From 32ea8edd36648251e73464c62681244758fedc0b Mon Sep 17 00:00:00 2001 From: Andres Breton Date: Mon, 27 Mar 2017 15:50:09 -0400 Subject: [PATCH] ok, really need to keep these out of master --- cover_db/chomp-pl--branch.html | 51 --- cover_db/chomp-pl--condition.html | 35 -- cover_db/chomp-pl--subroutine.html | 53 --- cover_db/chomp-pl.html | 335 ------------------ cover_db/cover.14 | 1 - cover_db/cover.css | 75 ---- cover_db/coverage.html | 41 --- cover_db/digests | 1 - cover_db/lib-SS-pm--branch.html | 31 -- cover_db/lib-SS-pm--subroutine.html | 40 --- cover_db/lib-SS-pm.html | 126 ------- cover_db/lib-Search-pm--branch.html | 37 -- cover_db/lib-Search-pm--subroutine.html | 46 --- cover_db/lib-Search-pm.html | 298 ---------------- .../0bf19b40fe954a61ff714e5a05d832e5 | 1 - .../1b2c97fff00e27eb6ce9144ab0b0a673 | 1 - .../b520b978413d49a88b29a3c144a06873 | 1 - .../e6845289bc529cbfc889f530bf091645 | 1 - cover_db/t-chomp-t--branch.html | 31 -- cover_db/t-chomp-t--subroutine.html | 96 ----- cover_db/t-chomp-t.html | 171 --------- 21 files changed, 1472 deletions(-) delete mode 100644 cover_db/chomp-pl--branch.html delete mode 100644 cover_db/chomp-pl--condition.html delete mode 100644 cover_db/chomp-pl--subroutine.html delete mode 100644 cover_db/chomp-pl.html delete mode 100644 cover_db/cover.14 delete mode 100644 cover_db/cover.css delete mode 100644 cover_db/coverage.html delete mode 100644 cover_db/digests delete mode 100644 cover_db/lib-SS-pm--branch.html delete mode 100644 cover_db/lib-SS-pm--subroutine.html delete mode 100644 cover_db/lib-SS-pm.html delete mode 100644 cover_db/lib-Search-pm--branch.html delete mode 100644 cover_db/lib-Search-pm--subroutine.html delete mode 100644 cover_db/lib-Search-pm.html delete mode 100644 cover_db/structure/0bf19b40fe954a61ff714e5a05d832e5 delete mode 100644 cover_db/structure/1b2c97fff00e27eb6ce9144ab0b0a673 delete mode 100644 cover_db/structure/b520b978413d49a88b29a3c144a06873 delete mode 100644 cover_db/structure/e6845289bc529cbfc889f530bf091645 delete mode 100644 cover_db/t-chomp-t--branch.html delete mode 100644 cover_db/t-chomp-t--subroutine.html delete mode 100644 cover_db/t-chomp-t.html diff --git a/cover_db/chomp-pl--branch.html b/cover_db/chomp-pl--branch.html deleted file mode 100644 index cc5cd64..0000000 --- a/cover_db/chomp-pl--branch.html +++ /dev/null @@ -1,51 +0,0 @@ - - - - - - - - - Branch Coverage: chomp.pl - - -

Branch Coverage

- - - -
File:chomp.pl
Coverage:66.7%
-

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line%coveragebranch
9950TFunless $SEQ
1000TFunless $OUTFILE
1030TFunless $DOWNSEQ and $VERBOSE
1040TFunless $UPSEQ and $VERBOSE
12250TFif (@SUBJECTS) { }
50TFelsif ($SEQ) { }
1300TFif $SS
146100TFunless @_ == 6
173100TFif (not $down || $up) { }
100TFelsif ($down and not $up) { }
100TFelsif (not $down and $up) { }
210100TFunless @_ == 1
243100TFunless @_ == 2
25350TFif $SS
27450TFunless @_ == 1
29450TFif @{$targets{$gRNA}{$subject}{'info'};}[0]->{'numhits'} == 0
304100TFif grep {$_ == $value;} @unqIdentities
332100TFunless $details{$a}{$subject}{'unqIdentities'}[0] <=> $details{$b}{$subject}{'unqIdentities'}[0]
349100TFunless @_ == 1
358100TFif $numMatches == 1
359100TFunless $nident == $WINDOWSIZE
- - diff --git a/cover_db/chomp-pl--condition.html b/cover_db/chomp-pl--condition.html deleted file mode 100644 index dfe2908..0000000 --- a/cover_db/chomp-pl--condition.html +++ /dev/null @@ -1,35 +0,0 @@ - - - - - - - - - Condition Coverage: chomp.pl - - -

Condition Coverage

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File:chomp.pl
Coverage:53.3%
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line%coveragecondition
1030
ABdec
0X0
100
111
$DOWNSEQ and $VERBOSE
1040
ABdec
0X0
100
111
$UPSEQ and $VERBOSE
17367
ABdec
0X0
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not $down and $up
100
ABdec
000
011
1X1
$down || $up
100
ABdec
0X0
100
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$down and not $up
- - diff --git a/cover_db/chomp-pl--subroutine.html b/cover_db/chomp-pl--subroutine.html deleted file mode 100644 index cf9215d..0000000 --- a/cover_db/chomp-pl--subroutine.html +++ /dev/null @@ -1,53 +0,0 @@ - - - - - - - - - Subroutine Coverage: chomp.pl - - -

Subroutine Coverage

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File:chomp.pl
Coverage:100.0%
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linesubroutine
4
BEGIN
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checks
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setParameters
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writeResults
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getSeqDetails
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writeFasta
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sortResults
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sortIdentities
- - diff --git a/cover_db/chomp-pl.html b/cover_db/chomp-pl.html deleted file mode 100644 index de227c7..0000000 --- a/cover_db/chomp-pl.html +++ /dev/null @@ -1,335 +0,0 @@ - - - - - - - - - File Coverage: chomp.pl - - -

