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1 : redwards 1.1 # -*- perl -*-
2 :    
3 :     =pod
4 :    
5 :     =head1
6 :    
7 :     Some routines and things that Rob uses. Please feel free to use at will and incorporate into
8 :     your own code or move them into FIG.pm or elsewhere.
9 :    
10 :     =cut
11 :    
12 :     package raelib;
13 :     use strict;
14 :     use FIG;
15 :     my $fig=new FIG;
16 :    
17 : redwards 1.5 =head2 new
18 :    
19 :     Just instantiate the object and return $self
20 :    
21 :     =cut
22 :    
23 :     sub new {
24 :     my $self=shift;
25 :     return $self
26 :     }
27 :    
28 :    
29 :    
30 :    
31 : redwards 1.4 =head2 features_on_contig
32 :    
33 :     Returns a reference to an array containing all the features on a contig in a genome.
34 :    
35 :     use:
36 :    
37 :     my $arrayref=$rae->features_on_contig($genome, $contig);
38 :    
39 :     or
40 :    
41 :     foreach my $peg (@{$rae->features_on_contig($genome, $contig)}) {
42 :     ... blah blah ...
43 :     }
44 :    
45 :     returns undef if contig is not a part of genome or there is nothing to return, otherwise returns a list of pegs
46 :    
47 :     v. experimental and guaranteed not to work!
48 :    
49 :     =cut
50 :    
51 :     sub features_on_contig {
52 :     my ($self, $genome, $contig)=@_;
53 :     # were this in FIG.pm you'd use this line:
54 :     #my $rdbH = $self->db_handle;
55 :    
56 :     my $rdbH = $fig->db_handle;
57 :     my $relational_db_response=$rdbH->SQL('SELECT id FROM features WHERE (genome = \'' . $genome . '\' AND location ~* \'' . $contig . '\')');
58 :     # this is complicated. A reference to an array of references to arrays, and we only want the first element.
59 :     # simplify.
60 :     my @results;
61 :     foreach my $res (@$relational_db_response) {push @results, $res->[0]}
62 :     return \@results;
63 :     }
64 :    
65 :    
66 :    
67 :    
68 :    
69 :    
70 :    
71 : redwards 1.7 =head2 pirsfcorrespondence
72 : redwards 1.1
73 : redwards 1.7 Generate the pirsf->fig id correspondence. This is only done once and the correspondence file is written.
74 : redwards 1.1 This is so that we can easily go back and forth.
75 :    
76 : redwards 1.7 The correspondence has PIR ID \t FIG ID\n, and is probably based on ftp://ftp.pir.georgetown.edu/pir_databases/pirsf/data/pirsfinfo.dat
77 : redwards 1.1
78 : redwards 1.9 This method takes three arguments:
79 :     from : pirsfinfo.dat file
80 :     to : file to write information to
81 :     verbose : report on progress
82 :    
83 :     Returns the number of lines in the pirsinfo file that were read.
84 :    
85 : redwards 1.1 =cut
86 :    
87 : redwards 1.7 sub pirsfcorrespondence {
88 : redwards 1.9 my ($self, $from, $to, $verbose)=@_;
89 : redwards 1.10 unless (-e $from) {
90 :     print STDERR "File $from does not exist as called in $0\n";
91 :     return 0;
92 :     }
93 : redwards 1.1 open (IN, $from) || die "Can't open $from";
94 : redwards 1.8 open (OUT, ">$to") || die "Can't write to $to";
95 : redwards 1.9 my $linecount;
96 : redwards 1.1 while (<IN>) {
97 : redwards 1.9 $linecount++;
98 :     unless ($linecount % 10000) {print STDERR "Correspondence of $linecount lines calculated\n"}
99 : redwards 1.1 if (/^>/) {print OUT; next}
100 :     chomp;
101 :     my $done;
102 : redwards 1.2 foreach my $peg ($fig->by_alias("uni|$_")) {
103 : redwards 1.1 print OUT $_, "\t", $peg, "\n";
104 :     $done=1;
105 :     }
106 : redwards 1.12 unless ($done) {
107 :     foreach my $peg ($fig->by_alias("tr|$_")) {
108 :     print OUT $_, "\t", $peg, "\n";
109 :     $done=1;
110 :     }
111 :     }
112 :     unless ($done) {
113 :     foreach my $peg ($fig->by_alias("sp|$_")) {
114 :     print OUT $_, "\t", $peg, "\n";
115 :     $done=1;
116 :     }
117 :     }
118 : redwards 1.1 unless ($done) {print OUT $_, "\t\n"}
119 :     }
120 :     close IN;
121 :     close OUT;
122 : redwards 1.9 return $linecount;
123 : redwards 1.1 }
124 :    
125 :    
126 :     =head2 ss_by_id
127 :    
128 :     Generate a list of subsystems that a peg occurs in. This is a ; separated list.
