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| 1 : | overbeek | 1.1 | ######################################################################## |
| 2 : | # -*- perl -*- | ||
| 3 : | # | ||
| 4 : | # Copyright (c) 2003-2006 University of Chicago and Fellowship | ||
| 5 : | # for Interpretations of Genomes. All Rights Reserved. | ||
| 6 : | # | ||
| 7 : | # This file is part of the SEED Toolkit. | ||
| 8 : | # | ||
| 9 : | # The SEED Toolkit is free software. You can redistribute | ||
| 10 : | # it and/or modify it under the terms of the SEED Toolkit | ||
| 11 : | # Public License. | ||
| 12 : | # | ||
| 13 : | # You should have received a copy of the SEED Toolkit Public License | ||
| 14 : | # along with this program; if not write to the University of Chicago | ||
| 15 : | # at info@ci.uchicago.edu or the Fellowship for Interpretation of | ||
| 16 : | # Genomes at veronika@thefig.info or download a copy from | ||
| 17 : | # http://www.theseed.org/LICENSE.TXT. | ||
| 18 : | # | ||
| 19 : | |||
| 20 : | use Carp; | ||
| 21 : | use Data::Dumper; | ||
| 22 : | use gjoseqlib; | ||
| 23 : | |||
| 24 : | use FIG; | ||
| 25 : | my $fig = new FIG; | ||
| 26 : | |||
| 27 : | use AliTree; | ||
| 28 : | use AliTrees; | ||
| 29 : | |||
| 30 : | # usage: ali_tree [DIR] | ||
| 31 : | |||
| 32 : | my $default_dir; | ||
| 33 : | if (@ARGV > 0) | ||
| 34 : | { | ||
| 35 : | $default_dir = shift @ARGV; | ||
| 36 : | } | ||
| 37 : | else | ||
| 38 : | { | ||
| 39 : | $default_dir = "$FIG_Config::data/AlignmentsAndTrees"; | ||
| 40 : | } | ||
| 41 : | |||
| 42 : | use AliTrees; | ||
| 43 : | my $ali_trees = new AliTrees($fig,$default_dir); | ||
| 44 : | |||
| 45 : | my $ali_tree; | ||
| 46 : | my($dir); | ||
| 47 : | while ($req = &get_req) | ||
| 48 : | { | ||
| 49 : | overbeek | 1.2 | if ($req =~ /^\s*set\s+(\d+\.\d+\.peg\.\S+)\s*$/) |
| 50 : | overbeek | 1.1 | { |
| 51 : | $id = $1; | ||
| 52 : | $ali_tree = new AliTree($id,$fig,$default_dir); | ||
| 53 : | $ali_tree | ||
| 54 : | || warn "could not handle $id in $default_dir\n"; | ||
| 55 : | } | ||
| 56 : | elsif ($req =~ /^\s*set_all\s*$/) | ||
| 57 : | { | ||
| 58 : | $ali_trees->set_all; | ||
| 59 : | print "set_all completed\n"; | ||
| 60 : | } | ||
| 61 : | elsif ($req =~ /^\s*all_alignments\s*$/) | ||
| 62 : | { | ||
| 63 : | foreach $_ ($ali_trees->all_alignments) | ||
| 64 : | { | ||
| 65 : | print "$_\n"; | ||
| 66 : | } | ||
| 67 : | print "\n"; | ||
| 68 : | } | ||
| 69 : | elsif ($req =~ /^\s*delete_ali\s+(\S+)\s*$/) | ||
| 70 : | { | ||
| 71 : | $ali = $1; | ||
| 72 : | $rc = $ali_trees->delete_ali($ali); | ||
