NAME

Utils

SYNOPSIS

    use Utils;

DESCRIPTION

A handy module comprising some commonly used helper functions in the TURNIP software.

FEEDBACK

Reporting Bugs

Please report bugs to the author.

AUTHOR

Rob Davey

APPENDIX

The rest of the documentation details each of the object methods. Internal (private) functions are preceded by an underscore (_)

hashcode

 Title   : hashcode
 Usage   : hashcode($s)
 Function: generates a hashcode from a scalar
 Returns : an integer scalar representing a hashcode
 Args    : the object from which to form the hashcode

use_config

 Title   : use_config
 Usage   : use_config($file)
 Function: reads in a Prefs config file and checks for sanity
 Returns : NONE
 Args    : a TURNIP .conf preferences file

slicestr

 Title   : slicestr
 Usage   : slicestr($string, $start, $end)
 Function: grab a slice of a string. This is different from substr in that you do not provide a length, but rather the start- and endpoints of the desired slice.
 Returns : the portion of the string that has been sliced
 Args    : a string, a start index and an end index

find_quality_alignment

 Title   : find_quality_alignment
 Usage   : find_quality_alignment($title, $strand, $start, $end, %dict)
 Function: find a slice of quality scores for a corresponding sequence alignment
 Returns : a slice of quality scores, separated by a whitespace character
 Args    : a read title, strand, slice start, slice end and corresponding sequence IndexDict

qual_to_prob

 Title   : qual_to_prob
 Usage   : qual_to_prob($quality)
 Function: converts a fastq quality score into an error probability
 Returns : an error probablity for this quality score
 Args    : a fastq quality integer, and an optional exponent and baseline

reverse_complement

 Title   : reverse_complement
 Usage   : reverse_complement($sequence)
 Function: computes the reverse complement for a given DNA sequence
 Returns : the reverse complement
 Args    : a string representing a DNA sequence

trim

 Title   : trim
 Usage   : trim($string)
 Function: trim function to remove whitespace from the start and end of the string
 Returns : the trimmed string
 Args    : a string

ltrim

 Title   : ltrim
 Usage   : ltrim($string)
 Function: left trim function to remove leading whitespace
 Returns : the left-trimmed string
 Args    : a string

rtrim

 Title   : rtrim
 Usage   : rtrim($string)
 Function: right trim function to remove trailing whitespace
 Returns : the right-trimmed string
 Args    : a string

zeros

 Title   : zeros
 Usage   : zeros($length)
 Function: generate a list of given length filled with zeros
 Returns : the zero-filled list
 Args    : the length of the list to generate

fisher_yates_shuffle

 Title   : fisher_yates_shuffle
 Usage   : fisher_yates_shuffle(\@list)
 Function: shuffles the contents of a given arrayref according to the Fisher-Yates shuffle algorithm
 Returns : NONE
 Args    : the arrayref to shuffle