[2] | 1 | #!/usr/bin/perl -w |
---|
| 2 | # a program to get indels |
---|
| 3 | # the input is a MAF format 3-way alignment file from 3-way blocks only |
---|
| 4 | # the output is a TABULAR format file containing the coordinates of indels determined based on the outgroup |
---|
| 5 | # the program translates seq2, seq3, etc coordinates to (5'-3') strand orientation if alignment orientation |
---|
| 6 | # is reverse complement |
---|
| 7 | # the program gets only indels that satisfy the following conditions: |
---|
| 8 | # 1. two gaps can not overlap unless they are identical, which means they start and end at the same coordinates |
---|
| 9 | # 2. the indel must start after at least three bases from the beginning of the block and finish before at least three bases from the end of the block |
---|
| 10 | # 3. a low score base (masked) can not exist within the indel interval in each of the three sequences |
---|
| 11 | # 4. at lease three high score bases (ummasked) must exist on each side of the indel in each of the three sequences |
---|
| 12 | |
---|
| 13 | |
---|
| 14 | use strict; |
---|
| 15 | use warnings; |
---|
| 16 | |
---|
| 17 | # declare and initialize variables |
---|
| 18 | my $fh; # variable to store filehandle |
---|
| 19 | my $record; |
---|
| 20 | my $offset; |
---|
| 21 | my $library = $ARGV[0]; |
---|
| 22 | my $count = 0; |
---|
| 23 | my $count2 = 0; |
---|
| 24 | my $count3 = 0; |
---|
| 25 | my $count4 = 0; |
---|
| 26 | my $start1 = my $start2 = my $start3 = my $start4 = my $start5 = my $start6 = 0; |
---|
| 27 | my $orient = ""; |
---|
| 28 | my $outgroup = $ARGV[2]; |
---|
| 29 | my $ingroup1 = my $ingroup2 = ""; |
---|
| 30 | my $count_seq1insert = my $count_seq1delete = 0; |
---|
| 31 | my $count_seq2insert = my $count_seq2delete = 0; |
---|
| 32 | my $count_seq3insert = my $count_seq3delete = 0; |
---|
| 33 | my @seq1_insert_lengths = my @seq1_delete_lengths = (); |
---|
| 34 | my @seq2_insert_lengths = my @seq2_delete_lengths = (); |
---|
| 35 | my @seq3_insert_lengths = my @seq3_delete_lengths = (); |
---|
| 36 | my @seq1_insert = my @seq1_delete = my @seq2_insert = my @seq2_delete = my @seq3_insert = my @seq3_delete = (); |
---|
| 37 | my @seq1_insert_startOnly = my @seq1_delete_startOnly = my @seq2_insert_startOnly = my @seq2_delete_startOnly = (); |
---|
| 38 | my @seq3_insert_startOnly = my @seq3_delete_startOnly = (); |
---|
| 39 | my @indels = (); |
---|
| 40 | |
---|
| 41 | # check to make sure correct files |
---|
| 42 | my $usage = "usage: parseMAF_smallIndels.pl [MAF.in] [small_Indels_summary_TABULAR.out] [outgroup]\n"; |
---|
| 43 | die $usage unless @ARGV == 3; |
---|
| 44 | |
---|
| 45 | # perform some standard subroutines |
---|
| 46 | $fh = open_file($library); |
---|
| 47 | |
---|
| 48 | $offset = tell($fh); |
---|
| 49 | |
---|
| 50 | my $ofile = $ARGV[1]; |
---|
| 51 | unless (open(OFILE, ">$ofile")){ |
---|
| 52 | print "Cannot open output file \"$ofile\"\n\n"; |
---|
| 53 | exit; |
---|
| 54 | } |
---|
| 55 | |
---|
| 56 | |
---|
| 57 | # header line for output files |
---|
| 58 | #print OFILE "# small indels summary, parsed from MAF 3-way alignment file, coords are translated from (-) to (+) if necessary\n"; |
---|
| 59 | print OFILE "#block\tindel_type\tindel_length\tingroup1\tingroup1_start\tingroup1_end\tingroup1_alignSize\tingroup1_orient\tingroup2\tingroup2_start\tingroup2_end\tingroup2_alignSize\tingroup2_orient\toutgroup\toutgroup_start\toutgroup_end\toutgroup_alignSize\toutgroup_orient\n"; |
---|
| 60 | |
---|
| 61 | # main body of program |
---|
| 62 | while ($record = get_next_record($fh) ){ |
---|
| 63 | if ($record=~ m/\s*##maf(.*)\s*# maf/s){ |
---|
| 64 | next; |
---|
| 65 | } |
---|
| 66 | |
---|
| 67 | my @sequences = get_sequences_within_block($record); |
---|
| 68 | my @seq_info = get_indels_within_block(@sequences); |
---|
| 69 | |
---|
| 70 | get_indels_lengths(@seq_info); |
---|
| 71 | $offset = tell($fh); |
---|
| 72 | $count++; |
---|
| 73 | |
---|
| 74 | } |
---|
| 75 | |
---|
| 76 | get_starts_only(@seq1_insert); |
---|
| 77 | get_starts_only(@seq1_delete); |
---|
| 78 | get_starts_only(@seq2_insert); |
---|
| 79 | get_starts_only(@seq2_delete); |
---|
| 80 | get_starts_only(@seq3_insert); |
---|
| 81 | get_starts_only(@seq3_delete); |
---|
| 82 | |
---|
| 83 | # print some things to keep track of progress |
---|
| 84 | #print "# $library\n"; |
---|
| 85 | #print "# number of records = $count\n"; |
---|
| 86 | #print "# number of sequence \"s\" lines = $count2\n"; |
---|
| 87 | |
---|
| 88 | if ($count3 != 0){ |
---|
| 89 | print "Skipped $count3 blocks with only 2 seqs;\n"; |
---|
| 90 | } |
---|
| 91 | #print "# number of records with only h-m = $count4\n\n"; |
---|
| 92 | |
---|
| 93 | print "Ingroup1 = $ingroup1; Ingroup2 = $ingroup2; Outgroup = $outgroup;\n"; |
---|
| 94 | print "# of ingroup1 inserts = $count_seq1insert;\n"; |
---|
| 95 | print "# of ingroup1 deletes = $count_seq1delete;\n"; |
---|
| 96 | print "# of ingroup2 inserts = $count_seq2insert;\n"; |
---|
| 97 | print "# of ingroup2 deletes = $count_seq2delete;\n"; |
---|
| 98 | print "# of outgroup3 inserts = $count_seq3insert;\n"; |
---|
| 99 | print "# of outgroup3 deletes = $count_seq3delete\n"; |
---|
| 100 | |
---|
| 101 | |
---|
| 102 | #close OFILE; |
---|
| 103 | |
---|
| 104 | if ($count == $count3){ |
---|
| 105 | print STDERR "Skipped all blocks since none of them contain 3-way alignments.\n"; |
---|
| 106 | exit -1; |
---|
| 107 | } |
---|
| 108 | |
---|
| 109 | ###################SUBROUTINES##################################### |
---|
| 110 | |
---|
| 111 | # subroutine to open file |
---|
| 112 | sub open_file { |
---|
| 113 | my($filename) = @_; |
---|
| 114 | my $fh; |
---|
| 115 | |
---|
| 116 | unless (open($fh, $filename)){ |
---|
| 117 | print "Cannot open file $filename\n"; |
---|
| 118 | exit; |
---|
| 119 | } |
---|
| 120 | return $fh; |
---|
| 121 | } |
---|
| 122 | |
---|
| 123 | # get next record |
---|
| 124 | sub get_next_record { |
---|
| 125 | my ($fh) = @_; |
---|
| 126 | my ($offset); |
---|
| 127 | my ($record) = ""; |
---|
| 128 | my ($save_input_separator) = $/; |
---|
| 129 | |
---|
| 130 | $/ = "a score"; |
---|
| 131 | |
---|
| 132 | $record = <$fh>; |
---|
| 133 | |
---|
| 134 | $/ = $save_input_separator; |
---|
| 135 | |
---|
| 136 | return $record; |
---|
| 137 | } |
---|
| 138 | |
---|
| 139 | # get header info |
---|
| 140 | sub get_sequences_within_block{ |
---|
| 141 | my (@alignment) = @_; |
---|
| 142 | my @lines = (); |
---|
| 143 | |
---|
| 144 | my @sequences = (); |
---|
| 145 | |
---|
| 146 | @lines = split ("\n", $record); |
---|
| 147 | foreach (@lines){ |
---|
| 148 | chomp($_); |
---|
| 149 | if (m/^\s*$/){ |
---|
| 150 | next; |
---|
| 151 | } |
---|
| 152 | elsif (m/^\s*=(\d+\.*\d*)/){ |
---|
| 153 | |
---|
| 154 | }elsif (m/^\s*s(.*)$/){ |
---|
| 155 | $count2++; |
---|
| 156 | |
---|
| 157 | push (@sequences,$_); |
---|
| 158 | } |
---|
| 159 | } |
---|
| 160 | |
---|
| 161 | return @sequences; |
---|
| 162 | } |
---|
| 163 | |
---|
| 164 | #get the indels within the blocks |
---|
| 165 | sub get_indels_within_block{ |
---|
| 166 | my (@sequences) = @_; |
---|