| 73 : | print &Dumper($rc); | ||
| 74 : | print "\n"; | ||
| 75 : | } | ||
| 76 : | elsif ($req =~ /^\s*add_ali\s+(\S+)\s*$/) | ||
| 77 : | { | ||
| 78 : | $dir_to_add = $1; | ||
| 79 : | $rc = $ali_trees->add_ali($dir_to_add); | ||
| 80 : | print &Dumper($rc); | ||
| 81 : | print "\n"; | ||
| 82 : | } | ||
| 83 : | elsif ($req =~ /^\s*alignments_containing_peg\s+(\S+)\s*$/) | ||
| 84 : | { | ||
| 85 : | $peg = $1; | ||
| 86 : | foreach $_ ($ali_trees->alignments_containing_peg($peg)) | ||
| 87 : | { | ||
| 88 : | print "$_\n"; | ||
| 89 : | } | ||
| 90 : | print "\n"; | ||
| 91 : | } | ||
| 92 : | overbeek | 1.4 | elsif ($req =~ /^\s*functions_in(\s+(\S+))?\s*$/) |
| 93 : | { | ||
| 94 : | $ali_tree = $2 ? new AliTree($2,$fig,$default_dir) : $ali_tree; | ||
| 95 : | my $ali = $ali_tree->id; | ||
| 96 : | |||
| 97 : | my($pegM,$funcM); | ||
| 98 : | if ($ali =~ /^(\d+\.\d+\.peg\.\d+)/) | ||
| 99 : | { | ||
| 100 : | $pegM = 'fig|' . $1; | ||
| 101 : | $funcM = $fig->function_of($pegM); | ||
| 102 : | print "$ali\t$pegM\t$funcM\n\n"; | ||
| 103 : | } | ||
| 104 : | foreach $_ ($ali_tree->functions_in) | ||
| 105 : | { | ||
| 106 : | print join("\t",@$_),"\n"; | ||
| 107 : | } | ||
| 108 : | print "\n"; | ||
| 109 : | } | ||
| 110 : | overbeek | 1.1 | elsif ($req =~ /^\s*pegs_in_alignment(\s+(\S+))?\s*$/) |
| 111 : | { | ||
| 112 : | $ali_tree = $2 ? new AliTree($2,$fig,$default_dir) : $ali_tree; | ||
| 113 : | if (! $ali_tree) | ||
| 114 : | { | ||
| 115 : | print "you need to specify an alignment\n\n"; | ||
| 116 : | } | ||
| 117 : | else | ||
| 118 : | { | ||
| 119 : | my $h = $ali_tree->pegs_in_alignment($ali_tree->id); | ||
| 120 : | foreach $peg (sort { &FIG::by_fig_id($a,$b) } keys(%$h)) | ||
| 121 : | { | ||
| 122 : | my $coords = $h->{$peg}; | ||
| 123 : | print join("\t",($peg,@$coords)),"\n"; | ||
| 124 : | } | ||
| 125 : | } | ||
| 126 : | print "\n"; | ||
| 127 : | } | ||
| 128 : | elsif ($req =~ /^\s*merge\s+(\S+)\s+(\S+)\s*$/) | ||
| 129 : | { | ||
| 130 : | $aliID1 = $1; | ||
| 131 : | $aliID2 = $2; | ||
| 132 : | $aliID3 = $ali_trees->merge_ali($aliID1,$aliID2); | ||
| 133 : | print defined($aliID3) ? $aliID3 : "failed to merge $aliID1 and $aliID2","\n\n"; | ||
| 134 : | } | ||
| 135 : | elsif ($req =~ /^\s*indel_ratio(\s+(\S+))?\s*$/) | ||
| 136 : | { | ||
| 137 : | $ali_tree = $2 ? new AliTree($2,$fig,$default_dir) : $ali_tree; | ||
| 138 : | if (! $ali_tree) | ||
| 139 : | { | ||
| 140 : | print "you need to specify an alignment\n\n"; | ||
| 141 : | } | ||
| 142 : | else | ||
| 143 : | { | ||
| 144 : | print $ali_tree->indel_ratio,"\n"; | ||
