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Revision 1.10 - (view) (download) (as text)
| 1 : | olson | 1.1 | |
| 2 : | package FFserver; | ||
| 3 : | |||
| 4 : | use LWP::UserAgent; | ||
| 5 : | use Data::Dumper; | ||
| 6 : | olson | 1.3 | use YAML; |
| 7 : | olson | 1.1 | |
| 8 : | use strict; | ||
| 9 : | |||
| 10 : | sub new | ||
| 11 : | { | ||
| 12 : | my($class, $server_url) = @_; | ||
| 13 : | |||
| 14 : | olson | 1.3 | $server_url = "http://servers.nmpdr.org/figfam/server.cgi" unless $server_url; |
| 15 : | olson | 1.1 | |
| 16 : | |||
| 17 : | my $self = { | ||
| 18 : | server_url => $server_url, | ||
| 19 : | ua => LWP::UserAgent->new(), | ||
| 20 : | }; | ||
| 21 : | |||
| 22 : | return bless $self, $class; | ||
| 23 : | } | ||
| 24 : | |||
| 25 : | olson | 1.3 | sub members_of_families |
| 26 : | { | ||
| 27 : | my($self, @ids) = @_; | ||
| 28 : | olson | 1.4 | return $self->run_query('members_of_families', @ids); |
| 29 : | } | ||
| 30 : | |||
| 31 : | olson | 1.6 | sub families_containing_peg |
| 32 : | { | ||
| 33 : | my($self, @ids) = @_; | ||
| 34 : | return $self->run_query('families_containing_peg', @ids); | ||
| 35 : | } | ||
| 36 : | |||
| 37 : | arodri7 | 1.9 | sub function_of |
| 38 : | { | ||
| 39 : | my($self, @ids) = @_; | ||
| 40 : | return $self->run_query('function_of', @ids); | ||
| 41 : | } | ||
| 42 : | |||
| 43 : | sub org_of | ||
| 44 : | { | ||
| 45 : | my($self, @ids) = @_; | ||
| 46 : | return $self->run_query('org_of', @ids); | ||
| 47 : | } | ||
| 48 : | |||
| 49 : | sub seq_of | ||
| 50 : | { | ||
| 51 : | my($self, @ids) = @_; | ||
| 52 : | return $self->run_query('seq_of', @ids); | ||
| 53 : | } | ||
| 54 : | |||
| 55 : | sub aliases_of | ||
| 56 : | { | ||
| 57 : | my($self, @ids) = @_; | ||
| 58 : | return $self->run_query('aliases_of', @ids); | ||
| 59 : | } | ||
| 60 : | |||
| 61 : | sub families_implementing_role | ||
| 62 : | { | ||
| 63 : | my($self,@roles) = @_; | ||
| 64 : | return $self->run_query('families_implementing_role', @roles); | ||
| 65 : | } | ||
| 66 : | |||
| 67 : | sub families_with_function | ||
| 68 : | { | ||
| 69 : | my($self,@functions) = @_; | ||
| 70 : | return $self->run_query('families_with_function', @functions); | ||
| 71 : | } | ||
| 72 : | |||
| 73 : | sub families_in_genome | ||
| 74 : | { | ||
| 75 : | my($self,@genomes) = @_; | ||
| 76 : | return $self->run_query('families_in_genome', @genomes); | ||
| 77 : | } | ||
| 78 : | |||
| 79 : | sub get_subsystem_based_figfams | ||
| 80 : | { | ||
| 81 : | my ($self) = @_; | ||
| 82 : | return $self->run_query('get_subsystem_based_figfams'); | ||
| 83 : | } | ||
| 84 : | |||
| 85 : | olson | 1.4 | sub should_be_member |
| 86 : | { | ||
| 87 : | my($self, @id_seq_pairs) = @_; | ||
| 88 : | return $self->run_query('should_be_member', @id_seq_pairs); | ||
| 89 : | } | ||
| 90 : | |||
| 91 : | sub all_families | ||
| 92 : | { | ||
| 93 : | my($self) = @_; | ||
| 94 : | return $self->run_query('all_families'); | ||
| 95 : | } | ||
| 96 : | |||
| 97 : | sub run_query | ||
| 98 : | { | ||
| 99 : | my($self, $function, @args ) = @_; | ||
| 100 : | my $form = [function => $function, | ||