File Coverage

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File:chomp.pl
Coverage:87.3%
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linestmtbrancondsubtimecode
1#!/usr/bin/env perl
2return 1 if caller(); #tests
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use strict; use warnings; use diagnostics; use feature qw(say);
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use Getopt::Long; use Pod::Usage;
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use Readonly;
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use Bio::Seq; use Bio::SeqIO;
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use FindBin; use lib "$FindBin::RealBin/lib";
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use Search; use SS; # lib modules
10# Own Modules (https://github.com/bretonics/Modules)
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use MyConfig; use MyIO; use Handlers;
12
13# ==============================================================================
14#
15#   CAPITAN:        Andres Breton, http://andresbreton.com
16#   FILE:           chomp.pl
17#   LICENSE:        MIT
18#   USAGE:          Find guide RNA (gRNA) sequences for CRISPR targeting
19#   DEPENDENCIES:   - BioPerl modules
20#                   - Own 'Modules' repo
21#
22# ==============================================================================
23
24
25#-------------------------------------------------------------------------------
26# COMMAND LINE
27my $SEQ;
28my @SUBJECTS;
29my $DOWNSEQ;
30my $UPSEQ;
31my $SS;
32my $OUTFILE;
33my $VERBOSE;
34
35our $OUTDIR = 'gRNAs';
36our $WINDOWSIZE  = 23;
37
38
39my $USAGE       = "\n\n$0 [options]\n
40Options:
41    -seq                Sequence file to search gRNAs [required]
42    -subjects           Subject sequence file(s) to BLAST search (search instead of -seq)
43    -down               Down sequence to append
44    -up                 Up sequence to append
45    -window             Window size for gRNA sequence (default = 23)
46    -ss                 Secondary structure prediction
47    -out                Out file name [required]
48    -outdir             Out directory name
49    -help               Shows this message
50\n";
51
52# OPTIONS
53GetOptions(
54    'seq=s'             =>\$SEQ,
55    'subjects:s{,10}'   =>\@SUBJECTS,
56    'down:s'            =>\$DOWNSEQ,
57    'up:s'              =>\$UPSEQ,
58    'window:i'          =>\$WINDOWSIZE,
59    'ss!'               =>\$SS,
60    'out=s'             =>\$OUTFILE,
61    'outdir:s'          =>\$OUTDIR,
62    'verbose!'          =>\$VERBOSE,
63    help                =>sub{pod2usage($USAGE);}
64)or pod2usage(2);
65
66checks(); # check CL arguments
67
68#-------------------------------------------------------------------------------
69# VARIABLES
70my $AUTHOR = 'Andres Breton, <dev@andresbreton.com>';
71
72my $REALBIN = $FindBin::RealBin;
73
74my ($seqDetails) = getSeqDetails($SEQ);
75my @SUBJSEQS; # sequence file to use in BLAST search
76
77#-------------------------------------------------------------------------------
78# CALLS
79mkDir($OUTDIR);
80my $gRNAs       = findOligo($seqDetails, $WINDOWSIZE); # gRNA HoH
81my $fastaFile   = writeFasta($gRNAs, $OUTFILE); # Write gRNAs fasta file
82my $targets     = Search::blast($fastaFile, \@SUBJSEQS, $OUTFILE); # gRNA target hits
83writeResults($gRNAs, $targets, $DOWNSEQ, $UPSEQ, $WINDOWSIZE, $OUTFILE);
84
85#-------------------------------------------------------------------------------
86# SUBS
87
88#- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
89# $input = checks();
90#- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
91# This function checks for arguments passed on the command-line using global variables.
92#- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
93# $return = Prompts users and exits if errors
94#- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
95sub checks {
96    # Command line arguments passed
97
98    # Exits
99
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    die 'Did not provide an input file, -seq <infile>', $USAGE unless ($SEQ);
100
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    die 'Did not provide an output file, -out <outfile>', $USAGE unless ($OUTFILE) ;
101
102    # Warnings
103
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    say 'Did not provide a DOWN stream sequence to append to gRNA seq, -down <seq>' unless ($DOWNSEQ && $VERBOSE);
104
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    say 'Did not provide an UP stream sequence to append to gRNA seq, -up <seq>' unless ($UPSEQ && $VERBOSE);
105
106
107
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    setParameters(); # set parameters to use in calls
108
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    return;
110}
111
112#- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
113# $input = ();
114#- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
115# This function takes no arguments, uses global variables to decide which set of
116# variables to use and set for calls.
117#- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
118# $output = sets sequence file to use for BLAST search
119#- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
120sub setParameters {
121    # Set up Variables
122
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    if (@SUBJECTS) {
123
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        @SUBJSEQS = @SUBJECTS;
124    } elsif ($SEQ) {
125
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        @SUBJSEQS = $SEQ;
126    } else {
127
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        die 'Could not determine which file(s) to use as search sequence.'
128    }
129
130
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    mkDir($OUTDIR); mkDir("$OUTDIR/ss") if($SS);
131
132
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    return;
133}
134
135#- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
136# $input = ();
137#- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
138# This function takes 5 arguments; gRNAs HoH, BLAST target HoA containing matches
139# throughout the sequence, the down/up stream sequences to append to gRNA
140# sequences, and the output file name
141#- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
142# $output = File containing gRNAs sequences and relative information on results
143#- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
144sub writeResults {
145
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    my $filledUsage = 'Usage: ' . (caller(0))[3] . '(\%gRNAs, \%targets, $DOWNSEQ, $UPSEQ, $WINDOWSIZE, $OUTFILE)';
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    @_ == 6 or die wrongNumberArguments(), $filledUsage;
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    my ($gRNAs, $targets, $down, $up, $window, $file) = @_;
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    my %targets = %$targets;
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    my $num     = keys %$gRNAs; # number of gRNA sequences
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    my $outFile = "$OUTDIR/$file.txt";
153
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    my $FH = getFH(">", $outFile);
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    say $FH "Name\tSequence\tStrand\tPalindrome\tSubject\tStart\tOccurrences\tIdentities";
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    my ($subjects, $sortedgRNAs, $details) = sortResults(\%targets);
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    my @subjects    = @$subjects;
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    my %sortedgRNAs = %$sortedgRNAs;
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    my %details     = %$details;
161
162
163    # Get ordered gRNA sequences + info to print
164
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    foreach my $subject (@subjects) {
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        foreach my $gRNA ( @{$sortedgRNAs{$subject}} ) {
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            my $sequence    = $gRNAs->{$gRNA}->{'sequence'};
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            my $palindrome  = $gRNAs->{$gRNA}{'palindrome'};
168
169            # Complete oligo sequence:
170            # + DOWN flanking target region
171            # + gRNA sequence
172            # + UP flanking target region
173
170
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            if (!$down and !$up) {
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                $sequence = $sequence;
175            } elsif ($down and !$up) {
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                $sequence = $down . $sequence;
177            } elsif (!$down and $up) {
178
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                $sequence = $sequence . $up;
179            } else {
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                $sequence = $down . $sequence . $up;
181            }
182
183            # Get all details to print to file
184
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            my $position    = $gRNAs->{$gRNA}{'start'}; # gRNA sequence position
185
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            my $strand      = $gRNAs->{$gRNA}{'strand'};
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            my $occurrence  = $details->{$gRNA}{$subject}->{'occurrences'};
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            my $identities  = join("," , @{ $details->{$gRNA}{$subject}->{'unqIdentities'} } ); # get string of identities
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            my $sStart      = @{ $targets{$gRNA}{$subject}{'hsps'} }[0]->{'sstart'}; # get location of BLAST match hit in subject (reference) for gRNA found
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            say $FH "$gRNA\t$sequence\t$strand\t$palindrome\t$subject\t$sStart\t$occurrence\t$identities"; # print to file
191        }
192
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    } close $FH;
193
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    say "gRNAs file written to $outFile";
195
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    return;
196}
197#-------------------------------------------------------------------------------
198# HELPERS
199
200#- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
201# $input = ($seqFile);
202#- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
203# This function takes 1 argument, the sequence file to get details using
204# BioPerl modules
205#- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
206# $return = ( \%seqInfo ); Returns sequence details hash
207#- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
208sub getSeqDetails {
209
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    my $filledUsage = 'Usage: ' . (caller(0))[3] . '($seqFile)';
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    @_ == 1 or die wrongNumberArguments(), $filledUsage;
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    my ($seqFile) = @_;
213
214    # Sequence OO
215
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    my $seqInObj    = Bio::SeqIO->new(-file => $seqFile, -alphabet => "dna");
216
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    my $format      = $seqInObj->_guess_format($seqFile); #check format of input file
217
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    my $seqObj      = $seqInObj->next_seq;
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    my $sequence    = uc $seqObj->seq;
219
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    my $reverse     = uc $seqObj->revcom->seq;
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    my %seqInfo = (
222        'seqInObj'  => $seqInObj,
223        'format'    => $format,
224        'seqObj'    => $seqObj,
225        'sequence'  => $sequence,
226        'reverse'   => $reverse,
227    );
228
229
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    return(\%seqInfo);
230}
231
232#- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