129 :     This is a wrapper that removes roles and ignores essential things
130 :    
131 :     =cut
132 :    
133 :     sub ss_by_id {
134 :     my ($self, $peg)=@_;
135 :     my $ssout;
136 :     foreach my $ss (sort $fig->subsystems_for_peg($peg))
137 :     {
138 :     next if ($$ss[0] =~ /essential/i); # Ignore the Essential B-subtilis subsystems
139 :     $ssout.=$$ss[0]."; ";
140 :     }
141 :     $ssout =~ s/; $//;
142 :     return $ssout;
143 :     }
144 :    
145 : redwards 1.3 =head2 ss_by_homol
146 :    
147 :     Generate a list of subsystems that homologs of a peg occur in. This is a ; separated list.
148 :     This is also a wrapper around sims and ss, but makes everything unified
149 :    
150 :     =cut
151 :    
152 :     sub ss_by_homol {
153 :     my ($self, $peg)=@_;
154 :     return unless ($peg);
155 :     my ($maxN, $maxP)=(50, 1e-20);
156 :    
157 :     # find the sims
158 :     my @sims=$fig->sims($peg, $maxN, $maxP, 'fig');
159 :    
160 :     # we are only going to keep the best hit for each peg
161 :     # in a subsystem
162 :     my $best_ss_score; my $best_ss_id;
163 :     foreach my $sim (@sims)
164 :     {
165 :     my $simpeg=$$sim[1];
166 :     my $simscore=$$sim[10];
167 :     my @subsys=$fig->subsystems_for_peg($simpeg);
168 :     foreach my $ss (@subsys)
169 :     {
170 :     if (! defined $best_ss_score->{$$ss[0]}) {$best_ss_score->{$$ss[0]}=$simscore; $best_ss_id->{$$ss[0]}=$simpeg}
171 :     elsif ($best_ss_score->{$$ss[0]} > $simscore)
172 :     {
173 :     $best_ss_score->{$$ss[0]}=$simscore;
174 :     $best_ss_id->{$$ss[0]}=$simpeg;
175 :     }
176 :     }
177 :     }
178 :    
179 :     my $ssoutput=join "", (map {"$_ (".$best_ss_id->{$_}."), "} keys %$best_ss_id);
180 :    
181 :     $ssoutput =~ s/, $//;
182 :     return $ssoutput;
183 :     }
184 :    
185 :     =head2 tagvalue
186 :    
187 :     This will just check for tag value pairs and return either an array of values or a single ; separated list (if called as a scalar)
188 :    
189 :     e.g. $values=raelib->tagvalue($peg, "PIRSF"); print join "\n", @$values;
190 :    
191 :     Returns an empty array if no tag/value appropriate.
192 :    
193 :     Just because I use this a lot I don't want to waste rewriting it.
194 :    
195 :     =cut
196 :    
197 :     sub tagvalue {
198 :     my ($self, $peg, $tag)=@_;
199 :     my @return;
200 :     my @attr=$fig->feature_attributes($peg);
201 :     foreach my $attr (@attr) {
202 : redwards 1.11 my ($gotpeg, $gottag, $val, $link)=@$attr;
203 : redwards 1.3 push @return, $val if ($gottag eq $tag);
204 :     }
205 :     return wantarray ? @return : join "; ", @return;
206 :     }
207 : redwards 1.1
208 : redwards 1.5 =head2 locations_on_contig
209 :    
210 :     Return the locations of a sequence on a contig.
211 :    
212 :     This will look for exact matches to a sequence on a contig, and return a reference to an array that has all the locations.
213 :    
214 :     my $locations=$raelib->locations_on_contig($genome, $contig, 'GATC', undef);
215 :     foreach my $bp (@$locations) { ... do something ... }
216 :    
217 :     first argument : genome number
218 :     second argument : contig name
219 :     third argument : sequence to look for
220 :     fourth argument : beginning position to start looking from (can be undef)
221 :     fifth argument : end position to stop looking from (can be undef)
222 :     sixth argument : check reverse complement (0 or undef will check forward, 1 or true will check rc)
223 :    
224 :     Note, the position is calculated before the sequence is rc'd
225 :    
226 :     =cut
227 :    
228 :     sub locations_on_contig {
229 :     my ($self, $genome, $contig, $sequence, $from, $to, $check_reverse)=@_;
230 :     my $return=[];
231 :    
232 :     # get the dna sequence of the contig, and make sure it is uppercase
233 :     my $contig_ln=$fig->contig_ln($genome, $contig);
234 :     return $return unless ($contig_ln);
235 :     unless ($from) {$from=1}
236 :     unless ($to) {$to=$contig_ln}
237 :     if ($from > $to) {($from, $to)=($to, $from)}
238 :     my $dna_seq=$fig->dna_seq($genome, $contig."_".$from."_".$to);
239 :     $dna_seq=uc($dna_seq);
240 :    
241 :     # if we want to check the rc, we actually rc the query
242 :     $sequence=$fig->reverse_comp($sequence) if ($check_reverse);
243 :     $sequence=uc($sequence);
244 :    
245 :     # now find all the matches
246 :     my $posn=index($dna_seq, $sequence, 0);
247 :     while ($posn > -1) {
248 :     push @$return, $posn;
249 :     $posn=index($dna_seq, $sequence, $posn+1);
250 :     }
251 :     return $return;
252 :     }
253 :    
254 :    
255 :     =head2 scrolling_org_list
256 :    
257 :     This is the list from index.cgi, that I call often. It has one minor modification: the value returned is solely the organisms id and does not contain genus_species information. I abstracted this here: 1, so I could call it often, and 2, so I could edit it once.