| 101 : | args => YAML::Dump(@args), | ||
| 102 : | ]; | ||
| 103 : | olson | 1.3 | return $self->run_query_form($form); |
| 104 : | } | ||
| 105 : | |||
| 106 : | sub run_query_form | ||
| 107 : | { | ||
| 108 : | my($self, $form) = @_; | ||
| 109 : | |||
| 110 : | my $res = $self->{ua}->post($self->{server_url}, $form); | ||
| 111 : | |||
| 112 : | if ($res->is_success) | ||
| 113 : | { | ||
| 114 : | return Load($res->content); | ||
| 115 : | } | ||
| 116 : | else | ||
| 117 : | { | ||
| 118 : | olson | 1.7 | die "error on post " . $res->status_line . " " . $res->content; |
| 119 : | olson | 1.3 | } |
| 120 : | } | ||
| 121 : | |||
| 122 : | olson | 1.1 | sub assign_function_to_prot |
| 123 : | { | ||
| 124 : | olson | 1.10 | my($self, $input, $blast, $min_hits) = @_; |
| 125 : | olson | 1.1 | |
| 126 : | olson | 1.2 | my $wq; |
| 127 : | olson | 1.10 | |
| 128 : | my $params = [blast => $blast, min_hits => $min_hits]; | ||
| 129 : | olson | 1.2 | |
| 130 : | olson | 1.1 | if (ref($input) eq 'ARRAY') |
| 131 : | { | ||
| 132 : | olson | 1.2 | $wq = SequenceListWorkQueue->new($input); |
| 133 : | olson | 1.1 | } |
| 134 : | else | ||
| 135 : | { | ||
| 136 : | olson | 1.2 | $wq = FastaWorkQueue->new($input); |
| 137 : | olson | 1.1 | } |
| 138 : | olson | 1.2 | |
| 139 : | olson | 1.10 | return ResultHandler->new($wq, $self->{server_url}, 'assign_function_to_prot', \&id_seq_pair_bundler, |
| 140 : | #\&tab_delimited_output_parser, | ||
| 141 : | \&YAML::Load, | ||
| 142 : | $params); | ||
| 143 : | olson | 1.1 | } |
| 144 : | |||
| 145 : | olson | 1.2 | sub assign_functions_to_dna |
| 146 : | olson | 1.1 | { |
| 147 : | olson | 1.10 | my($self, $input, $min_hits, $max_gap, $blast) = @_; |
| 148 : | olson | 1.1 | |
| 149 : | olson | 1.2 | my $wq; |
| 150 : | olson | 1.1 | |
| 151 : | olson | 1.2 | if (ref($input) eq 'ARRAY') |
| 152 : | olson | 1.1 | { |
| 153 : | olson | 1.2 | $wq = SequenceListWorkQueue->new($input); |
| 154 : | olson | 1.1 | } |
| 155 : | else | ||
| 156 : | { | ||
| 157 : | olson | 1.2 | $wq = FastaWorkQueue->new($input); |
| 158 : | olson | 1.1 | } |
| 159 : | olson | 1.2 | |
| 160 : | olson | 1.10 | my $params = [min_hits => $min_hits, max_gap => $max_gap, blast => $blast]; |
| 161 : | return ResultHandler->new($wq, $self->{server_url}, 'assign_functions_to_DNA', | ||
| 162 : | \&id_seq_pair_bundler, | ||
| 163 : | \&tab_delimited_output_parser, $params); | ||
| 164 : | olson | 1.2 | } |
| 165 : | |||
| 166 : | sub id_seq_pair_bundler | ||
| 167 : | { | ||
| 168 : | my($item) = @_; | ||
| 169 : | my($id, $seq) = @$item[0,2]; | ||
| 170 : | return "id_seq", join(",", $id, (ref($seq) eq 'SCALAR' ? $$seq : $seq)); | ||
| 171 : | } | ||
| 172 : | |||
| 173 : | sub tab_delimited_output_parser | ||
| 174 : | { | ||
| 175 : | my($line) = @_; | ||
| 176 : | chomp $line; | ||
| 177 : | my @cols = split(/\t/, $line); | ||
| 178 : | return \@cols; | ||
| 179 : | } | ||
| 180 : | |||
| 181 : | |||
| 182 : | sub tab_delimited_dna_data_output_parser | ||
| 183 : | { | ||
| 184 : | my($line) = @_; | ||
| 185 : | chomp $line; | ||
| 186 : | my ($id, $idbe, $fam) = split(/\t/, $line); | ||
| 187 : | my ($beg, $end) = $idbe =~ /_(\d+)_(\d+)$/; | ||