233# $input = ($gRNAs, $OUTDIR, $OUTFILE);
234#- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
235# This function takes 3 arguments; HoH reference of gRNA sequences,
236# the output diretory, and the output file name. Writes each gRNA
237# sequence found in FASTA and returns file location.
238#- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
239# $return = ($outFile);
240#- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
241sub writeFasta {
242
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    my $filledUsage = 'Usage: ' . (caller(0))[3] . '($gRNAs, $OUTFILE)';
243
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    @_ == 2 or die wrongNumberArguments(), $filledUsage;
244
245
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    my ($gRNAs, $out) = @_;
246
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    my $outFile = "$OUTDIR/$out.fasta";
247
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    my $FH      = getFH(">", $outFile);
248
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    my $num     = keys %$gRNAs; # number of gRNA sequences
249
250
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    for (my $i = 0; $i < $num; $i++) { # get sequences in numerical order
251
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        my $name = "gRNA_$i";
252
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        my $sequence = $gRNAs->{$name}->{'sequence'};
253
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        ss($name, $sequence) if($SS); # secondary structure prediction if desired
254
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        say $FH ">$name:" . $gRNAs->{$name}->{'start'}; # 'gRNA_0:start_position'
255
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        say $FH $sequence;
256
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    } close $FH;
257
258
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    return $outFile;
259}
260
261#- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
262# $input = ($targetsRef);
263#- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
264# This function takes 1 arguments: $target hash of array of hashes
265# references returned from Search::blast. Returns a numerically
266# ordered array of gRNA sequence names based on lowest identity
267# base pair matches, then occurrences and a details hash with sorted
268# identities and number of occurrences per gRNA sequence.
269#- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
270# $return = ( \@sortedgRNAs, \%details );
271#- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
272sub sortResults {
273
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    my $filledUsage = 'Usage: ' . (caller(0))[3] . '($targetsRef)';
274
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    @_ == 1 or die wrongNumberArguments(), $filledUsage;
275
276
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    my ($targetsRef) = @_;
277    # %targets HoHoAoH:
278    # -- Hash key == gRNA name
279    # -- Hash key == Subject name
280    # -- Hash key == 'info'
281    # -- Hash key == 'hsps'
282    # -- Array accounts for multiple hits for each gRNA sequence
283    # -- Hash contains BLAST match info
284
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    my %targets = %$targetsRef;
285
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    my @gRNAs = keys %targets;
286
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    my (@subjects, @noHits, @sorted, %sortedgRNAs, %details);
287
288    # Get number of occurrences from BLAST call per gRNA sequence in %targets Hash of Hashes of Array of Hashes
289
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    foreach my $gRNA (@gRNAs) { # iterate through each gRNA instance
290
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        @subjects = sort keys $targets{$gRNA}; # @subjects == BLAST subject instances in Hash of Arrays of Hash
291
292
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        foreach my $subject (@subjects) { # iterate through each BLAST subject instance
293            # Handle gRNA sequences having 'No hits', skip sorting
294
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            next if ( @{ $targets{$gRNA}{$subject}{'info'} }[0]->{'numhits'} == 0 );
295
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170
88
            my @identities;
297
170
212
            my @ids = sortIdentities( $targets{$gRNA}{$subject}{'hsps'} ); # get sorted list of all BLAST hits (and for all subjects) for each gRNA query
298
170
196
            push @identities, @ids; # push identities list for each subject
299
300            # Remove duplicates
301
170
62
            my @unqIdentities;
302
170
95
            foreach my $value (@identities) {
303                # Push identitities value unless already recorded
304
460
620
100
288
409
                next if ( grep { $_ == $value} @unqIdentities );
305
310
247
                push @unqIdentities, $value;
306            }
307
308            # Sort identities from all HSPs
309
170
480
121
193
            @identities     = ( sort {$b <=> $a} @identities );
310
170
210
95
91
            @unqIdentities  = ( sort {$b <=> $a} @unqIdentities );
311
312            # Number of hashes in array == number of matches for same gRNA sequence throughout the whole sequence
313
170
91
            my $occurrences = @identities; # number of occcurrences per gRNA
314
315            # %details
316            # -- Hash key == gRNA name
317            # -- Hash key == subject
318            # -- Hash keys == 'identities', 'unique identities', and 'number of occurrences'
319
170
469
            $details{$gRNA}{$subject} = {
320                'identities'    => \@identities,
321                'unqIdentities' => \@unqIdentities,
322                'occurrences'   => $occurrences,
323            };
324        }
325    }
326
327    # Return sorted gRNA names based on lowest identity base pair matches, then occurrences
328
15
21
    foreach my $subject ( @subjects ) {
329        # Get only gRNAs having hits in current subject, remove others
330
10
170
170
12
63
160
        my @gRNAsHit = grep { @{ $targets{$_}{$subject}{'info'} }[0]->{'numhits'} != 0 } @gRNAs;
331
332
10
505
100
11
811
        my @sorted = ( sort { $details{$a}{$subject}{'unqIdentities'}[0] <=> $details{$b}{$subject}{'unqIdentities'}[0] || $details{$a}{$subject}{'occurrences'} <=> $details{$b}{$subject}{'occurrences'} } @gRNAsHit );
333
10
21
        $sortedgRNAs{$subject} = \@sorted;
334    }
335
336
15
46
    return (\@subjects, \%sortedgRNAs, \%details);
337}
338
339#- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
340# $input = ($targets{$name});
341#- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
342# This function takes 1 argument: an array reference containing
343# all gRNA matches for a given gRNA sequence name
344#- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
345# $return = sorted identities ascending numerically
346#- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
347sub sortIdentities {
348
182
182
195
    my $filledUsage = 'Usage: ' . (caller(0))[3] . '($targets{$gRNA}{$subject}{\'hsps\'})';
349
182
100
3737
    @_ == 1 or die wrongNumberArguments(), $filledUsage;
350
351
176
100
    my ($hsps) = @_;
352
176
193
    my @hsps = @$hsps;
353
172
85
    my $numMatches = @hsps;
354
172
79
    my @identities;
355
356
172
105
    foreach my $hash (@hsps) {
357
620
620
437
265
        my $nident = $hash->{'nident'}; chomp($nident);
358
620
100
445
        return ($nident) if ($numMatches == 1); # return single match (when $nident == $WINDOWSIZE is only match)
359
600
100
661
        push @identities, $nident unless ($nident == $WINDOWSIZE);
360    }
361
362
152
488
150
226
    @identities = ( sort {$b <=> $a} @identities ); # sort descending numerically
363
152
282
    return (@identities); # return sorted identity hits
364}
- - diff --git a/cover_db/cover.14 b/cover_db/cover.14 deleted file mode 100644 index d8a5875..0000000 --- a/cover_db/cover.14 +++ /dev/null @@ -1 +0,0 @@ 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use Exporter qw(import);
4our @ISA = qw(Exporter);
5our @EXPORT = qw(ss); # functions exported by default
6our @EXPORT_OK = qw(); # functions for explicit export
7
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use strict; use warnings; use diagnostics; use feature qw(say);
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use Carp;
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use MyConfig; use MyIO;
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use RNA; # ViennaRNA
14
15# ==============================================================================
16#
17#   CAPITAN:        Andres Breton
18#   FILE:           SSpm
19#   LICENSE:        [LICENSE]
20#   USAGE:          Predict RNA secondary structures
21#   DEPENDENCIES:   ViennaRNA (http://www.tbi.univie.ac.at/RNA/)
22#
23# ==============================================================================
24
25 - 48
=head1 NAME
-
-SS - package for prediction and comparison of RNA secondary structures using ViennaRNA
-
-=head1 SYNOPSIS
-
-Creation:
-    use SS;
-
-=head1 DESCRIPTION
-
-    This module is designed to predictic secondary structures of nucleotide sequences using ViennaRNA package
-
-=head1 EXPORTS
-
-=head2 Default Behaviors
-
-Exports ss subroutine by default
-
-use SS;
-
-=head1 FUNCTIONS
-
-=cut
49
50#-------------------------------------------------------------------------------
51# MAIN
52
53 - 67
=head2 ss
-
-    Arg [1]     : Name string
-
-    Arg [2]     : Sequence string
-
-    Example     : ss($name, $sequence)
-
-    Description : Predict secondary structures and output plots
-
-    Returntype  : undef
-
-    Status      : Stable
-
-=cut
68sub ss {
69
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    my $filledUsage = 'Usage: ' . (caller(0))[3] . '($name, $sequence)';
70
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    @_ == 2 or confess wrongNumberArguments(), $filledUsage;
71
72
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    my ($name, $sequence) = @_;
73
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    my $outFile = "$main::OUTDIR/ss/$name";
74
38
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    my $rnaPlot = "$outFile\_rna.ps";
75
38
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    my $dotPlot = "$outFile\_dot.ps";
76
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    my $rssPlot = "$outFile\_rss.ps";
77
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    my $F = RNA::pf_fold($sequence);   # compute partition function and pair pobabilities
79
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    my ($ss, $mfe) = RNA::fold($sequence);
80
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    RNA::PS_rna_plot($sequence, $ss, $rnaPlot);  # write PS plot to gRNA_#_rna.ps
81
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    RNA::PS_dot_plot($sequence, $dotPlot);       # write dot plot to dot.ps
82
83
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    my $command = "relplot.pl $rnaPlot $dotPlot > $rssPlot";
84
19
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    say "Running relative secondary structure command --> '$command'";
85
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    `$command`;
86
87
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    return;
88}
89
90 - 108
=head1 COPYRIGHT AND LICENSE
-
-    Andres Breton (C)
-
-    [LICENSE]
-
-    =head1 CONTACT
-
-    Please email comments or questions to Andres Breton, me@andresbreton.com
-
-    =head1 SETTING PATH
-
-    If PERL5LIB was not set, do something like this:
-
-    use FindBin; use lib "$FindBin::RealBin/lib";
-
-    This finds and uses subdirectory 'lib' in current directoy as library location
-
-=cut
109
1101;
- - diff --git a/cover_db/lib-Search-pm--branch.html b/cover_db/lib-Search-pm--branch.html deleted file mode 100644 index 5b0a6d4..0000000 --- a/cover_db/lib-Search-pm--branch.html +++ /dev/null @@ -1,37 +0,0 @@ - - - - - - - - - Branch Coverage: lib/Search.pm - - -