258 :    
259 :     use like this push @$html, $raelib->scrolling_org_list($cgi, $multiple);
260 :    
261 :     multiple selections will only be set if $multiple is true
262 :    
263 :     =cut
264 :    
265 :     sub scrolling_org_list {
266 :     my ($self, $cgi, $multiple)=@_;
267 :     unless ($multiple) {$multiple=0}
268 :    
269 :     my @display = ( 'All', 'Archaea', 'Bacteria', 'Eucarya', 'Viruses', 'Environmental samples' );
270 :    
271 :     #
272 :     # Canonical names must match the keywords used in the DBMS. They are
273 :     # defined in compute_genome_counts.pl
274 :     #
275 :     my %canonical = (
276 :     'All' => undef,
277 :     'Archaea' => 'Archaea',
278 :     'Bacteria' => 'Bacteria',
279 :     'Eucarya' => 'Eukaryota',
280 :     'Viruses' => 'Virus',
281 :     'Environmental samples' => 'Environmental Sample'
282 :     );
283 :    
284 :     my $req_dom = $cgi->param( 'domain' ) || 'All';
285 :     my @domains = $cgi->radio_group( -name => 'domain',
286 :     -default => $req_dom,
287 :     -override => 1,
288 :     -values => [ @display ]
289 :     );
290 :    
291 :     my $n_domain = 0;
292 :     my %dom_num = map { ( $_, $n_domain++ ) } @display;
293 :     my $req_dom_num = $dom_num{ $req_dom } || 0;
294 :    
295 :     #
296 :     # Viruses and Environmental samples must have completeness = All (that is
297 :     # how they are in the database). Otherwise, default is Only "complete".
298 :     #
299 :     my $req_comp = ( $req_dom_num > $dom_num{ 'Eucarya' } ) ? 'All'
300 :     : $cgi->param( 'complete' ) || 'Only "complete"';
301 :     my @complete = $cgi->radio_group( -name => 'complete',
302 :     -default => $req_comp,
303 :     -override => 1,
304 :     -values => [ 'All', 'Only "complete"' ]
305 :     );
306 :     #
307 :     # Use $fig->genomes( complete, restricted, domain ) to get org list:
308 :     #
309 :     my $complete = ( $req_comp =~ /^all$/i ) ? undef : "complete";
310 :    
311 :     my $orgs; my $label;
312 :     @$orgs = $fig->genomes( $complete, undef, $canonical{ $req_dom } );
313 :    
314 :     foreach (@$orgs) {
315 :     my $gs = $fig->genus_species($_);
316 :     my $gc=scalar $fig->all_contigs($_);
317 :     $label->{$_} = "$gs ($_) [$gc contigs]";
318 :     }
319 :    
320 :     @$orgs = sort {$label->{$a} cmp $label->{$b}} @$orgs;
321 :    
322 :     my $n_genomes = @$orgs;
323 :    
324 :     return ( "<TABLE>\n",
325 :     " <TR>\n",
326 :     " <TD>",
327 : redwards 1.6 $cgi->scrolling_list( -name => 'korgs',
328 :     -values => $orgs,
329 :     -labels => $label,
330 :     -size => 10,
331 :     -multiple => $multiple,
332 : redwards 1.5 ), $cgi->br,
333 :     "$n_genomes genomes shown ",
334 :     $cgi->submit( 'Update List' ), $cgi->reset, $cgi->br,
335 :     " </TD>",
336 :     " <TD>",
337 :     join( "<br>", "<b>Domain(s) to show:</b>", @domains), "<br>\n",
338 :     join( "<br>", "<b>Completeness?</b>", @complete), "\n",
339 :     "</TD>",
340 :     " </TR>\n",
341 :     "</TABLE>\n",
342 :     $cgi->hr
343 :     );
344 :     }
345 :    
346 :    
347 : redwards 1.1
348 :    
349 :    
350 :     1;

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