| 188 : | return [$id, $beg, $end, $fam]; | ||
| 189 : | olson | 1.1 | } |
| 190 : | |||
| 191 : | olson | 1.2 | package ResultHandler; |
| 192 : | olson | 1.1 | use strict; |
| 193 : | olson | 1.2 | use Data::Dumper; |
| 194 : | olson | 1.1 | |
| 195 : | sub new | ||
| 196 : | { | ||
| 197 : | olson | 1.5 | my($class, $work_queue, $server_url, $function, $input_bundler, $output_parser, $form_vars) = @_; |
| 198 : | olson | 1.2 | |
| 199 : | olson | 1.1 | my $self = { |
| 200 : | olson | 1.2 | work_queue => $work_queue, |
| 201 : | server_url => $server_url, | ||
| 202 : | function => $function, | ||
| 203 : | input_bundler => $input_bundler, | ||
| 204 : | output_parser => $output_parser, | ||
| 205 : | ua => LWP::UserAgent->new(), | ||
| 206 : | cur_result => undef, | ||
| 207 : | olson | 1.5 | form_vars => $form_vars ? $form_vars : [], |
| 208 : | olson | 1.1 | }; |
| 209 : | return bless $self, $class; | ||
| 210 : | } | ||
| 211 : | |||
| 212 : | sub get_next | ||
| 213 : | { | ||
| 214 : | my($self) = @_; | ||
| 215 : | |||
| 216 : | olson | 1.10 | my $res = $self->get_next_from_result(); |
| 217 : | |||
| 218 : | if ($res) | ||
| 219 : | olson | 1.2 | { |
| 220 : | olson | 1.10 | return $res; |
| 221 : | olson | 1.2 | } |
| 222 : | else | ||
| 223 : | { | ||
| 224 : | my @inp = $self->{work_queue}->get_next_n_bytes(16000); | ||
| 225 : | if (@inp) | ||
| 226 : | { | ||
| 227 : | olson | 1.5 | my $form = [@{$self->{form_vars}}]; |
| 228 : | push(@$form, function => $self->{function}, | ||
| 229 : | map { &{$self->{input_bundler}}($_) } @inp); | ||
| 230 : | olson | 1.8 | # print "Invoke " .Dumper($form); |
| 231 : | olson | 1.2 | |
| 232 : | my $res = $self->{ua}->post($self->{server_url}, $form); | ||
| 233 : | if ($res->is_success) | ||
| 234 : | { | ||
| 235 : | olson | 1.10 | $self->{cur_result} = [YAML::Load($res->content)]; |
| 236 : | olson | 1.2 | #print "res: $self->{cur_result}\n"; |
| 237 : | return $self->get_next_from_result(); | ||
| 238 : | } | ||
| 239 : | else | ||
| 240 : | { | ||
| 241 : | olson | 1.3 | die "error " . $res->status_line . " on post " . $res->content; |
| 242 : | olson | 1.2 | } |
| 243 : | } | ||
| 244 : | else | ||
| 245 : | { | ||
| 246 : | return; | ||
| 247 : | } | ||
| 248 : | } | ||
| 249 : | } | ||
| 250 : | |||
| 251 : | sub get_next_from_result | ||
| 252 : | { | ||
| 253 : | my($self) = @_; | ||
| 254 : | olson | 1.10 | my $l = $self->{cur_result}; |
| 255 : | if ($l and @$l) | ||
| 256 : | { | ||
| 257 : | return shift(@$l); | ||
| 258 : | } | ||
| 259 : | else | ||
| 260 : | olson | 1.2 | { |
| 261 : | olson | 1.10 | delete $self->{cur_result}; |
| 262 : | return undef; | ||
| 263 : | olson | 1.2 | } |
| 264 : | } | ||
| 265 : | |||
| 266 : | package SequenceWorkQueue; | ||
| 267 : | use strict; | ||
| 268 : | |||
| 269 : | sub new | ||
| 270 : | { | ||
| 271 : | my($class) = @_; | ||
| 272 : | |||
| 273 : | my $self = {}; | ||
| 274 : | |||
| 275 : | return bless $self, $class; | ||
| 276 : | } | ||
| 277 : | olson | 1.1 | |
| 278 : | olson | 1.2 | sub get_next_n |
| 279 : | { | ||
| 280 : | my($self, $n) = @_; | ||
| 281 : | my @out; | ||
| 282 : | |||