Branch Coverage

- - - -
File:lib/Search.pm
Coverage:92.9%
-

- - - - - - - - - -
line%coveragebranch
75100TFunless @_ == 2
97100TFif length $window < $windowSize
99100TFif ($window =~ /(.+)(.GG)$/)
153100TFunless @_ == 3
18950TFif $numHits == 0
284100TFunless @_ == 1
290100TF$palindrome eq $sequence ? :
- - diff --git a/cover_db/lib-Search-pm--subroutine.html b/cover_db/lib-Search-pm--subroutine.html deleted file mode 100644 index 7bd89cc..0000000 --- a/cover_db/lib-Search-pm--subroutine.html +++ /dev/null @@ -1,46 +0,0 @@ - - - - - - - - - Subroutine Coverage: lib/Search.pm - - -

Subroutine Coverage

- - - -
File:lib/Search.pm
Coverage:100.0%
-

- - - - - - - - - - - - - - - - - - -
linesubroutine
3
BEGIN
8
BEGIN
BEGIN
BEGIN
BEGIN
9
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BEGIN
BEGIN
12
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13
BEGIN
BEGIN
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findOligo
84
__ANON__
152
blast
262
_getSeqName
283
_palindrome
- - diff --git a/cover_db/lib-Search-pm.html b/cover_db/lib-Search-pm.html deleted file mode 100644 index 9cfd708..0000000 --- a/cover_db/lib-Search-pm.html +++ /dev/null @@ -1,298 +0,0 @@ - - - - - - - - - File Coverage: lib/Search.pm - - -

