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Full Discussion: Need help comparing Base Pairs within PERL
Top Forums Shell Programming and Scripting Need help comparing Base Pairs within PERL Post 302651297 by drossy on Tuesday 5th of June 2012 09:46:21 AM
Old 06-05-2012
Need help comparing Base Pairs within PERL
Hi I have a multi-step project I am working on and have been finding it difficult to come up with the correct approach.
The data I have been given resembles:

Code:
 
Index      Chr       Genotype   Mutation Type
1           Chr1           TT            Intronic
2           Chr1           AA            Exonic
3           Chr1           AG            Exonic
4           Chr1           CC            Frameshift
5           Chr1           CA            Intronic
...         ...              ....

My goal here is to compare a large file such as this one to a set of references that are a single letter (T,A,C,G). I need to split the genotype in the given file into two individual letters and then compare this to the reference. If either matches the reference, then the program should move on to the next reference. If, however, neither letter is consistant, then the program should give an output of the index number and mutation type that corresponds to that data.
I am still fairly new to this so all help would be greatly appreciated.
Thanks!
 

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LEARN ABOUT DEBIAN

pc-compare

PC-COMPARE(1)							  Probcons Manual						     PC-COMPARE(1)

NAME

       pc-compare - Program for scoring alignments according to a reference alignment with respect to sum-of-pairs and column scores.

SYNOPSIS

       pc-compare [TEST_ALIGNMENT] [REFERENCE_ALIGNMENT] [BALIBASE_ANNOT_FILE] [-col] [-core] [-caps] [-annot FILENAME]

NOTE

       pc-compare is named compare in the original sources, but has been remamed to avoid collision with other program names.

SEE ALSO

       pc-makegnufile(1), pc-project(1),from the probcons-extra package, and probcons(1) and probcons-RNA(1) from the probcons package.

REFERENCE

       Please cite Do, C.B., Mahabhashyam, M.S.P., Brudno, M., and Batzoglou, S. 2005. PROBCONS: Probabilistic Consistency-based Multiple Sequence
       Alignment. Genome Research 15: 330-340.

AUTHORS

       Chuong Do <chuongdo@cs.stanford.edu>
	   Wrote probcons in collaboration with Michael Brudno in the research group of Serafim Batzoglou, Department of Computer Science,
	   Stanford University.

       Charles Plessy <charles-debian-nospam@plessy.org>
	   Wrote this manpage in DocBook XML for the Debian distribution.

COPYRIGHT

       This program and its manpage are in the public domain.

pc-compare 1.12 						    2007-04-04							     PC-COMPARE(1)
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