| 283 : | for (my $i = 0;$i < $n; $i++) | ||
| 284 : | olson | 1.1 | { |
| 285 : | olson | 1.2 | my($id, $com, $seqp) = $self->get_next(); |
| 286 : | if (defined($id)) | ||
| 287 : | { | ||
| 288 : | push(@out, [$id, $com, $seqp]); | ||
| 289 : | } | ||
| 290 : | else | ||
| 291 : | { | ||
| 292 : | last; | ||
| 293 : | } | ||
| 294 : | olson | 1.1 | } |
| 295 : | olson | 1.2 | return @out; |
| 296 : | } | ||
| 297 : | |||
| 298 : | sub get_next_n_bytes | ||
| 299 : | { | ||
| 300 : | my($self, $n) = @_; | ||
| 301 : | my @out; | ||
| 302 : | |||
| 303 : | my $size = 0; | ||
| 304 : | while ($size < $n) | ||
| 305 : | olson | 1.1 | { |
| 306 : | olson | 1.2 | my($id, $com, $seqp) = $self->get_next(); |
| 307 : | if (defined($id)) | ||
| 308 : | { | ||
| 309 : | push(@out, [$id, $com, $seqp]); | ||
| 310 : | $size += (ref($seqp) eq 'SCALAR') ? length($$seqp) : length($seqp); | ||
| 311 : | } | ||
| 312 : | else | ||
| 313 : | { | ||
| 314 : | last; | ||
| 315 : | } | ||
| 316 : | olson | 1.1 | } |
| 317 : | olson | 1.2 | return @out; |
| 318 : | olson | 1.1 | } |
| 319 : | |||
| 320 : | olson | 1.2 | package FastaWorkQueue; |
| 321 : | olson | 1.1 | use strict; |
| 322 : | olson | 1.2 | use base 'SequenceWorkQueue'; |
| 323 : | olson | 1.1 | use FileHandle; |
| 324 : | use FIG; | ||
| 325 : | |||
| 326 : | sub new | ||
| 327 : | { | ||
| 328 : | olson | 1.2 | my($class, $input) = @_; |
| 329 : | olson | 1.1 | |
| 330 : | my $fh; | ||
| 331 : | if (ref($input)) | ||
| 332 : | { | ||
| 333 : | $fh = $input; | ||
| 334 : | } | ||
| 335 : | else | ||
| 336 : | { | ||
| 337 : | $fh = new FileHandle("<$input"); | ||
| 338 : | } | ||
| 339 : | olson | 1.2 | |
| 340 : | my $self = $class->SUPER::new(); | ||
| 341 : | |||
| 342 : | $self->{fh} = $fh; | ||
| 343 : | |||
| 344 : | olson | 1.1 | return bless $self, $class; |
| 345 : | } | ||
| 346 : | |||
| 347 : | sub get_next | ||
| 348 : | { | ||
| 349 : | my($self) = @_; | ||
| 350 : | |||
| 351 : | olson | 1.2 | my($id, $seqp, $com) = &FIG::read_fasta_record($self->{fh}); |
| 352 : | return defined($id) ? ($id, $com, $seqp) : (); | ||
| 353 : | } | ||
| 354 : | |||
| 355 : | package SequenceListWorkQueue; | ||
| 356 : | use strict; | ||
| 357 : | use base 'SequenceWorkQueue'; | ||
| 358 : | olson | 1.1 | |
| 359 : | olson | 1.2 | sub new |
| 360 : | { | ||
| 361 : | my($class, $input) = @_; | ||
| 362 : | |||
| 363 : | my $fh; | ||
| 364 : | if (ref($input) ne 'ARRAY') | ||
| 365 : | olson | 1.1 | { |
| 366 : | olson | 1.2 | die "SequenceWorkQueue requires a list as input"; |
| 367 : | olson | 1.1 | } |
| 368 : | olson | 1.2 | |
| 369 : | my $self = $class->SUPER::new(); | ||
| 370 : | |||
| 371 : | $self->{list} = $input; | ||
| 372 : | |||
| 373 : | return bless $self, $class; | ||
| 374 : | } | ||
| 375 : | |||
| 376 : | sub get_next | ||
| 377 : | { | ||
| 378 : | my($self) = @_; | ||
| 379 : | |||
| 380 : | my $top = shift @{$self->{list}}; | ||
| 381 : | |||
| 382 : | return defined($top) ? @$top : (); | ||
| 383 : | olson | 1.1 | } |
| 384 : | olson | 1.2 | |
| 385 : | |||
| 386 : | olson | 1.1 | 1; |
| 387 : | olson | 1.2 |
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