File Coverage

- - - -
File:lib/Search.pm
Coverage:99.2%
-

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
linestmtbrancondsubtimecode
1package Search;
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use Exporter qw(import);
4our @ISA = qw(Exporter);
5our @EXPORT = qw(findOligo); #functions exported by default
6our @EXPORT_OK = qw(blast); #functions for explicit export
7
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use strict; use warnings; use diagnostics; use feature qw(say);
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use Carp;
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use Bio::Seq; use Bio::SeqIO;
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use Bio::Tools::Run::StandAloneBlastPlus;
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use MyConfig; use MyIO;
14
15
16# ==============================================================================
17#
18#   CAPITAN:        Andres Breton, http://andresbreton.com
19#   FILE:           Search.pm
20#   LICENSE:
21#   USAGE:
22#   DEPENDENCIES:   - NCBI's BLAST+ CL utility
23#
24# ==============================================================================
25
26 - 52
=head1 NAME
-
-Search - package searching gRNA sequences and offsite targets for CRISPR targeting
-
-=head1 SYNOPSIS
-
-Creation:
-    use Search;
-
-=head1 DESCRIPTION
-
-
-=head1 EXPORTS
-
-=head2 Default Behaviors
-
-Exports findOligo subroutine by default
-
-use Search;
-
-=head2 Optional Behaviors
-
-Search::blast;
-
-=head1 FUNCTIONS
-
-=cut
53
54#-------------------------------------------------------------------------------
55# MAIN
56
57#- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
58 - 72
=head2 findOligo
-
-    Arg [1]     : Sequence to be searched details hash
-
-    Arg [2]     : Window size of gRNA sequence
-
-    Example     : findOligo($seqDetails, $windowSize)
-
-    Description : Find gRNA sequences for CRISPR targeting
-
-    Returntype  : Hash of hashes reference
-
-    Status      : Stable
-
-=cut
73sub findOligo {
74
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    my $filledUsage = 'Usage: ' . (caller(0))[3] . '($seqDetails, $windowSize)';
75
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    @_ == 2 or confess wrongNumberArguments(), $filledUsage;
76
77
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    my ($seqDetails, $windowSize) = @_;
78
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    my %gRNAs;
79
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    my $instance = 0; # track gRNA count
80
81    # Anonymous subroutine to find gRNA sequences in forward and reverse strands.
82    # Stores both strand findings in same hash (%gRNAs) containing all information
83    my $go = sub {
84
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            my ($sequence, $strand) = @_;
85
86
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            say "Searching gRNA sequences on $strand strand";
87
88
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            my $seqLen = length($sequence);
89
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            my ($kmer, $PAM, $gRNA, $content, $contentG, $contentC, $GC);
90
91
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            for (my $i = 0; $i < $seqLen; $i++) {
92
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52106
                my $window = substr $sequence, $i, $windowSize;
93
94                # LAST STEP: When DONE LOOKING UP -- Return gRNA sequences and information.
95                # Returns references of HoH containing all gRNA instances found and
96                # respective information for each gRNA sequence
97
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100
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                return(\%gRNAs) if ( length($window) < $windowSize ); # don't go out of bounds when at end of sequence
98
99
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                if ($window =~ /(.+)(.GG)$/) {
100
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                    ($kmer, $PAM) = ($1, $2); # get first 'kmer' and PAM nucleotides in gRNA (kmer + PAM)
101
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4012
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                    my $name        = "gRNA_$instance"; $instance++;
102
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                    my $gRNA        = $kmer . $PAM; # kmer + PAM = gRNA sequence
103
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                    my $palindrome  = _palindrome($kmer);
104
105                    # GC Content
106
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                    $contentG   = $gRNA =~ tr/G//;
107
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                    $contentC   = $gRNA =~ tr/C//;
108
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                    $GC         = ($contentG + $contentC)/$windowSize;
109
110                    # Store gRNA sequences and info in Hash of Hashes
111
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                    $content = { # anonymous hash of relevant gRNA content
112                        'kmer'          => $kmer,
113                        'palindrome'    => $palindrome,
114                        'strand'        => $strand,
115                        'start'         => $i,
116                        'sequence'      => $gRNA,
117                        'PAM'           => $PAM,
118                        'G'             => $contentG,
119                        'C'             => $contentC,
120                        'GC'            => $GC,
121                    };
122                    # Hash key == gRNA sequence name
123                    # Hash value == Hash with gRNA content info
124
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                    $gRNAs{$name} = $content;
125                }
126            }
127
472
4267
    };
128
129    # Get all gRNA sequences in forward and reverse strands of sequence passed, -seq
130
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    $go->( $seqDetails->{'sequence'}, 'plus' );
131
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    $go->( $seqDetails->{'reverse'}, 'reverse' );
132}
133#- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
134 - 150
=head2 blast
-
-    Arg [1]     : gRNA fasta file
-
-    Arg [2]     : Array reference with subject sequence file(s) provided for search
-
-    Arg [3]     : Output file name
-
-    Example     : Search::blast($fastaFile, \@SUBJSEQS, $OUTFILE);
-
-    Description : Run BLAST+ search for gRNA sequences
-
-    Returntype  : Hash reference
-
-    Status      : Stable