| 167 | my $line1 = my $line2 = my $line3 = ""; |
---|
| 168 | my @line1 = my @line2 = my @line3 = (); |
---|
| 169 | my $score = 0; |
---|
| 170 | my $start1 = my $align_length1 = my $end1 = my $seq_length1 = 0; |
---|
| 171 | my $start2 = my $align_length2 = my $end2 = my $seq_length2 = 0; |
---|
| 172 | my $start3 = my $align_length3 = my $end3 = my $seq_length3 = 0; |
---|
| 173 | my $seq1 = my $orient1 = ""; |
---|
| 174 | my $seq2 = my $orient2 = ""; |
---|
| 175 | my $seq3 = my $orient3 = ""; |
---|
| 176 | my $start1_plus = my $end1_plus = 0; |
---|
| 177 | my $start2_plus = my $end2_plus = 0; |
---|
| 178 | my $start3_plus = my $end3_plus = 0; |
---|
| 179 | my @test = (); |
---|
| 180 | my $test = ""; |
---|
| 181 | my $header = ""; |
---|
| 182 | my @header = (); |
---|
| 183 | my $sequence1 = my $sequence2 = my $sequence3 =""; |
---|
| 184 | my @array_return = (); |
---|
| 185 | my $test1 = 0; |
---|
| 186 | my $line1_stat = my $line2_stat = my $line3_stat = ""; |
---|
| 187 | |
---|
| 188 | # process 3-way blocks only |
---|
| 189 | if (scalar(@sequences) == 3){ |
---|
| 190 | $line1 = $sequences[0]; |
---|
| 191 | chomp ($line1); |
---|
| 192 | $line2 = $sequences[1]; |
---|
| 193 | chomp ($line2); |
---|
| 194 | $line3 = $sequences[2]; |
---|
| 195 | chomp ($line3); |
---|
| 196 | |
---|
| 197 | # check order of sequences and assign uniformly seq1= human, seq2 = chimp, seq3 = macaque |
---|
| 198 | if ($line1 =~ m/$outgroup/){ |
---|
| 199 | $line1_stat = "out"; |
---|
| 200 | $line2=~ s/^\s*//; |
---|
| 201 | $line2 =~ s/\s+/\t/g; |
---|
| 202 | @line2 = split(/\t/, $line2); |
---|
| 203 | if (($ingroup1 eq "") || ($line2[1] =~ m/$ingroup1/)){ |
---|
| 204 | $line2_stat = "in1"; |
---|
| 205 | $line3_stat = "in2"; |
---|
| 206 | } |
---|
| 207 | else{ |
---|
| 208 | $line3_stat = "in1"; |
---|
| 209 | $line2_stat = "in2"; |
---|
| 210 | } |
---|
| 211 | } |
---|
| 212 | elsif ($line2 =~ m/$outgroup/){ |
---|
| 213 | $line2_stat = "out"; |
---|
| 214 | $line1=~ s/^\s*//; |
---|
| 215 | $line1 =~ s/\s+/\t/g; |
---|
| 216 | @line1 = split(/\t/, $line1); |
---|
| 217 | if (($ingroup1 eq "") || ($line1[1] =~ m/$ingroup1/)){ |
---|
| 218 | $line1_stat = "in1"; |
---|
| 219 | $line3_stat = "in2"; |
---|
| 220 | } |
---|
| 221 | else{ |
---|
| 222 | $line3_stat = "in1"; |
---|
| 223 | $line1_stat = "in2"; |
---|
| 224 | } |
---|
| 225 | } |
---|
| 226 | elsif ($line3 =~ m/$outgroup/){ |
---|
| 227 | $line3_stat = "out"; |
---|
| 228 | $line1=~ s/^\s*//; |
---|
| 229 | $line1 =~ s/\s+/\t/g; |
---|
| 230 | @line1 = split(/\t/, $line1); |
---|
| 231 | if (($ingroup1 eq "") || ($line1[1] =~ m/$ingroup1/)){ |
---|
| 232 | $line1_stat = "in1"; |
---|
| 233 | $line2_stat = "in2"; |
---|
| 234 | } |
---|
| 235 | else{ |
---|
| 236 | $line2_stat = "in1"; |
---|
| 237 | $line1_stat = "in2"; |
---|
| 238 | } |
---|
| 239 | } |
---|
| 240 | |
---|
| 241 | #print "# l1 = $line1_stat\n"; |
---|
| 242 | #print "# l2 = $line2_stat\n"; |
---|
| 243 | #print "# l3 = $line3_stat\n"; |
---|
| 244 | |
---|
| 245 | my $linei1 = my $linei2 = my $lineo = ""; |
---|
| 246 | my @linei1 = my @linei2 = my @lineo = (); |
---|
| 247 | |
---|
| 248 | if ($line1_stat eq "out"){ |
---|
| 249 | $lineo = $line1; |
---|
| 250 | } |
---|
| 251 | elsif ($line1_stat eq "in1"){ |
---|
| 252 | $linei1 = $line1; |
---|
| 253 | } |
---|
| 254 | else{ |
---|
| 255 | $linei2 = $line1; |
---|
| 256 | } |
---|
| 257 | |
---|
| 258 | if ($line2_stat eq "out"){ |
---|
| 259 | $lineo = $line2; |
---|
| 260 | } |
---|
| 261 | elsif ($line2_stat eq "in1"){ |
---|
| 262 | $linei1 = $line2; |
---|
| 263 | } |
---|
| 264 | else{ |
---|
| 265 | $linei2 = $line2; |
---|
| 266 | } |
---|
| 267 | |
---|
| 268 | if ($line3_stat eq "out"){ |
---|
| 269 | $lineo = $line3; |
---|
| 270 | } |
---|
| 271 | elsif ($line3_stat eq "in1"){ |
---|
| 272 | $linei1 = $line3; |
---|
| 273 | } |
---|
| 274 | else{ |
---|
| 275 | $linei2 = $line3; |
---|
| 276 | } |
---|
| 277 | |
---|
| 278 | $linei1=~ s/^\s*//; |
---|
| 279 | $linei1 =~ s/\s+/\t/g; |
---|
| 280 | @linei1 = split(/\t/, $linei1); |
---|
| 281 | $end1 =($linei1[2]+$linei1[3]-1); |
---|
| 282 | $seq1 = $linei1[1].":".$linei1[3]; |
---|
| 283 | $ingroup1 = (split(/\./, $seq1))[0]; |
---|
| 284 | $start1 = $linei1[2]; |
---|
| 285 | $align_length1 = $linei1[3]; |
---|
| 286 | $orient1 = $linei1[4]; |
---|
| 287 | $seq_length1 = $linei1[5]; |
---|
| 288 | $sequence1 = $linei1[6]; |
---|
| 289 | $test1 = length($sequence1); |
---|
| 290 | my $total_length1 = $test1+$start1; |
---|
| 291 | my @array1 = ($start1,$end1,$orient1,$seq_length1); |
---|
| 292 | ($start1_plus, $end1_plus) = convert_coords(@array1); |
---|
| 293 | |
---|
| 294 | $linei2=~ s/^\s*//; |
---|
| 295 | $linei2 =~ s/\s+/\t/g; |
---|
| 296 | @linei2 = split(/\t/, $linei2); |
---|
| 297 | $end2 =($linei2[2]+$linei2[3]-1); |
---|
| 298 | $seq2 = $linei2[1].":".$linei2[3]; |
---|
| 299 | $ingroup2 = (split(/\./, $seq2))[0]; |
---|
| 300 | $start2 = $linei2[2]; |
---|
| 301 | $align_length2 = $linei2[3]; |
---|
| 302 | $orient2 = $linei2[4]; |
---|
| 303 | $seq_length2 = $linei2[5]; |
---|
| 304 | $sequence2 = $linei2[6]; |
---|
| 305 | my $test2 = length($sequence2); |
---|
| 306 | my $total_length2 = $test2+$start2; |
---|
| 307 | my @array2 = ($start2,$end2,$orient2,$seq_length2); |
---|
| 308 | ($start2_plus, $end2_plus) = convert_coords(@array2); |
---|
| 309 | |
---|
| 310 | $lineo=~ s/^\s*//; |
---|
| 311 | $lineo =~ s/\s+/\t/g; |
---|
| 312 | @lineo = split(/\t/, $lineo); |
---|
| 313 | $end3 =($lineo[2]+$lineo[3]-1); |
---|
| 314 | $seq3 = $lineo[1].":".$lineo[3]; |
---|
| 315 | $start3 = $lineo[2]; |
---|
| 316 | $align_length3 = $lineo[3]; |
---|
| 317 | $orient3 = $lineo[4]; |
---|
| 318 | $seq_length3 = $lineo[5]; |
---|
| 319 | $sequence3 = $lineo[6]; |
---|
| 320 | my $test3 = length($sequence3); |
---|
| 321 | my $total_length3 = $test3+$start3; |
---|
| 322 | my @array3 = ($start3,$end3,$orient3,$seq_length3); |
---|
| 323 | ($start3_plus, $end3_plus) = convert_coords(@array3); |
---|
| 324 | |
---|
| 325 | #print "# l1 = $ingroup1\n"; |
---|
| 326 | #print "# l2 = $ingroup2\n"; |
---|
| 327 | #print "# l3 = $outgroup\n"; |
---|
| 328 | |
---|
| 329 | my $ABC = ""; |
---|
| 330 | my $coord1 = my $coord2 = my $coord3 = 0; |
---|
| 331 | $coord1 = $start1_plus; |
---|
| 332 | $coord2 = $start2_plus; |
---|
| 333 | $coord3 = $start3_plus; |
---|
| 334 | |
---|
| 335 | #variables to store the lengths of gaps in each sequence |
---|
| 336 | my $gapLenth = my $gapLenth1 = my $gapLenth2 = my $gapLenth3 = 0; |
---|
| 337 | |
---|
| 338 | #variables to store the index of the start of a gap in each sequence |
---|
| 339 | my $gapStartPos = my $gapStartPos1 = my $gapStartPos2 = my $gapStartPos3 = 0; |
---|
| 340 | my $gapEndPos = 0; |
---|
| 341 | |
---|
| 342 | #variable to determine if there is a valid gap |
---|
| 343 | my $getValidGap = 0; |
---|
| 344 | |
---|
| 345 | #scan the block from left to right looking for gaps |
---|
| 346 | for (my $position = 0; $position < $test1; $position++) { |
---|
| 347 | my $indelType = ""; |
---|
| 348 | my $indel_line = ""; |
---|
| 349 | |
---|
| 350 | #print($position ." position\n"); |
