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 <robert.davey@bbsrc.ac.uk>

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