothy Bates <timothy.c.bates at 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...

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