---|
| 351 | #print($sequence1 ." sequence1\n"); |
---|
| 352 | #print($sequence2 ." sequence2\n"); |
---|
| 353 | #print($sequence3 ." sequence3\n"); |
---|
| 354 | #if ($position > 2 && $position < ($test1 - 3)){ |
---|
| 355 | #print(substr($sequence1,$position - 3, 3) . " before " . substr($sequence1, $position + 1, 3) . " after\n"); |
---|
| 356 | #print(substr($sequence2,$position - 3, 3) . " before " . substr($sequence2, $position + 1, 3) . " after\n"); |
---|
| 357 | #print(substr($sequence3,$position - 3, 3) . " before " . substr($sequence3, $position + 1, 3) . " after\n"); |
---|
| 358 | #} |
---|
| 359 | |
---|
| 360 | #if the current position is the start of a gap, look for any overlapping gaps in the other two sequences |
---|
| 361 | if (substr($sequence1,$position,1) eq "-" || substr($sequence2,$position,1) eq "-" || substr($sequence3,$position,1) eq "-"){ |
---|
| 362 | |
---|
| 363 | #print($gapStartPos . " gapStartPos\n"); |
---|
| 364 | #print("starting a gap\n"); |
---|
| 365 | |
---|
| 366 | #reset all gap related variables to 0 |
---|
| 367 | $gapLenth = $gapLenth1 = $gapLenth2 = $gapLenth3 = 0; |
---|
| 368 | $gapStartPos = $gapStartPos1 = $gapStartPos2 = $gapStartPos3 = 0; |
---|
| 369 | $gapEndPos = 0; |
---|
| 370 | $getValidGap = 0; |
---|
| 371 | |
---|
| 372 | #if($position > 2 && $position < $test1 - 3){ |
---|
| 373 | #print(substr($sequence1,$position - 3, 3) . " before " . substr($sequence1, $position + 1, 3) . " after\n"); |
---|
| 374 | #print(substr($sequence2,$position - 3, 3) . " before " . substr($sequence2, $position + 1, 3) . " after\n"); |
---|
| 375 | #print(substr($sequence3,$position - 3, 3) . " before " . substr($sequence3, $position + 1, 3) . " after\n"); |
---|
| 376 | #} |
---|
| 377 | |
---|
| 378 | #check if this position is the start of a gap |
---|
| 379 | if ($gapStartPos == 0){ |
---|
| 380 | |
---|
| 381 | #the variables $gapStartPos and $gapEndPos are initialized with the current position value $position |
---|
| 382 | $gapStartPos = $gapEndPos = $position; |
---|
| 383 | |
---|
| 384 | #iterate till the end of the gap and/or the end of any overlapping gap, whichever is greater |
---|
| 385 | while (substr($sequence1, $gapEndPos, 1) eq "-" || substr($sequence2, $gapEndPos, 1) eq "-" || substr($sequence3,$gapEndPos,1) eq "-"){ |
---|
| 386 | |
---|
| 387 | #check if the current single gap is in sequence1 |
---|
| 388 | if(substr($sequence1, $gapEndPos, 1) eq "-" && $gapEndPos < $test1){ |
---|
| 389 | $gapLenth1++; |
---|
| 390 | if ($gapLenth1 == 1){ |
---|
| 391 | $gapStartPos1 = $gapEndPos; |
---|
| 392 | } |
---|
| 393 | } |
---|
| 394 | |
---|
| 395 | #check if the current single gap is in sequence2 |
---|
| 396 | if(substr($sequence2, $gapEndPos, 1) eq "-" && $gapEndPos < $test1){ |
---|
| 397 | $gapLenth2++; |
---|
| 398 | if ($gapLenth2 == 1){ |
---|
| 399 | $gapStartPos2 = $gapEndPos; |
---|
| 400 | } |
---|
| 401 | } |
---|
| 402 | |
---|
| 403 | #check if the current single gap is in sequence3 |
---|
| 404 | if(substr($sequence3, $gapEndPos, 1) eq "-" && $gapEndPos < $test1){ |
---|
| 405 | $gapLenth3++; |
---|
| 406 | if ($gapLenth3 == 1){ |
---|
| 407 | $gapStartPos3 = $gapEndPos; |
---|
| 408 | } |
---|
| 409 | } |
---|
| 410 | $gapEndPos++; |
---|
| 411 | } |
---|
| 412 | |
---|
| 413 | #readjust the value of $gapStartPos to represent the index of the end of the gap |
---|
| 414 | #and/or the end of any overlapping gaps, whichever is greater |
---|
| 415 | $gapEndPos--; |
---|
| 416 | |
---|
| 417 | #print($gapStartPos . " - " . $gapEndPos . " gapStartPos - gapEndPos\n"); |
---|
| 418 | #print($gapStartPos1 . " - " . $gapLenth1 . " gapStartPos1 - gapLenth1\n"); |
---|
| 419 | #print($gapStartPos2 . " - " . $gapLenth2 . " gapStartPos2 - gapLenth2\n"); |
---|
| 420 | #print($gapStartPos3 . " - " . $gapLenth3 . " gapStartPos3 - gapLenth3\n"); |
---|
| 421 | |
---|
| 422 | #variable $gapLength stores the length of the max gap among the three gaps if any |
---|
| 423 | if ($gapLenth < $gapLenth1){ |
---|
| 424 | $gapLenth = $gapLenth1; |
---|
| 425 | } |
---|
| 426 | if ($gapLenth < $gapLenth2){ |
---|
| 427 | $gapLenth = $gapLenth2; |
---|
| 428 | } |
---|
| 429 | if ($gapLenth < $gapLenth3){ |
---|
| 430 | $gapLenth = $gapLenth3; |
---|
| 431 | } |
---|
| 432 | |
---|
| 433 | #print("The length of the longest gap is: " . $gapLenth . "\n"); |
---|
| 434 | |
---|
| 435 | #check if there are two overlapping gaps from sequence1 and sequence2 but not from sequence3 |
---|
| 436 | if ($gapLenth1 > 0 && $gapLenth2 > 0 && $gapLenth3 == 0){ |
---|
| 437 | if ($gapLenth1 != $gapLenth2 || $gapStartPos1 != $gapStartPos2){ |
---|
| 438 | |
---|
| 439 | #print("Invalid case: gaps are overlapping starting at position: " . $position . "\n"); |
---|
| 440 | |
---|
| 441 | # readjust the value of the variable $gapLenth to include all unequal-lenght gaps |
---|
| 442 | $gapLenth = $gapEndPos - $position + 1; |
---|
| 443 | |
---|
| 444 | # readjust the value of the variable $position to the next non-gap character |
---|
| 445 | $position = $position + $gapLenth - 1; |
---|
| 446 | |
---|
| 447 | #print("The total length of the overlapping gaps is: " . $gapLenth . "\n"); |
---|
| 448 | |
---|
| 449 | #add as many characters "N" as the length of $gapLenth to the sequence $ABC as if there is no gap |
---|
| 450 | while($gapLenth > 0){ |
---|
| 451 | $ABC = join("",($ABC,"N")); |
---|
| 452 | $coord1++; $coord2++; $coord3++; |
---|
| 453 | $gapLenth--; |
---|
| 454 | } |
---|
| 455 | } |
---|
| 456 | } |
---|
| 457 | else{ #check if there are two overlapping gaps from sequence1 and sequence3 but not from sequence2 |
---|
| 458 | if ($gapLenth1 > 0 && $gapLenth3 > 0 && $gapLenth2 == 0){ |
---|
| 459 | |
---|
| 460 | if ($gapLenth1 != $gapLenth3 || $gapStartPos1 != $gapStartPos3){ |
---|
| 461 | |
---|
| 462 | #print("Invalid case: gaps are overlapping starting at position: " . $position . "\n"); |
---|
| 463 | |
---|
| 464 | # readjust the value of the variable $gapLenth to include all unequal-lenght gaps |
---|
| 465 | $gapLenth = $gapEndPos - $position + 1; |
---|
| 466 | |
---|
| 467 | # readjust the value of the variable $position to the next non-gap character |
---|
| 468 | $position = $position + $gapLenth - 1; |
---|
| 469 | |
---|
| 470 | #print("The total length of the overlapping gaps is: " . $gapLenth . "\n"); |
---|
| 471 | |
---|
| 472 | #add as many characters "N" as the length of $gapLenth to the sequence $ABC as if there is no gap |
---|
| 473 | while($gapLenth > 0){ |
---|
| 474 | $ABC = join("",($ABC,"N")); |
---|
| 475 | $coord1++; $coord2++; $coord3++; |
---|
| 476 | $gapLenth--; |
---|
| 477 | } |
---|
| 478 | } |
---|
| 479 | } |
---|
| 480 | else{ #check if there are two overlapping gaps from sequence2 and sequence3 but not from sequence1 |
---|
| 481 | if ($gapLenth2 > 0 && $gapLenth3 > 0 && $gapLenth1 == 0){ |
---|
| 482 | if ($gapLenth2 != $gapLenth3 || $gapStartPos2 != $gapStartPos3){ |
---|
| 483 | |
---|
| 484 | #print("Invalid case: gaps are overlapping starting at position: " . $position . "\n"); |
---|
| 485 | |
---|
| 486 | # readjust the value of the variable $gapLenth to include all unequal-lenght gaps |