-
-=cut
151sub blast {
152
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    my $filledUsage = 'Usage: ' . (caller(0))[3] . '(\%fastaFile, \@SUBJSEQS, $OUTFILE)';
153
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    @_ == 3 or confess wrongNumberArguments(), $filledUsage;
154
155
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    my ($fasta, $SUBJSEQS, $OUTFILE) = @_;
156
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    my @SUBJSEQS = @$SUBJSEQS;
157
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    my (%targets, $info, $hsps);
158
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    my $outDir = $main::OUTDIR;
159
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    my $wordSize = 7;
160
161
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    mkDir("$outDir/blast");
162
163
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    foreach my $subject (@SUBJSEQS) {
164
154
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        my $subjName = _getSeqName($subject);
165
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        my $outFile = "$outDir/blast/$subjName\_$OUTFILE\_blast.txt";
166
167
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        say "Searching gRNA sequences against $subject";
168
169        # Create StandAloneBlastPlus Factory
170
154
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        my $fac = Bio::Tools::Run::StandAloneBlastPlus->new(
171                    -db_data    => $subject,
172                );
173
174        # Perform BLAST call
175
154
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        $fac->blastn(   -query          => $fasta,
176                        -outfile        => $outFile,
177                        -method_args    => [ -word_size => 7],
178                    );
179
180        # Rewind to beginning of results and get all
181
154
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        $fac->rewind_results;
182
183        # Process each gRNA sequence
184
154
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        while ( my $result = $fac->next_result ) {
185
2618
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            my ($gRNA)  = $result->query_name =~ /(.*):\d+/;; # gRNA sequence name ex.) 'gRNA_0', removes appendend positioning
186
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            my $numHits = $result->num_hits;
187
188            # Resolve when gRNA sequences has no matches in subject
189
2618
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            say "\t$gRNA has $numHits hits here" if ($numHits == 0);
190
191            # Default anonymous hashes for storing BLAST results
192            # $info hash stores each gRNA BLAST result's info
193            # $hsps hash stores that match's High-scoring Segment Pairs (HSPs) result
194
2618
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            $info = {
195                'numhits'       => $numHits,
196                'occurrences'   => 0,
197            };
198
199
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            $hsps = {
200                'rank'          => 0,
201                'qstart'        => 0,
202                'qend'          => 0,
203                'sstart'        => 0,
204                'send'          => 0,
205                'sstrand'       => 0,
206                'pident'        => 0,
207                'nident'        => 0,
208                'gaps'          => 0,
209            };
210
211            # Process each gRNA hit
212
2618
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            while ( my $hit = $result->next_hit ) {
213
214
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                $info->{'occurrences'} = $hit->num_hsps;
215
216                # Process each match (HSP) in iterative fashion
217
2618
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                while( my $hsp = $hit->next_hsp ) {
218                    # Get all values to store in hashes
219
9394
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                    $hsps = {
220                        'rank'          => $hsp->rank,
221                        'qstart'        => $hsp->start('query'),
222                        'qend'          => $hsp->end('query'),
223                        'qstrand'       => $hsp->strand('query'),
224                        'sstart'        => $hsp->start('hit'),
225                        'send'          => $hsp->end('hit'),
226                        'sstrand'       => $hsp->strand('hit'),
227                        'pident'        => $hsp->percent_identity,
228                        'nident'        => $hsp->num_identical,
229                        'gaps'          => $hsp->gaps,
230                    };
231
9394
9394
10608404
48657
                    push @{ $targets{$gRNA}{$subjName}{'hsps'} } , $hsps;
232                }
233            }
234
2618
2618
76153
15630
            push @{ $targets{$gRNA}{$subjName}{'info'} } , $info;
235        }
236
154
61504
        $fac->cleanup; #clean up temp database files
237    }
238
239
196
206889
    say "\nBLAST files saved in: '$outDir/blast' ";
240
241    # Hash of Hashes of Hashes of Arrays of Hash to store BLAST results for each query
242    # -- Hash key == gRNA name
243    # -- Hash key == Subject name
244    # -- Hash key == 'info'
245    # -- Hash key == 'hsps'
246    # -- Array accounts for multiple hits for each gRNA sequence as hashes....
247    # -- Hash contains BLAST match info
248
196
2793
    return(\%targets);
249}
250
251#-------------------------------------------------------------------------------
252# HELPERS
253
254#- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
255# $input = ($seq);
256#- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
257# This function takes 1 argument, a record file and extracts relevant information
258#- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
259# $return = ($name); Name of sequence record
260#- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
261sub _getSeqName {
262
154
154
462
    my ($seq) = @_;
263
264    # Sequence OO
265
154
2700
    my $seqInObj    = Bio::SeqIO->new(-file => $seq, -alphabet => "dna");
266
154
102705
    my $format      = $seqInObj->_guess_format($seq); #check format of input file
267
154
2326
    my $seqObj      = $seqInObj->next_seq;
268
154
18261
    my $name        = $seqObj->display_id;
269
270
154
3074
    return $name;
271}
272
273#- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
274# $input = ($sequence);
275#- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
276# This function takes 1 argument, a sequence string and determines if string is
277# palindrome.