| 145 : | } | ||
| 146 : | print "\n"; | ||
| 147 : | } | ||
| 148 : | elsif ($req =~ /^\s*overlaps(\s+(\S+))?\s*$/) | ||
| 149 : | { | ||
| 150 : | $ali_tree = $2 ? new AliTree($2,$fig,$default_dir) : $ali_tree; | ||
| 151 : | if (! $ali_tree) | ||
| 152 : | { | ||
| 153 : | print "you need to specify an alignment\n\n"; | ||
| 154 : | } | ||
| 155 : | else | ||
| 156 : | { | ||
| 157 : | $sz = $ali_tree->sz; | ||
| 158 : | print "Overlaps for ",$ali_tree->id,", which contains $sz seqauences\n\n"; | ||
| 159 : | $overlaps = $ali_tree->overlaps; | ||
| 160 : | @tmp = (); | ||
| 161 : | foreach $ali1 (keys(%$overlaps)) | ||
| 162 : | { | ||
| 163 : | my $ali_tree1 = new AliTree($ali1,$fig,$default_dir); | ||
| 164 : | push(@tmp,[$ali1,scalar @{$overlaps->{$ali1}},$ali_tree1->sz]); | ||
| 165 : | } | ||
| 166 : | @tmp = sort { $b->[1] <=> $a->[1] } @tmp; | ||
| 167 : | foreach $tuple (@tmp) | ||
| 168 : | { | ||
| 169 : | print join("\t",@$tuple),"\n"; | ||
| 170 : | } | ||
| 171 : | } | ||
| 172 : | print "\n"; | ||
| 173 : | } | ||
| 174 : | elsif ($req =~ /^\s*tree(\s+(\S+))?\s*$/) | ||
| 175 : | { | ||
| 176 : | $ali_tree = $2 ? new AliTree($2,$fig,$default_dir) : $ali_tree; | ||
| 177 : | if (! $ali_tree) | ||
| 178 : | { | ||
| 179 : | print "you need to specify an alignment\n\n"; | ||
| 180 : | } | ||
| 181 : | else | ||
| 182 : | { | ||
| 183 : | $id = $ali_tree->id; | ||
| 184 : | $tree = $ali_tree->tree; | ||
| 185 : | overbeek | 1.3 | if (-s "$default_dir/Library/$id/tree.newick") |
| 186 : | overbeek | 1.1 | { |
| 187 : | overbeek | 1.3 | system "sketch_tree -a $default_dir/Library/$id/tree.newick"; |
| 188 : | overbeek | 1.1 | } |
| 189 : | else | ||
| 190 : | { | ||
| 191 : | print "no tree for $id\n"; | ||
| 192 : | } | ||
| 193 : | } | ||
| 194 : | print "\n"; | ||
| 195 : | } | ||
| 196 : | elsif ($req =~ /^\s*sz(\s+(\S+))?\s*$/) | ||
| 197 : | { | ||
| 198 : | $ali_tree = $2 ? new AliTree($2,$fig,$default_dir) : $ali_tree; | ||
| 199 : | if (! $ali_tree) | ||
| 200 : | { | ||
| 201 : | print "you need to specify an alignment\n\n"; | ||
| 202 : | } | ||
| 203 : | else | ||
| 204 : | { | ||
| 205 : | print $ali_tree->sz;; | ||
| 206 : | } | ||
| 207 : | print "\n"; | ||
| 208 : | } | ||
| 209 : | elsif ($req =~ /^\s*display(\s+(\S+))?\s*$/) | ||
| 210 : | { | ||
| 211 : | $ali_tree = $2 ? new AliTree($2,$fig,$default_dir) : $ali_tree; | ||
| 212 : | if (! $ali_tree) | ||
| 213 : | { | ||
| 214 : | print "you need to specify an alignment\n\n"; | ||
| 215 : | } | ||
| 216 : | else | ||
| 217 : | { | ||