---|
| 487 | $gapLenth = $gapEndPos - $position + 1; |
---|
| 488 | |
---|
| 489 | # readjust the value of the variable $position to the next non-gap character |
---|
| 490 | $position = $position + $gapLenth - 1; |
---|
| 491 | |
---|
| 492 | #print("The total length of the overlapping gaps is: " . $gapLenth . "\n"); |
---|
| 493 | |
---|
| 494 | #add as many characters "N" as the length of $gapLenth to the sequence $ABC as if there is no gap |
---|
| 495 | while($gapLenth > 0){ |
---|
| 496 | $ABC = join("",($ABC,"N")); |
---|
| 497 | $coord1++; $coord2++; $coord3++; |
---|
| 498 | $gapLenth--; |
---|
| 499 | } |
---|
| 500 | } |
---|
| 501 | } |
---|
| 502 | else{ #check if there are three overlapping gaps from the three sequences |
---|
| 503 | if ($gapLenth1 > 0 && $gapLenth2 > 0 && $gapLenth3 > 0){ |
---|
| 504 | if ($gapLenth1 != $gapLenth2 || $gapLenth1 != $gapLenth3 || $gapLenth2 != $gapLenth3 |
---|
| 505 | || $gapStartPos1 != $gapStartPos2 || $gapStartPos1 != $gapStartPos3 |
---|
| 506 | || $gapStartPos2 != $gapStartPos3){ |
---|
| 507 | |
---|
| 508 | #print("Invalid case: gaps are overlapping starting at position: " . $position . "\n"); |
---|
| 509 | |
---|
| 510 | # readjust the value of the variable $gapLenth to include all unequal-lenght gaps |
---|
| 511 | $gapLenth = $gapEndPos - $position + 1; |
---|
| 512 | |
---|
| 513 | # readjust the value of the variable $position to the next non-gap character |
---|
| 514 | $position = $position + $gapLenth - 1; |
---|
| 515 | |
---|
| 516 | #print("The total length of the overlapping gaps is: " . $gapLenth . "\n"); |
---|
| 517 | |
---|
| 518 | #add as many characters "N" as the length of $gapLenth to the sequence $ABC as if there is no gap |
---|
| 519 | while($gapLenth > 0){ |
---|
| 520 | $ABC = join("",($ABC,"N")); |
---|
| 521 | $coord1++; $coord2++; $coord3++; |
---|
| 522 | $gapLenth--; |
---|
| 523 | } |
---|
| 524 | } |
---|
| 525 | } |
---|
| 526 | } |
---|
| 527 | } |
---|
| 528 | } |
---|
| 529 | |
---|
| 530 | #check if the gaps are overlapping |
---|
| 531 | if ($gapLenth == 0){ |
---|
| 532 | |
---|
| 533 | #check if the overlapping gaps are also within less than three base from either end of the block |
---|
| 534 | if ($gapStartPos <= 2 || $gapEndPos >= ($test1 - 3)){ |
---|
| 535 | if ($gapStartPos <= 2){ |
---|
| 536 | #print("Invalid case: at least one of the overlapping gaps is within less than 3 bases from the left end of the block starting at position: " . $gapStartPos . "\n"); |
---|
| 537 | } |
---|
| 538 | elsif ($gapEndPos >= $test1 - 3){ |
---|
| 539 | #print("Invalid case: at least one of the overlapping gaps is within less than 3 bases from the right end of the block starting at position: " . $gapStartPos . "\n"); |
---|
| 540 | } |
---|
| 541 | elsif ($gapStartPos <= 2 && $gapEndPos >= ($test1 - 3)){ |
---|
| 542 | #print("Invalid case: at least one of the overlapping gaps is within less than 3 bases from each end of the block starting at position: " . $gapStartPos . "\n"); |
---|
| 543 | } |
---|
| 544 | } |
---|
| 545 | |
---|
| 546 | #check if the gap starts at position located within three bases from the start of the block |
---|
| 547 | my $preSubSeqLength = 0; |
---|
| 548 | if ($gapStartPos - 3 < 0){ |
---|
| 549 | $preSubSeqLength = $gapStartPos; |
---|
| 550 | } |
---|
| 551 | else{ |
---|
| 552 | $preSubSeqLength = 3; |
---|
| 553 | } |
---|
| 554 | |
---|
| 555 | #check if the there is a masked character among the three bases on at least one side of the gap |
---|
| 556 | if ((substr($sequence1, $gapStartPos - $preSubSeqLength, $preSubSeqLength) =~ m/[-\#$?^@]/) |
---|
| 557 | || (substr($sequence2, $gapStartPos - $preSubSeqLength, $preSubSeqLength) =~ m/[-\#$?^@]/) |
---|
| 558 | || (substr($sequence3, $gapStartPos - $preSubSeqLength, $preSubSeqLength) =~ m/[-\#$?^@]/) |
---|
| 559 | || (substr($sequence1, $gapEndPos + 1, 3) =~ m/[-\#$?^@]/) |
---|
| 560 | || (substr($sequence2, $gapEndPos + 1, 3) =~ m/[-\#$?^@]/) |
---|
| 561 | || (substr($sequence3, $gapEndPos + 1, 3) =~ m/[-\#$?^@]/)){ |
---|
| 562 | |
---|
| 563 | #print("Invalid case: at least one masked character is within 3 bases from at least one of overlapping gaps starting at position: " . $gapStartPos . "\n"); |
---|
| 564 | } |
---|
| 565 | |
---|
| 566 | #check if there is at least one base with low score (maskd) within the gap interval |
---|
| 567 | if((substr($sequence1, $gapStartPos, $gapEndPos - $gapStartPos + 1) =~ m/[\#$?^@]/) |
---|
| 568 | || (substr($sequence2, $gapStartPos, $gapEndPos - $gapStartPos + 1) =~ m/[\#$?^@]/) |
---|
| 569 | || (substr($sequence3, $gapStartPos, $gapEndPos - $gapStartPos + 1) =~ m/[\#$?^@]/)){ |
---|
| 570 | |
---|
| 571 | #print("Invalid case: at least one masked character is within the gap interval starting at position: " . $gapStartPos . "\n"); |
---|
| 572 | } |
---|
| 573 | |
---|
| 574 | #print($sequence1 ." sequence1\n"); |
---|
| 575 | #print($sequence2 ." sequence2\n"); |
---|
| 576 | #print($sequence3 ." sequence3\n"); |
---|
| 577 | #print("________________________________________________________________\n"); |
---|
| 578 | } |
---|
| 579 | |
---|
| 580 | |
---|
| 581 | #if $gapLenth > 0, then there is no overlapping gaps, which means that either there is only one gap |
---|
| 582 | # or two gaps that have equal lengths and start at the same position |
---|
| 583 | if ($gapLenth > 0){ |
---|
| 584 | |
---|
| 585 | #variable indicating if the gap is within less than three bases from the end of the blocks |
---|
| 586 | my $blockEndGap = 0; |
---|
| 587 | #variable indicating if the gap is within less than three bases from the end of the blocks |
---|
| 588 | my $maskedCharWithinGap = 0; |
---|
| 589 | #variable indicating if there is any masked character among the three bases flanking the gap from each side |
---|
| 590 | my $maskedCharNearGap = 0; |
---|
| 591 | |
---|
| 592 | #check if there are at least there bases on each side of the gap |
---|
| 593 | if ($position > 2 && ($position + $gapLenth - 1) < ($test1 - 3)){ |
---|
| 594 | $blockEndGap = 0; |
---|
| 595 | } |
---|
| 596 | else{ #the gap is within less than 3 bases from the end of the block |
---|
| 597 | |
---|
| 598 | $blockEndGap = 1; |
---|
| 599 | } |
---|
| 600 | |
---|
| 601 | #variable $preSubSeqLength stores the number of bases available on the left side of the gap |
---|
| 602 | my $preSubSeqLength = 0; |
---|
| 603 | #variable $leftStartCheckingPosition stores the index of the base at which |
---|
| 604 | #we start checking the number of bases available on the left side of the gap |
---|
| 605 | my $leftStartCheckingPosition = 0; |
---|
| 606 | |
---|
| 607 | if ($gapStartPos - 3 < 0){ |
---|
| 608 | $preSubSeqLength = $gapStartPos; |
---|
| 609 | } |
---|
| 610 | else{ |
---|
| 611 | $preSubSeqLength = 3; |
---|
| 612 | $leftStartCheckingPosition = $position - 3; |
---|
| 613 | } |
---|
| 614 | #check if all the three bases on each side of the gap have high scores (unmasked) |
---|
| 615 | if ((substr($sequence1, $leftStartCheckingPosition, $preSubSeqLength) !~ m/[-\#$?^@]/) |
---|
| 616 | && (substr($sequence2, $leftStartCheckingPosition, $preSubSeqLength) !~ m/[-\#$?^@]/) |
---|