278#- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
279# $return = Returns yes/no if palindrome found
280#- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
281
282sub _palindrome {
283
4440
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6832
    my $filledUsage = 'Usage: ' . (caller(0))[3] . '($sequence)';
284
4440
100
117569
    @_ == 1 or confess wrongNumberArguments(), $filledUsage;
285
286
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3645
    my ($sequence) = @_;
287
288
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3161
    my $palindrome = reverse $sequence;
289
290
4333
100
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    $palindrome eq $sequence ? return("Yes") : return("No");
291}
292
293
294
295 - 313
=head1 COPYRIGHT AND LICENSE
-
-Andres Breton ©
-
-[LICENSE]
-
-=head1 CONTACT
-
-Please email comments or questions to Andres Breton, <dev@andresbreton.com>
-
-=head1 SETTING PATH
-
-If PERL5LIB was not set, do something like this:
-
-use FindBin; use lib "$FindBin::RealBin/lib";
-
-This finds and uses subdirectory 'lib' in current directoy as library location
-
-=cut
3141;
- - diff --git a/cover_db/structure/0bf19b40fe954a61ff714e5a05d832e5 b/cover_db/structure/0bf19b40fe954a61ff714e5a05d832e5 deleted file mode 100644 index 213590b..0000000 --- a/cover_db/structure/0bf19b40fe954a61ff714e5a05d832e5 +++ /dev/null @@ -1 +0,0 @@ -{"statement":[3,3,3,8,8,8,8,8,8,8,8,8,8,8,8,9,9,9,11,11,11,11,11,11,12,12,12,13,13,13,13,13,13,74,75,77,78,79,127,84,86,88,89,91,92,97,99,100,101,101,102,103,106,107,108,111,124,130,131,152,153,155,156,157,158,159,161,163,164,165,167,170,175,181,184,185,186,189,194,199,212,214,217,219,231,231,234,234,236,239,248,262,265,266,267,268,270,283,284,286,288,290],"branch":[[75,{"text":"unless @_ == 2"}],[97,{"text":"if length $window < $windowSize"}],[99,{"text":"if ($window =~ /(.+)(.GG)$/)"}],[153,{"text":"unless @_ == 3"}],[189,{"text":"if $numHits == 0"}],[284,{"text":"unless @_ == 1"}],[290,{"text":"$palindrome eq $sequence ? 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use strict; use warnings; use diagnostics; use feature qw(say);
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1606
26512
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use IO::Detect qw(is_filehandle);
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1450
41293
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use Test::More tests => 73;
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1
1
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1331
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use Test::Exception; #need this to get dies_ok and lives_ok to work
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417
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use FindBin; use lib "$FindBin::RealBin/../lib";
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my $SEQ = 'usr/test.fasta';
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1
2
my @SUBJSEQS = $SEQ;
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1
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my $OUTFILE = 'test';
14
1
2
our $OUTDIR = 'tests';
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1
1
our $WINDOWSIZE  = 23;
16
1
1
my $VERBOSE;
17
1
1
my $SS;
18
1
1
our $HTML;
19
1
1
my $USAGE = "Usage message";
20
21
1
5
mkDir($OUTDIR);
22
23#-------------------------------------------------------------------------------
24# TESTS
25
26
1
119
require_ok 'chomp.pl';
27
28# Modules
29
1
1
1
1
1
1
1
113
508
4424
1
61
BEGIN { use_ok('MyIO') }
30
1
1
1
1
1
1
1
226
87
1
0
25
BEGIN { use_ok('MyConfig') }
31
1
1
1
1
1
1
1
195
576
300
1
13
BEGIN { use_ok('Handlers') }
32
1
1
1
1
1
1
1
183
393
2
1
21
BEGIN { use_ok('Search') }
33
1
1
1
1
1
1
1
228
438
3
1
23
BEGIN { use_ok('SS') }
34
35
36#- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
37# MAIN
38
39#-------------------------------------------------------------------------------
40# checks
41
1
268
print "\nTesting checks()...\n";
42
1
1
1
5
17
dies_ok { checks() } 'dies ok when no arguments passed in checks()';
43
44#-------------------------------------------------------------------------------
45# setParameters
46# print "\nTesting setParameters()...\n";
47
1
1
1
755
45
dies_ok { setParameters() } 'dies ok when no arguments passed in setParameters()';
48
49#-------------------------------------------------------------------------------
50# getSeqDetails
51
1
218
print "\nTesting getSeqDetails()...\n";
52
1
1
1
5
34
dies_ok { getSeqDetails() } 'dies ok when no argument passed in getSeqDetails()';
53
1
1
1
358
21
dies_ok { getSeqDetails(1) } 'dies ok when 1 incorrect argument is passed in getSeqDetails()';
54
1
1
1
1617
17
dies_ok { getSeqDetails(1,2) } 'dies ok when >1 arguments are passed in getSeqDetails()';
55
1
1
1
257
18
dies_ok { getSeqDetails("not.fasta") } 'dies ok when argument is not FASTA file in getSeqDetails()';
56
1
1
1
4811
16
lives_ok { getSeqDetails($SEQ) } 'lives ok when file is passed in getSeqDetails()';
57
1
475
my ($seqDetails) = getSeqDetails($SEQ);
58
59#-------------------------------------------------------------------------------
60# findOligo()
61
1
16
print "\nTesting findOligo()...\n";
62
1
1
1
9
32
dies_ok { findOligo() } 'dies ok when no argument passed in findOligo()';
63
1
1
1
690
13
dies_ok { findOligo(1) } 'dies ok when 1 argument is passed in findOligo()';
64
1
1
1
585
16
dies_ok { findOligo(1, $WINDOWSIZE) } 'dies ok when 2 incorrect arguments passed in findOligo()';
65
1
1
1
173
12
dies_ok { findOligo(1, $WINDOWSIZE) } 'dies ok when 2 arguments passed, but 1 is incorrect in findOligo()';
66
1
1
1
205
36
dies_ok { findOligo(1,2,3) } 'dies ok when 3 arguments are passed in findOligo()';
67
1
1
1
546
12
lives_ok { findOligo($seqDetails, $WINDOWSIZE) } 'lives ok when right paramaterers passed in findOligo()';
68
69
1
212
my ($gRNAs, $CRPseqs) = findOligo($seqDetails, $WINDOWSIZE);
70
1
5
is(ref($gRNAs), "HASH", "gRNA hash reference returned");
71
1
406
is($gRNAs->{'gRNA_0'}->{'sequence'}, 'ATGTAGCTAGCTAGCTAGTAGGG', 'gRNA_0 sequence is correct');
72
1
177
is($gRNAs->{'gRNA_1'}->{'sequence'}, 'AAAAAATTTTCTCTATCTAACGG', 'gRNA_1 sequence is correct');
73
1
158
is($gRNAs->{'gRNA_2'}->{'sequence'}, 'AAAAATTTTCTCTATCTAACGGG', 'gRNA_2 sequence is correct');
74
1
149
is($gRNAs->{'gRNA_3'}->{'sequence'}, 'TGTGATCACGTACTATTATGCGG', 'gRNA_3 sequence is correct');
75
1
133
is($gRNAs->{'gRNA_4'}->{'sequence'}, 'AAAAATCCCATCGATCTAGCAGG', 'gRNA_4 sequence is correct');
76
1
150
is($gRNAs->{'gRNA_5'}->{'sequence'}, 'TCCCATCGATCTAGCAGGCCCGG', 'gRNA_5 sequence is correct');
77
1
133
is($gRNAs->{'gRNA_6'}->{'sequence'}, 'CGAAAAAAAATTTTCCCTATCGG', 'gRNA_6 sequence is correct');
78
1
147