| 218 : | print $ali_tree->display; | ||
| 219 : | } | ||
| 220 : | print "\n"; | ||
| 221 : | } | ||
| 222 : | elsif ($req =~ /^\s*html(\s+(\S+))?\s*$/) | ||
| 223 : | { | ||
| 224 : | $ali_tree = $2 ? new AliTree($2,$fig,$default_dir) : $ali_tree; | ||
| 225 : | if (! $ali_tree) | ||
| 226 : | { | ||
| 227 : | print "you need to specify an alignment\n\n"; | ||
| 228 : | } | ||
| 229 : | else | ||
| 230 : | { | ||
| 231 : | my $id = $ali_tree->id; | ||
| 232 : | my $tmpdir = "$FIG_Config::fig/Tmp/Alignments"; | ||
| 233 : | &FIG::verify_dir($tmpdir); | ||
| 234 : | if (! -s "$tmpdir/$id.html") | ||
| 235 : | { | ||
| 236 : | if (open(HTML,">$tmpdir/$id.html")) | ||
| 237 : | { | ||
| 238 : | print HTML $ali_tree->html,"\n"; | ||
| 239 : | close(HTML); | ||
| 240 : | } | ||
| 241 : | } | ||
| 242 : | } | ||
| 243 : | print "\n"; | ||
| 244 : | } | ||
| 245 : | elsif ($req =~ /^\s*load_db\s*$/) | ||
| 246 : | { | ||
| 247 : | $ali_trees->load_db; | ||
| 248 : | } | ||
| 249 : | elsif ($req =~ /^\s*h\s*$/ || $req =~ /^\s*help\s*$/) | ||
| 250 : | { | ||
| 251 : | &help; | ||
| 252 : | } | ||
| 253 : | else | ||
| 254 : | { | ||
| 255 : | print "invalid command\n"; | ||
| 256 : | } | ||
| 257 : | print "\n"; | ||
| 258 : | } | ||
| 259 : | |||
| 260 : | sub get_req { | ||
| 261 : | my($x); | ||
| 262 : | |||
| 263 : | print "?? "; | ||
| 264 : | $x = <STDIN>; | ||
| 265 : | while (defined($x) && ($x =~ /^h$/i) ) | ||
| 266 : | { | ||
| 267 : | &help; | ||
| 268 : | print "?? "; | ||
| 269 : | $x = <STDIN>; | ||
| 270 : | } | ||
| 271 : | |||
| 272 : | if ((! defined($x)) || ($x =~ /^\s*[qQxX]/)) | ||
| 273 : | { | ||
| 274 : | return ""; | ||
| 275 : | } | ||
| 276 : | else | ||
| 277 : | { | ||
| 278 : | if ($echo) | ||
| 279 : | { | ||
| 280 : | print ">> $x\n"; | ||
| 281 : | } | ||
| 282 : | return $x; | ||
| 283 : | } | ||
| 284 : | } | ||
| 285 : | |||
| 286 : | |||
| 287 : | sub help { | ||
| 288 : | print <<END; | ||
| 289 : | |||
| 290 : | add_ali Ali | ||
| 291 : | alignments_containing_peg PEG | ||
| 292 : | all_alignments | ||
| 293 : | delete_ali Ali | ||
| 294 : | display [Ali] | ||
| 295 : | overbeek | 1.4 | functions_in [Ali] |
| 296 : | overbeek | 1.1 | h |
| 297 : | html Ali | ||
| 298 : | indel_ratio [Ali] | ||
| 299 : | load_db | ||
| 300 : | merge Ali1 Ali2 [creates Ali1-n and displays the computed ID] | ||
| 301 : | overlaps [Ali] | ||
| 302 : | pegs_in_alignment [Ali] | ||
| 303 : | set Ali | ||
| 304 : | set_all | ||
| 305 : | sz [Ali] | ||
| 306 : | tree [Ali] | ||
| 307 : | END | ||
| 308 : | } |
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