| 617 | && (substr($sequence3, $leftStartCheckingPosition, $preSubSeqLength) !~ m/[-\#$?^@]/) |
---|
| 618 | && (substr($sequence1, $position + $gapLenth, 3) !~ m/[-\#$?^@]/) |
---|
| 619 | && (substr($sequence2, $position + $gapLenth, 3) !~ m/[-\#$?^@]/) |
---|
| 620 | && (substr($sequence3, $position + $gapLenth, 3) !~ m/[-\#$?^@]/)){ |
---|
| 621 | |
---|
| 622 | #there are three bases with high scores (unmasked) on each side of the gap |
---|
| 623 | $maskedCharNearGap = 0; |
---|
| 624 | } |
---|
| 625 | else{ #three is a masked character among the three bases on at least one side of the gap |
---|
| 626 | $maskedCharNearGap = 1; |
---|
| 627 | } |
---|
| 628 | |
---|
| 629 | #check if there is at least one base with low score (maskd) within the gap interval |
---|
| 630 | if((substr($sequence1, $position, $gapLenth) !~ m/[\#$?^@]/) |
---|
| 631 | && (substr($sequence2, $position, $gapLenth) !~ m/[\#$?^@]/) |
---|
| 632 | && (substr($sequence3, $position, $gapLenth) !~ m/[\#$?^@]/)){ |
---|
| 633 | |
---|
| 634 | #there is no base with low score (unmasked) within the gap interval |
---|
| 635 | $maskedCharWithinGap = 0; |
---|
| 636 | } |
---|
| 637 | else{ #there is at least one base with low score (maskd) within the gap interval |
---|
| 638 | $maskedCharWithinGap = 1; |
---|
| 639 | } |
---|
| 640 | |
---|
| 641 | #check if the gap is, valid which means: |
---|
| 642 | #check if the gap is within at least 3 bases from each end of the block, |
---|
| 643 | #and that all the three bases on each side of the block have high scores (unmasked), |
---|
| 644 | #and that there is no base with low score (masked) within the gap interval at the same time |
---|
| 645 | if ($blockEndGap == 0 && $maskedCharNearGap == 0 && $maskedCharWithinGap == 0){ |
---|
| 646 | |
---|
| 647 | #print("The gap is valid and will be treated accordingly\n"); |
---|
| 648 | $getValidGap = 1 |
---|
| 649 | } |
---|
| 650 | |
---|
| 651 | #the gap is not valid, which means: |
---|
| 652 | #the gap is not valid, so check if the gap is within less than 3 bases from the end of the block, |
---|
| 653 | #and that there is a masked character among the three bases on at least one side of the gap, |
---|
| 654 | #and that there is a masked character within the gap interval at the same time |
---|
| 655 | elsif ($blockEndGap == 1 && $maskedCharNearGap == 1 && $maskedCharWithinGap == 1){ |
---|
| 656 | #print("Invalid case: the gap is within less than 3 bases from the end of the block starting at position: " . $position . "\n"); |
---|
| 657 | #print("Invalid case: at least one masked character is within 3 bases from the gap starting at position: " . $position . "\n"); |
---|
| 658 | #print("Invalid case: at least one masked character is within the gap interval starting at position: " . $position . "\n"); |
---|
| 659 | #print("The total length of the overlapping gaps is: " . $gapLenth . "\n"); |
---|
| 660 | } |
---|
| 661 | #check if the gap is within less than 3 bases from the end of the block, and |
---|
| 662 | #that there is a masked character among the three bases on at least one side of the gap at the same time |
---|
| 663 | elsif ($blockEndGap == 1 && $maskedCharNearGap == 1){ |
---|
| 664 | #print("Invalid case: the gap is within less than 3 bases from the end of the block starting at position: " . $position . "\n"); |
---|
| 665 | #print("Invalid case: at least one masked character is within 3 bases from the gap starting at position: " . $position . "\n"); |
---|
| 666 | #print("The total length of the overlapping gaps is: " . $gapLenth . "\n"); |
---|
| 667 | } |
---|
| 668 | #check if the gap is within less than 3 bases from the end of the block and |
---|
| 669 | #and that there is a masked character within the gap interval at the same time |
---|
| 670 | elsif ($blockEndGap == 1 && $maskedCharWithinGap == 1){ |
---|
| 671 | #print("Invalid case: the gap is within less than 3 bases from the end of the block starting at position: " . $position . "\n"); |
---|
| 672 | #print("Invalid case: at least one masked character is within the gap interval starting at position: " . $position . "\n"); |
---|
| 673 | #print("The total length of the overlapping gaps is: " . $gapLenth . "\n"); |
---|
| 674 | } |
---|
| 675 | #check if there is a masked character among the three bases on at least one side of the gap |
---|
| 676 | #and that there is a masked character within the gap interval at the same time |
---|
| 677 | elsif ($maskedCharNearGap == 1 && $maskedCharWithinGap == 1){ |
---|
| 678 | #print("Invalid case: at least one masked character is within 3 bases from the gap starting at position: " . $position . "\n"); |
---|
| 679 | #print("Invalid case: at least one masked character is within the gap interval starting at position: " . $position . "\n"); |
---|
| 680 | #print("The total length of the overlapping gaps is: " . $gapLenth . "\n"); |
---|
| 681 | } |
---|
| 682 | #check if the gap is within less than 3 bases from the end of the block |
---|
| 683 | elsif ($blockEndGap == 1){ |
---|
| 684 | #print("Invalid case: the gap is within less than 3 bases from the end of the block starting at position: " . $position . "\n"); |
---|
| 685 | #print("The total length of the overlapping gaps is: " . $gapLenth . "\n"); |
---|
| 686 | } |
---|
| 687 | #check if there is a masked character within 3 bases on each side of the gap |
---|
| 688 | elsif ($maskedCharNearGap == 1){ |
---|
| 689 | #print("Invalid case: at least one masked character is within 3 bases from the gap starting at position: " . $position . "\n"); |
---|
| 690 | #print("The total length of the overlapping gaps is: " . $gapLenth . "\n"); |
---|
| 691 | } |
---|
| 692 | #check if there is a masked character within the gap interval |
---|
| 693 | elsif ($maskedCharWithinGap == 1){ |
---|
| 694 | #print("Invalid case: at least one masked character is within the gap interval starting at position: " . $position . "\n"); |
---|
| 695 | #print("The total length of the overlapping gaps is: " . $gapLenth . "\n"); |
---|
| 696 | } |
---|
| 697 | |
---|
| 698 | #check if the gap is not valid in order to readjust the $position value and increment coordinates varaibles |
---|
| 699 | if ($getValidGap == 0){ |
---|
| 700 | #print($sequence1 . " sequence1\n"); |
---|
| 701 | #print($sequence2 . " sequence2\n"); |
---|
| 702 | #print($sequence3 . " sequence3\n"); |
---|
| 703 | #print("________________________________________________________________\n"); |
---|
| 704 | |
---|
| 705 | # readjust the value of the variable $position to the next non-gap character |
---|
| 706 | $position = $position + $gapLenth - 1; |
---|
| 707 | |
---|
| 708 | #add as many characters "N" as the length of $gapLenth to the sequence $ABC as if there is no gap |
---|
| 709 | while($gapLenth > 0){ |
---|
| 710 | $ABC = join("",($ABC,"N")); |
---|
| 711 | $coord1++; $coord2++; $coord3++; |
---|
| 712 | $gapLenth--; |
---|
| 713 | } |
---|
| 714 | } |
---|
| 715 | } |
---|
| 716 | } |
---|
| 717 | } |
---|
| 718 | else{ #there is no gap at this position |
---|
| 719 | #if ($position <= 2){ |
---|
| 720 | #print("invalid case\n"); |
---|
| 721 | #print(substr($sequence1, 0, $position) ." before\n"); |