is($gRNAs->{'gRNA_7'}->{'sequence'}, 'GAAAAAAAATTTTCCCTATCGGG', 'gRNA_7 sequence is correct');
79
1
131
is($gRNAs->{'gRNA_8'}->{'sequence'}, 'AAAAAAAATTTTCCCTATCGGGG', 'gRNA_8 sequence is correct');
80
1
150
is($gRNAs->{'gRNA_9'}->{'sequence'}, 'AAAAAAATTTTCCCTATCGGGGG', 'gRNA_9 sequence is correct');
81
1
130
is($gRNAs->{'gRNA_10'}->{'sequence'}, 'CTATAGCATGGGCCCCCGATAGG', 'gRNA_10 sequence is correct');
82
1
151
is($gRNAs->{'gRNA_11'}->{'sequence'}, 'TATAGCATGGGCCCCCGATAGGG', 'gRNA_11 sequence is correct');
83
1
131
is($gRNAs->{'gRNA_12'}->{'sequence'}, 'TTCGTCATGCATGCTCGCTCCGG', 'gRNA_12 sequence is correct');
84
1
148
is($gRNAs->{'gRNA_13'}->{'sequence'}, 'TCGTCATGCATGCTCGCTCCGGG', 'gRNA_13 sequence is correct');
85
1
134
is($gRNAs->{'gRNA_14'}->{'sequence'}, 'CTCCGGGCCTGCTAGATCGATGG', 'gRNA_14 sequence is correct');
86
1
150
is($gRNAs->{'gRNA_15'}->{'sequence'}, 'TCCGGGCCTGCTAGATCGATGGG', 'gRNA_15 sequence is correct');
87
1
130
is($gRNAs->{'gRNA_16'}->{'sequence'}, 'ATAGTACGTGATCACAGTCATGG', 'gRNA_16 sequence is correct');
88
89#-------------------------------------------------------------------------------
90# writeFasta
91
1
153
print "\nTesting writeFasta()...\n";
92
1
1
1
7
25
dies_ok { writeFasta() } 'dies ok when no argument passed in writeFasta()';
93
1
1
1
263
39
dies_ok { writeFasta(1) } 'dies ok when 1 argument is passed in writeFasta()';
94
1
1
1
193
13
dies_ok { writeFasta(1,2) } 'dies ok when 2 incorrect arguments passed in writeFasta()';
95
1
1
1
201
22
dies_ok { writeFasta(1, $OUTFILE) } 'dies ok when 2 arguments passed, but 1 is incorrect in writeFasta()';
96
1
1
1
206
17
dies_ok { writeFasta(1,2,3) } 'dies ok when 3 arguments are passed in writeFasta()';
97
1
1
1
229
20
lives_ok { writeFasta($gRNAs, $OUTFILE) } 'lives ok when right parameters are passed in writeFasta()';
98
1
352
my $fastaFile = writeFasta($gRNAs, $OUTFILE);
99
100#-------------------------------------------------------------------------------
101# ss
102
1
6
mkDir("$OUTDIR/ss");
103
1
1
1
79
21
dies_ok { ss() } 'dies ok when no argument passed in ss()';
104
1
1
1
635
10
dies_ok { ss(1) } 'dies ok when 1 argument passed in ss()';
105
1
1
1
703
12
dies_ok { ss(1,2) } 'dies ok when 2 invalid arguments passed in ss()';
106
1
1
1
285
19
lives_ok { ss('gRNA_0', $gRNAs->{'gRNA_0'}->{'sequence'} ) } 'lives ok when correct arguments passed in ss()';
107
108#-------------------------------------------------------------------------------
109# Search::blast
110
1
740
print "\nTesting Search::blast()...\n";
111
1
1
1
63
63
dies_ok { Search::blast() } 'dies ok when no argument passed in Search::blast()';
112
1
1
1
878
18
dies_ok { Search::blast(1) } 'dies ok when 1 argument is passed in Search::blast()';
113
1
1
1
611
26
dies_ok { Search::blast(1,2,) } 'dies ok when 2 arguments passed, but at least 1 is incorrect in Search::blast()';
114
1
1
1
573
14
dies_ok { Search::blast(1,2, $OUTFILE) } 'dies ok when 3 arguments passed, but 1 is incorrect in Search::blast()';
115
1
1
1
182
23
dies_ok { Search::blast(1, $fastaFile, $OUTFILE) } 'dies ok when 3 arguments passed, but 2 are incorrect in Search::blast()';
116
1
1
1
171
21
dies_ok { Search::blast(1,2,3) } 'dies ok when 3 incorrect arguments are passed in Search::blast()';
117
1
1
1
178
22
lives_ok { Search::blast($fastaFile, \@SUBJSEQS, $OUTFILE) } 'lives ok when right parameters are passed in Search::blast()';
118
1
762
my $targets = Search::blast($fastaFile, \@SUBJSEQS, $OUTFILE);
119
120#-------------------------------------------------------------------------------
121# _palindrome
122
1
6
print "\nTesting Search::_palindrome()...\n";
123
1
1
1
26
50
dies_ok { Search::_palindrome() } 'dies ok when no argument passed in Search::_palindrome()';
124# dies_ok { Search::_palindrome(1) } 'dies ok when argument passed is incorrect in Search::_palindrome()';
125
1
1
1
938
22
lives_ok { Search::_palindrome('ATGTA') } 'lives ok when right parameters are passed in Search::_palindrome()';
126
1
225
is ( Search::_palindrome('ATGTA') , 'Yes', 'YES palindrome found is correct');
127
1
235
is ( Search::_palindrome('ATGTAA') , 'No', 'NO palindrome found is correct');
128
129#-------------------------------------------------------------------------------
130# writeResults
131
1
267
print "\nTesting writeResults()...\n";
132
1
1
1
10
42
dies_ok { writeResults() } 'dies ok when no argument passed in writeResults()';
133
1
1
1
318
22
dies_ok { writeResults(1) } 'dies ok when 1 argument is passed in writeResults()';
134
1
1
1
271
23
dies_ok { writeResults(1,2) } 'dies ok when 2 incorrect arguments passed in writeResults()';
135
1
1
1
310
19
dies_ok { writeResults(1,2,3) } 'dies ok when 3 incorrect arguments passed in writeResults()';
136
1
1
1
218
12
dies_ok { writeResults(1,2,3,4) } 'dies ok when 4 incorrect arguments passed in writeResults()';
137
1
1
1
250
17
dies_ok { writeResults(1,2,3,4,5) } 'dies ok when 5 incorrect arguments passed in writeResults()';
138
1
1
1
237
16
dies_ok { writeResults(1,2,3,4,5,6) } 'dies ok when 6 incorrect arguments passed in writeResults()';
139
140
1
169
my $DOWNSEQ;
141
1
1
my $UPSEQ;
142
1
1
1
13
14
lives_ok { writeResults($gRNAs, $targets, $DOWNSEQ, $UPSEQ, $WINDOWSIZE, $OUTFILE) } 'lives ok whith both undef DOWN/UP-SEQ parameters are passed in writeResults()';
143
144
1
314
$DOWNSEQ = "DWDWDW";
145
1
1
1
8
31
lives_ok { writeResults($gRNAs, $targets, $DOWNSEQ, $UPSEQ, $WINDOWSIZE, $OUTFILE) } 'lives ok whith undef UPSEQ parameter is passed in writeResults()';
146
147
1
320
$DOWNSEQ = "";
148
1
2
$UPSEQ = "UPUPUP";
149
1
1
1
48
24
lives_ok { writeResults($gRNAs, $targets, $DOWNSEQ, $UPSEQ, $WINDOWSIZE, $OUTFILE) } 'lives ok whith undef DOWNSEQ & defined $UPSEQ parameter is passed in writeResults()';
150
151
152
1
262
$DOWNSEQ = "DWDWDW";
153
1
3
$UPSEQ = "UPUPUP";
154
1
1
1
26
22
lives_ok { writeResults($gRNAs, $targets, $DOWNSEQ, $UPSEQ, $WINDOWSIZE, $OUTFILE) } 'lives ok when right parameters are passed in writeResults()';
155
1
287
writeResults($gRNAs, $targets, $DOWNSEQ, $UPSEQ, $WINDOWSIZE, $OUTFILE);
156
157#-------------------------------------------------------------------------------
158# sortIdentities
159
1
4
print "\nTesting sortIdentities()...\n";
160
1
1
1
25
31
dies_ok { sortIdentities() } 'dies ok when no arguments passed';
161
1
1
1
317
15
dies_ok { sortIdentities(1) } 'dies ok when invalid argument passed';
162
1
1
1
184
17
dies_ok { sortIdentities(1,2) } 'dies ok when 2 arguments passed';
163
1
1
1
198
13
lives_ok { sortIdentities( $targets->{'gRNA_0'}{'test'}{'hsps'} ) } 'lives ok when 1 correct arguments passed';
164
165
166#-------------------------------------------------------------------------------
167# Clean Up
168
1
4770
`rm -r ./$OUTDIR`;
169
170
1
41
done_testing();
- -