[Bioperl-l] Alignment excision script
Stephen Gordon Lenk
slenk at emich.edu
Wed Aug 31 14:16:21 EDT 2005
Thank you! Following is thinking out loud.
I will accept your advice and reconvert to 100% script, easy. No new
object type will be created. Actually, I already have a seperate
script with AlignIO objects, just did not explain well.
- The script will create AlignIO objects with format defined by user
(or have Bioperl guess format if user does not specify ...). All IO
will be done using them. Flexible, 'any' format in, 'any' format out
with CD excised via X. We will use this in our analysis pipeline.
- The alignment must be treated as a whole as the default 'X'ing out
(partial excision) considers if a whole column is part of a CD. I
first X out designated CD residues, then look to see if the whole
column is X'd out before making the final excision on a copy of the
original sequences. I can return eiher a full (all designated CD) or
partial (only columns that all have X). I have this code solid, and
plan to use it internally to script. Reuse what works well already.
- I have extracted needed information from the input AlignIO object
already and process it using the above method. The internal excised
alignment data is right. Just a matter of loading it into the output
- I can use AlignIO methods to add excised sequences etc to output
object formatted as requested by user, sounds easy. Will look at
Utilities for any shortcuts.
- I will further examine the Bio::Tools::Analysis for Bioperl methods
to get the needed CD data, which is really just start/end pairs for a
given protein sequence. Nothing fancy needed as far as representation
for the already working code. All I use is "$start $end" to represent
excision regions for given CD for given protein sequence. I make an
array of these for a given protein and use that when I do the initial
Xing out. I'd like to have internal reuse of existing reliable code.
- I have a t/ directory for the earlier script. I will expand and
reuse this. POD documentation is in the code. I will modify it to
reflect current status.
Again, thank you.
slenk at emich.edu
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