---|
| 722 | #print(substr($sequence2, 0, $position) ." before\n"); |
---|
| 723 | #print(substr($sequence3, 0, $position) ." before\n"); |
---|
| 724 | #} |
---|
| 725 | #if ($position >= ($test1 - 3)){ |
---|
| 726 | #print("invalid case\n"); |
---|
| 727 | #print(substr($sequence1, $position - $test1) . " after\n"); |
---|
| 728 | #print(substr($sequence2, $position - $test1) . " after\n"); |
---|
| 729 | #print(substr($sequence3, $position - $test1) . " after\n"); |
---|
| 730 | #} |
---|
| 731 | |
---|
| 732 | #add as many characters "N" as the length of $gapLenth to the sequence $ABC becasue there is no gap |
---|
| 733 | $ABC = join("",($ABC,"N")); |
---|
| 734 | $coord1++; $coord2++; $coord3++; |
---|
| 735 | |
---|
| 736 | # reset the value of the variable $gapStartPos to 0 |
---|
| 737 | if ($gapStartPos > 0){ |
---|
| 738 | $gapStartPos = 0; |
---|
| 739 | } |
---|
| 740 | |
---|
| 741 | # reset the value of the variable $getValidGap to 0 |
---|
| 742 | if ($getValidGap > 0){ |
---|
| 743 | $getValidGap = 0; |
---|
| 744 | } |
---|
| 745 | } |
---|
| 746 | |
---|
| 747 | #The gap is valid and will be treated accordingly |
---|
| 748 | if ($getValidGap > 0){ |
---|
| 749 | |
---|
| 750 | my $localGap = $gapLenth; |
---|
| 751 | |
---|
| 752 | # seq1 deletes |
---|
| 753 | if ((substr($sequence1,$position,1) eq "-") |
---|
| 754 | && (substr($sequence2,$position,1) !~ m/[-*\#$?^@]/) |
---|
| 755 | && (substr($sequence3,$position,1) !~ m/[-*\#$?^@]/)){ |
---|
| 756 | |
---|
| 757 | while($gapLenth > 0){ |
---|
| 758 | $ABC = join("",($ABC,"X")); |
---|
| 759 | my @s = split(/:/, $seq1); |
---|
| 760 | $indelType = $s[0]."_delete"; |
---|
| 761 | |
---|
| 762 | #print OFILE "$count\t$seq1\t$coord1\t$orient1\t$seq2\t$coord2\t$orient2\t$seq3\t$coord3\t$orient3\t$indelType\n"; |
---|
| 763 | $indel_line = join("\t",($count,$seq1,$coord1,$orient1,$seq2,$coord2,$orient2,$seq3,$coord3,$orient3,$indelType)); |
---|
| 764 | push (@indels,$indel_line); |
---|
| 765 | push (@seq1_delete,$indel_line); |
---|
| 766 | $coord2++; |
---|
| 767 | $coord3++; |
---|
| 768 | |
---|
| 769 | $gapLenth--; |
---|
| 770 | } |
---|
| 771 | } |
---|
| 772 | # seq2 deletes |
---|
| 773 | elsif ((substr($sequence1,$position,1) !~ m/[-*\#$?^@]/) |
---|
| 774 | && (substr($sequence2,$position,1) eq "-") |
---|
| 775 | && (substr($sequence3,$position,1) !~ m/[-*\#$?^@]/)){ |
---|
| 776 | |
---|
| 777 | while($gapLenth > 0){ |
---|
| 778 | $ABC = join("",($ABC,"Y")); |
---|
| 779 | my @s = split(/:/, $seq2); |
---|
| 780 | $indelType = $s[0]."_delete"; |
---|
| 781 | |
---|
| 782 | #print OFILE "$count\t$seq1\t$coord1\t$orient1\t$seq2\t$coord2\t$orient2\t$seq3\t$coord3\t$orient3\t$indelType\n"; |
---|
| 783 | $indel_line = join("\t",($count,$seq1,$coord1,$orient1,$seq2,$coord2,$orient2,$seq3,$coord3,$orient3,$indelType)); |
---|
| 784 | push (@indels,$indel_line); |
---|
| 785 | push (@seq2_delete,$indel_line); |
---|
| 786 | $coord1++; |
---|
| 787 | $coord3++; |
---|
| 788 | |
---|
| 789 | $gapLenth--; |
---|
| 790 | } |
---|
| 791 | } |
---|
| 792 | # seq1 inserts |
---|
| 793 | elsif ((substr($sequence1,$position,1) !~ m/[-*\#$?^@]/) |
---|
| 794 | && (substr($sequence2,$position,1) eq "-") |
---|
| 795 | && (substr($sequence3,$position,1) eq "-")){ |
---|
| 796 | |
---|
| 797 | while($gapLenth > 0){ |
---|
| 798 | $ABC = join("",($ABC,"Z")); |
---|
| 799 | my @s = split(/:/, $seq1); |
---|
| 800 | $indelType = $s[0]."_insert"; |
---|
| 801 | |
---|
| 802 | #print OFILE "$count\t$seq1\t$coord1\t$orient1\t$seq2\t$coord2\t$orient2\t$seq3\t$coord3\t$orient3\t$indelType\n"; |
---|
| 803 | $indel_line = join("\t",($count,$seq1,$coord1,$orient1,$seq2,$coord2,$orient2,$seq3,$coord3,$orient3,$indelType)); |
---|
| 804 | push (@indels,$indel_line); |
---|
| 805 | push (@seq1_insert,$indel_line); |
---|
| 806 | $coord1++; |
---|
| 807 | |
---|
| 808 | $gapLenth--; |
---|
| 809 | } |
---|
| 810 | } |
---|
| 811 | # seq2 inserts |
---|
| 812 | elsif ((substr($sequence1,$position,1) eq "-") |
---|
| 813 | && (substr($sequence2,$position,1) !~ m/[-*\#$?^@]/) |
---|
| 814 | && (substr($sequence3,$position,1) eq "-")){ |
---|
| 815 | |
---|
| 816 | while($gapLenth > 0){ |
---|
| 817 | $ABC = join("",($ABC,"W")); |
---|
| 818 | my @s = split(/:/, $seq2); |
---|
| 819 | $indelType = $s[0]."_insert"; |
---|
| 820 | |
---|
| 821 | #print OFILE "$count\t$seq1\t$coord1\t$orient1\t$seq2\t$coord2\t$orient2\t$seq3\t$coord3\t$orient3\t$indelType\n"; |
---|
| 822 | $indel_line = join("\t",($count,$seq1,$coord1,$orient1,$seq2,$coord2,$orient2,$seq3,$coord3,$orient3,$indelType)); |
---|
| 823 | push (@indels,$indel_line); |
---|
| 824 | push (@seq2_insert,$indel_line); |
---|
| 825 | $coord2++; |
---|
| 826 | |
---|
| 827 | $gapLenth--; |
---|
| 828 | } |
---|
| 829 | } |
---|
| 830 | # seq3 deletes |
---|
| 831 | elsif ((substr($sequence1,$position,1) !~ m/[-*\#$?^@]/) |
---|
| 832 | && (substr($sequence2,$position,1) !~ m/[-*\#$?^@]/) |
---|
| 833 | && (substr($sequence3,$position,1) eq "-")){ |
---|
| 834 | |
---|
| 835 | while($gapLenth > 0){ |
---|
| 836 | $ABC = join("",($ABC,"S")); |
---|
| 837 | my @s = split(/:/, $seq3); |
---|
| 838 | $indelType = $s[0]."_delete"; |
---|
| 839 | |
---|
| 840 | #print OFILE "$count\t$seq1\t$coord1\t$orient1\t$seq2\t$coord2\t$orient2\t$seq3\t$coord3\t$orient3\t$indelType\n"; |
---|
| 841 | $indel_line = join("\t",($count,$seq1,$coord1,$orient1,$seq2,$coord2,$orient2,$seq3,$coord3,$orient3,$indelType)); |
---|
| 842 | push (@indels,$indel_line); |
---|
| 843 | push (@seq3_delete,$indel_line); |
---|
| 844 | $coord1++; |
---|
| 845 | $coord2++; |
---|
| 846 | |
---|
| 847 | $gapLenth--; |
---|
| 848 | } |
---|
| 849 | } |
---|
| 850 | # seq3 inserts |
---|
| 851 | elsif ((substr($sequence1,$position,1) eq "-") |
---|
| 852 | && (substr($sequence2,$position,1) eq "-") |
---|
| 853 | && (substr($sequence3,$position,1) !~ m/[-*\#$?^@]/)){ |
---|
| 854 | |
---|
| 855 | while($gapLenth > 0){ |
---|
| 856 | $ABC = join("",($ABC,"T")); |
---|
| 857 | my @s = split(/:/, $seq3); |
---|
| 858 | $indelType = $s[0]."_insert"; |
---|
| 859 | |
---|
| 860 | #print OFILE "$count\t$seq1\t$coord1\t$orient1\t$seq2\t$coord2\t$orient2\t$seq3\t$coord3\t$orient3\t$indelType\n"; |
---|
| 861 | $indel_line = join("\t",($count,$seq1,$coord1,$orient1,$seq2,$coord2,$orient2,$seq3,$coord3,$orient3,$indelType)); |
---|
| 862 | push (@indels,$indel_line); |
---|
| 863 | push (@seq3_insert,$indel_line); |
---|
| 864 | $coord3++; |
---|
| 865 | |
---|
| 866 | $gapLenth--; |
---|
| 867 | } |
---|
| 868 | }else{ |
---|
| 869 | while($gapLenth > 0){ |
---|
| 870 | $ABC = join("",($ABC,"N")); |
---|
| 871 | $coord1++; $coord2++; $coord3++; |
---|
| 872 | |
---|
| 873 | $gapLenth--; |
---|
| 874 | } |
---|
| 875 | } |
---|
| 876 | |
---|
| 877 | # readjust the value of the variable $position to indicate the last character of the gap |
---|
| 878 | $position = $position + $localGap - 1; |
---|
| 879 | } |
---|
| 880 | |
---|
| 881 | } |
---|
| 882 | @array_return=($seq1,$seq2,$seq3,$ABC); |
---|
| 883 | return (@array_return); |
---|
| 884 | |
---|
| 885 | } |
---|
| 886 | # ignore pairwise cases for now, just count the number of blocks |
