06-16-2016
OK. Seeing your code and the output it produces makes it very clear that none of the sample input files you have shown us in the past in this thread were used as input to this script. You have never said that your input files contain an additional field at the start of each line that is to be ignored by your script. Your descriptions up until now have said that you are looking at the stings in the first two fields in your input, but your script never looks at the first field in your input file; it only looks at the second and third fields in your input.
You have now shown us your script and the output it produces. Thank you for both.
Now, PLEASE show us three more things:
- the input that was given to your script to produce the output you supplied in post #7 in this thread,
- the output that you WANT your script to produce (including the percentages that you want to be produced), and
- a clear description of what determines whether or not the string in field three of your input file is "similar" to the string in field two of your input file. (Is the requirement that the string in field 3 is a substring of field 2 where the comparison performed is case insensitive?)
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LEARN ABOUT DEBIAN
bio::matrix::scoring
Bio::Matrix::Scoring(3pm) User Contributed Perl Documentation Bio::Matrix::Scoring(3pm)
NAME
Bio::Matrix::Scoring - Object which can hold scoring matrix information
SYNOPSIS
use Bio::Matrix::Scoring;
DESCRIPTION
An object which can handle AA or NT scoring matrix information. Some transformation properties are available too.
FEEDBACK
Mailing Lists
User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the
Bioperl mailing list. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Support
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address
it. Please include a thorough description of the problem with code and data examples if at all possible.
Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the
web:
https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Jason Stajich
Email jason-at-bioperl-dot-org
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
new
Title : new
Usage : my $obj = Bio::Matrix::Scoring->new();
Function: Builds a new Bio::Matrix::Scoring object
Returns : an instance of Bio::Matrix::Scoring
Args :
entropy
Title : entropy
Usage : $obj->entropy($newval)
Function:
Example :
Returns : value of entropy (a scalar)
Args : on set, new value (a scalar or undef, optional)
expected_score
Title : expected_score
Usage : $obj->expected_score($newval)
Function:
Example :
Returns : value of expected (a scalar)
Args : on set, new value (a scalar or undef, optional)
scale
Title : scale
Usage : $obj->scale($newval)
Function:
Example :
Returns : value of scale (a scalar)
Args : on set, new value (a scalar or undef, optional)
scale_value
Title : scale_value
Usage : $obj->scale_value($newval)
Function:
Example :
Returns : value of scale_value (a scalar)
Args : on set, new value (a scalar or undef, optional)
description
Title : description
Usage : $obj->description($newval)
Function:
Example :
Returns : value of description (a scalar)
Args : on set, new value (a scalar or undef, optional)
database
Title : database
Usage : $obj->database($newval)
Function:
Example :
Returns : value of database (a scalar)
Args : on set, new value (a scalar or undef, optional)
lowest_score
Title : lowest_score
Usage : $obj->lowest_score($newval)
Function:
Example :
Returns : value of lowest_score (a scalar)
Args : on set, new value (a scalar or undef, optional)
highest_score
Title : highest_score
Usage : $obj->highest_score($newval)
Function:
Example :
Returns : value of highest_score (a scalar)
Args : on set, new value (a scalar or undef, optional)
lambda
Title : lambda
Usage : $obj->lambda($newval)
Function:
Example :
Returns : value of lambda (a scalar)
Args : on set, new value (a scalar or undef, optional)
H
Title : H
Usage : $obj->H($newval)
Function:
Example :
Returns : value of H (a scalar)
Args : on set, new value (a scalar or undef, optional)
perl v5.14.2 2012-03-02 Bio::Matrix::Scoring(3pm)