---|
| 887 | elsif (scalar(@sequences) == 2){ |
---|
| 888 | my $ABC = ""; |
---|
| 889 | my $coord1 = my $coord2 = my $coord3 = 0; |
---|
| 890 | $count3++; |
---|
| 891 | |
---|
| 892 | $line1 = $sequences[0]; |
---|
| 893 | $line2 = $sequences[1]; |
---|
| 894 | chomp ($line1); |
---|
| 895 | chomp ($line2); |
---|
| 896 | |
---|
| 897 | if ($line2 !~ m/$ingroup2/){ |
---|
| 898 | $count4++; |
---|
| 899 | } |
---|
| 900 | } |
---|
| 901 | } |
---|
| 902 | |
---|
| 903 | |
---|
| 904 | sub get_indels_lengths{ |
---|
| 905 | my (@array) = @_; |
---|
| 906 | if (scalar(@array) == 4){ |
---|
| 907 | my $seq1 = $array[0]; my $seq2 = $array[1]; my $seq3 = $array[2]; my $ABC = $array[3]; |
---|
| 908 | |
---|
| 909 | while ($ABC =~ m/(X+)/g) { |
---|
| 910 | push (@seq1_delete_lengths,length($1)); |
---|
| 911 | $count_seq1delete++; |
---|
| 912 | } |
---|
| 913 | |
---|
| 914 | while ($ABC =~ m/(Y+)/g) { |
---|
| 915 | push (@seq2_delete_lengths,length($1)); |
---|
| 916 | $count_seq2delete++; |
---|
| 917 | } |
---|
| 918 | while ($ABC =~ m/(S+)/g) { |
---|
| 919 | push (@seq3_delete_lengths,length($1)); |
---|
| 920 | $count_seq3delete++; |
---|
| 921 | } |
---|
| 922 | while ($ABC =~ m/(Z+)/g) { |
---|
| 923 | push (@seq1_insert_lengths,length($1)); |
---|
| 924 | $count_seq1insert++; |
---|
| 925 | } |
---|
| 926 | while ($ABC =~ m/(W+)/g) { |
---|
| 927 | push(@seq2_insert_lengths,length($1)); |
---|
| 928 | $count_seq2insert++; |
---|
| 929 | } |
---|
| 930 | while ($ABC =~ m/(T+)/g) { |
---|
| 931 | push (@seq3_insert_lengths,length($1)); |
---|
| 932 | $count_seq3insert++; |
---|
| 933 | } |
---|
| 934 | } |
---|
| 935 | elsif (scalar(@array) == 0){ |
---|
| 936 | next; |
---|
| 937 | } |
---|
| 938 | |
---|
| 939 | } |
---|
| 940 | # convert to coordinates to + strand if align orient = - |
---|
| 941 | sub convert_coords{ |
---|
| 942 | my (@array) = @_; |
---|
| 943 | my $s = $array[0]; |
---|
| 944 | my $e = $array[1]; |
---|
| 945 | my $o = $array[2]; |
---|
| 946 | my $l = $array[3]; |
---|
| 947 | my $start_plus = my $end_plus = 0; |
---|
| 948 | |
---|
| 949 | if ($o eq "-"){ |
---|
| 950 | $start_plus = ($l - $e); |
---|
| 951 | $end_plus = ($l - $s); |
---|
| 952 | }elsif ($o eq "+"){ |
---|
| 953 | $start_plus = $s; |
---|
| 954 | $end_plus = $e; |
---|
| 955 | } |
---|
| 956 | |
---|
| 957 | return ($start_plus, $end_plus); |
---|
| 958 | } |
---|
| 959 | |
---|
| 960 | # get first line only for each event |
---|
| 961 | sub get_starts_only{ |
---|
| 962 | my (@test) = @_; |
---|
| 963 | my $seq1 = my $seq2 = my $seq3 = my $indelType = my $old_seq1 = my $old_seq2 = my $old_seq3 = my $old_indelType = my $old_line = ""; |
---|
| 964 | my $coord1 = my $coord2 = my $coord3 = my $old_coord1 = my $old_coord2 = my $old_coord3 = 0; |
---|
| 965 | |
---|
| 966 | my @matches = (); |
---|
| 967 | my @seq1_insert = my @seq1_delete = my @seq2_insert = my @seq2_delete = my @seq3_insert = my @seq3_delete = (); |
---|
| 968 | |
---|
| 969 | |
---|
| 970 | foreach my $line (@test){ |
---|
| 971 | chomp($line); |
---|
| 972 | $line =~ s/^\s*//; |
---|
| 973 | $line =~ s/\s+/\t/g; |
---|
| 974 | my @line1 = split(/\t/, $line); |
---|
| 975 | $seq1 = $line1[1]; |
---|
| 976 | $coord1 = $line1[2]; |
---|
| 977 | $seq2 = $line1[4]; |
---|
| 978 | $coord2 = $line1[5]; |
---|
| 979 | $seq3 = $line1[7]; |
---|
| 980 | $coord3 = $line1[8]; |
---|
| 981 | $indelType = $line1[10]; |
---|
| 982 | |
---|
| 983 | if ($indelType =~ m/$ingroup1/ && $indelType =~ m/insert/){ |
---|
| 984 | if ($coord1 != $old_coord1+1 || ($coord2 != $old_coord2 || $coord3 != $old_coord3)){ |
---|
| 985 | $start1++; |
---|
| 986 | push (@seq1_insert_startOnly,$line); |
---|
| 987 | } |
---|
| 988 | } |
---|
| 989 | elsif ($indelType =~ m/$ingroup1/ && $indelType =~ m/delete/){ |
---|
| 990 | if ($coord1 != $old_coord1 || ($coord2 != $old_coord2+1 || $coord3 != $old_coord3+1)){ |
---|
| 991 | $start2++; |
---|
| 992 | push(@seq1_delete_startOnly,$line); |
---|
| 993 | } |
---|
| 994 | } |
---|
| 995 | elsif ($indelType =~ m/$ingroup2/ && $indelType =~ m/insert/){ |
---|
| 996 | if ($coord2 != $old_coord2+1 || ($coord1 != $old_coord1 || $coord3 != $old_coord3)){ |
---|
| 997 | $start3++; |
---|
| 998 | push(@seq2_insert_startOnly,$line); |
---|
| 999 | } |
---|
| 1000 | } |
---|
| 1001 | elsif ($indelType =~ m/$ingroup2/ && $indelType =~ m/delete/){ |
---|
| 1002 | if ($coord2 != $old_coord2 || ($coord1 != $old_coord1+1 || $coord3 != $old_coord3+1)){ |
---|
| 1003 | $start4++; |
---|
| 1004 | push(@seq2_delete_startOnly,$line); |
---|
| 1005 | } |
---|
| 1006 | } |
---|
| 1007 | elsif ($indelType =~ m/$outgroup/ && $indelType =~ m/insert/){ |
---|
| 1008 | if ($coord3 != $old_coord3+1 || ($coord1 != $old_coord1 || $coord2 != $old_coord2)){ |
---|
| 1009 | $start5++; |
---|
| 1010 | push(@seq3_insert_startOnly,$line); |
---|
| 1011 | } |
---|
| 1012 | } |
---|
| 1013 | elsif ($indelType =~ m/$outgroup/ && $indelType =~ m/delete/){ |
---|
| 1014 | if ($coord3 != $old_coord3 || ($coord1 != $old_coord1+1 ||$coord2 != $old_coord2+1)){ |
---|
| 1015 | $start6++; |
---|
| 1016 | push(@seq3_delete_startOnly,$line); |
---|
| 1017 | } |
---|
| 1018 | } |
---|
| 1019 | |
---|
| 1020 | $old_indelType = $indelType; |
---|
| 1021 | $old_seq1 = $seq1; |
---|
| 1022 | $old_coord1 = $coord1; |
---|
| 1023 | $old_seq2 = $seq2; |
---|
| 1024 | $old_coord2 = $coord2; |
---|
| 1025 | $old_seq3 = $seq3; |
---|
| 1026 | $old_coord3 = $coord3; |
---|
| 1027 | $old_line = $line; |
---|
| 1028 | } |
---|
| 1029 | } |
---|
| 1030 | # append lengths to each event start line |
---|
| 1031 | my $counter1; my $counter2; my $counter3; my $counter4; my $counter5; my $counter6; |
---|
| 1032 | my @final1 = my @final2 = my @final3 = my @final4 = my @final5 = my @final6 = (); |
---|
| 1033 | my $final_line1 = my $final_line2 = my $final_line3 = my $final_line4 = my $final_line5 = my $final_line6 = ""; |
---|
| 1034 | |
---|
| 1035 | |
---|
| 1036 | for ($counter1 = 0; $counter1 < @seq3_insert_startOnly; $counter1++){ |
---|
| 1037 | $final_line1 = join("\t",($seq3_insert_startOnly[$counter1],$seq3_insert_lengths[$counter1])); |
---|
| 1038 | push (@final1,$final_line1); |
---|
| 1039 | } |
---|
| 1040 | |
---|
| 1041 | for ($counter2 = 0; $counter2 < @seq3_delete_startOnly; $counter2++){ |
---|
| 1042 | $final_line2 = join("\t",($seq3_delete_startOnly[$counter2],$seq3_delete_lengths[$counter2])); |
---|
| 1043 | push(@final2,$final_line2); |
---|
| 1044 | } |
---|
| 1045 | |
---|
| 1046 | for ($counter3 = 0; $counter3 < @seq2_insert_startOnly; $counter3++){ |
---|
| 1047 | $final_line3 = join("\t",($seq2_insert_startOnly[$counter3],$seq2_insert_lengths[$counter3])); |
---|
| 1048 | push(@final3,$final_line3); |
---|
| 1049 | } |
---|
| 1050 | |
---|
| 1051 | for ($counter4 = 0; $counter4 < @seq2_delete_startOnly; $counter4++){ |
---|
| 1052 | $final_line4 = join("\t",($seq2_delete_startOnly[$counter4],$seq2_delete_lengths[$counter4])); |
---|
| 1053 | push(@final4,$final_line4); |
---|
| 1054 | } |
---|
| 1055 | |
---|
| 1056 | for ($counter5 = 0; $counter5 < @seq1_insert_startOnly; $counter5++){ |
---|
| 1057 | $final_line5 = join("\t",($seq1_insert_startOnly[$counter5],$seq1_insert_lengths[$counter5])); |
---|
| 1058 | push(@final5,$final_line5); |
---|
| 1059 | } |
---|
| 1060 | |
---|
| 1061 | for ($counter6 = 0; $counter6 < @seq1_delete_startOnly; $counter6++){ |
---|
| 1062 | $final_line6 = join("\t",($seq1_delete_startOnly[$counter6],$seq1_delete_lengths[$counter6])); |
---|
| 1063 | push(@final6,$final_line6); |
---|
| 1064 | } |
---|
| 1065 | |
---|
| 1066 | # format final output |
---|
| 1067 | # # if inserts, increase coords for the sequence inserted, other sequences give coords for 5' and 3' bases flanking the gap |
---|
| 1068 | # # for deletes, increase coords for other 2 sequences and the one deleted give coords for 5' and 3' bases flanking the gap |
---|
| 1069 | |
---|
| 1070 | get_final_format(@final5); |
---|
| 1071 | get_final_format(@final6); |
---|
| 1072 | get_final_format(@final3); |
---|
| 1073 | get_final_format(@final4); |
---|
| 1074 | get_final_format(@final1); |
---|
| 1075 | get_final_format(@final2); |
---|
| 1076 | |
---|
| 1077 | sub get_final_format{ |
---|
| 1078 | my (@final) = @_; |
---|
| 1079 | foreach (@final){ |
---|
| 1080 | my $event_line = $_; |
---|
| 1081 | my @events = split(/\t/, $event_line); |
---|
| 1082 | my $event_type = $events[10]; |
---|
| 1083 | my @name_align1 = split(/:/, $events[1]); |
---|
| 1084 | my @name_align2 = split(/:/, $events[4]); |
---|
| 1085 | my @name_align3 = split(/:/, $events[7]); |
---|
| 1086 | my $seq1_event_start = my $seq1_event_end = my $seq2_event_start = my $seq2_event_end = my $seq3_event_start = my $seq3_event_end = 0; |
---|
| 1087 | my $final_event_line = ""; |
---|
| 1088 | # seq1_insert |
---|
| 1089 | if ($event_type =~ m/$ingroup1/ && $event_type =~ m/insert/){ |
---|
| 1090 | # only increase coord for human |
---|
| 1091 | # remember that other two sequnences, the gap spans (coord - 1) --> coord |
---|
| 1092 | $seq1_event_start = ($events[2]); |
---|
| 1093 | $seq1_event_end = ($events[2]+$events[11]-1); |
---|
| 1094 | $seq2_event_start = ($events[5]-1); |
---|
| 1095 | $seq2_event_end = ($events[5]); |
---|
| 1096 | $seq3_event_start = ($events[8]-1); |
---|
| 1097 | $seq3_event_end = ($events[8]); |
---|
| 1098 | $final_event_line = join("\t",($events[0],$event_type,$events[11],$name_align1[0],$seq1_event_start,$seq1_event_end,$name_align1[1],$events[3],$name_align2[0],$seq2_event_start,$seq2_event_end,$name_align2[1],$events[6],$name_align3[0],$seq3_event_start,$seq3_event_end,$name_align3[1],$events[9])); |
---|
| 1099 | } |
---|
| 1100 | # seq1_delete |
---|
| 1101 | elsif ($event_type =~ m/$ingroup1/ && $event_type =~ m/delete/){ |
---|
| 1102 | # only increase coords for seq2 and seq3 |
---|
| 1103 | # remember for seq1, the gap spans (coord - 1) --> coord |
---|
| 1104 | $seq1_event_start = ($events[2]-1); |
---|
| 1105 | $seq1_event_end = ($events[2]); |
---|
| 1106 | $seq2_event_start = ($events[5]); |
---|
| 1107 | $seq2_event_end = ($events[5]+$events[11]-1); |
---|
| 1108 | $seq3_event_start = ($events[8]); |
---|
| 1109 | $seq3_event_end = ($events[8]+$events[11]-1); |
---|
| 1110 | $final_event_line = join("\t",($events[0],$event_type,$events[11],$name_align1[0],$seq1_event_start,$seq1_event_end,$name_align1[1],$events[3],$name_align2[0],$seq2_event_start,$seq2_event_end,$name_align2[1],$events[6],$name_align3[0],$seq3_event_start,$seq3_event_end,$name_align3[1],$events[9])); |
---|
| 1111 | } |
---|
| 1112 | # seq2_insert |
---|
| 1113 | elsif ($event_type =~ m/$ingroup2/ && $event_type =~ m/insert/){ |
---|
| 1114 | # only increase coords for seq2 |
---|
| 1115 | # remember that other two sequnences, the gap spans (coord - 1) --> coord |
---|
| 1116 | $seq1_event_start = ($events[2]-1); |
---|
| 1117 | $seq1_event_end = ($events[2]); |
---|
| 1118 | $seq2_event_start = ($events[5]); |
---|
| 1119 | $seq2_event_end = ($events[5]+$events[11]-1); |
---|
| 1120 | $seq3_event_start = ($events[8]-1); |
---|
| 1121 | $seq3_event_end = ($events[8]); |
---|
| 1122 | $final_event_line = join("\t",($events[0],$event_type,$events[11],$name_align1[0],$seq1_event_start,$seq1_event_end,$name_align1[1],$events[3],$name_align2[0],$seq2_event_start,$seq2_event_end,$name_align2[1],$events[6],$name_align3[0],$seq3_event_start,$seq3_event_end,$name_align3[1],$events[9])); |
---|
| 1123 | } |
---|
| 1124 | # seq2_delete |
---|
| 1125 | elsif ($event_type =~ m/$ingroup2/ && $event_type =~ m/delete/){ |
---|
| 1126 | # only increase coords for seq1 and seq3 |
---|
| 1127 | # remember for seq2, the gap spans (coord - 1) --> coord |
---|
| 1128 | $seq1_event_start = ($events[2]); |
---|
| 1129 | $seq1_event_end = ($events[2]+$events[11]-1); |
---|
| 1130 | $seq2_event_start = ($events[5]-1); |
---|
| 1131 | $seq2_event_end = ($events[5]); |
---|
| 1132 | $seq3_event_start = ($events[8]); |
---|
| 1133 | $seq3_event_end = ($events[8]+$events[11]-1); |
---|
| 1134 | $final_event_line = join("\t",($events[0],$event_type,$events[11],$name_align1[0],$seq1_event_start,$seq1_event_end,$name_align1[1],$events[3],$name_align2[0],$seq2_event_start,$seq2_event_end,$name_align2[1],$events[6],$name_align3[0],$seq3_event_start,$seq3_event_end,$name_align3[1],$events[9])); |
---|
| 1135 | } |
---|
| 1136 | # start testing w/seq3_insert |
---|
| 1137 | elsif ($event_type =~ m/$outgroup/ && $event_type =~ m/insert/){ |
---|
| 1138 | # only increase coord for rheMac |
---|
| 1139 | # remember that other two sequnences, the gap spans (coord - 1) --> coord |
---|
| 1140 | $seq1_event_start = ($events[2]-1); |
---|
| 1141 | $seq1_event_end = ($events[2]); |
---|
| 1142 | $seq2_event_start = ($events[5]-1); |
---|
| 1143 | $seq2_event_end = ($events[5]); |
---|
| 1144 | $seq3_event_start = ($events[8]); |
---|
| 1145 | $seq3_event_end = ($events[8]+$events[11]-1); |
---|
| 1146 | $final_event_line = join("\t",($events[0],$event_type,$events[11],$name_align1[0],$seq1_event_start,$seq1_event_end,$name_align1[1],$events[3],$name_align2[0],$seq2_event_start,$seq2_event_end,$name_align2[1],$events[6],$name_align3[0],$seq3_event_start,$seq3_event_end,$name_align3[1],$events[9])); |
---|
| 1147 | } |
---|
| 1148 | # seq3_delete |
---|
| 1149 | elsif ($event_type =~ m/$outgroup/ && $event_type =~ m/delete/){ |
---|
| 1150 | # only increase coords for seq1 and seq2 |
---|
| 1151 | # remember for seq3, the gap spans (coord - 1) --> coord |
---|
| 1152 | $seq1_event_start = ($events[2]); |
---|
| 1153 | $seq1_event_end = ($events[2]+$events[11]-1); |
---|
| 1154 | $seq2_event_start = ($events[5]); |
---|
| 1155 | $seq2_event_end = ($events[5]+$events[11]-1); |
---|
| 1156 | $seq3_event_start = ($events[8]-1); |
---|
| 1157 | $seq3_event_end = ($events[8]); |
---|
| 1158 | $final_event_line = join("\t",($events[0],$event_type,$events[11],$name_align1[0],$seq1_event_start,$seq1_event_end,$name_align1[1],$events[3],$name_align2[0],$seq2_event_start,$seq2_event_end,$name_align2[1],$events[6],$name_align3[0],$seq3_event_start,$seq3_event_end,$name_align3[1],$events[9])); |
---|
| 1159 | |
---|
| 1160 | } |
---|
| 1161 | |
---|
| 1162 | print OFILE "$final_event_line\n"; |
---|
| 1163 | } |
---|
| 1164 | } |
---|
| 1165 | close OFILE; |
---|