Mercurial > repos > plus91-technologies-pvt-ltd > ss_test_tool
comparison 2.4/src/blat_parse.pl @ 0:00b9898b8510 draft
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| author | plus91-technologies-pvt-ltd |
|---|---|
| date | Wed, 04 Jun 2014 03:41:27 -0400 |
| parents | |
| children |
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| -1:000000000000 | 0:00b9898b8510 |
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| 1 ##################################################################################################################################################### | |
| 2 #Purpose: To parse blat psl file | |
| 3 #Date: 07-30-2013 | |
| 4 ##################################################################################################################################################### | |
| 5 use Getopt::Long; | |
| 6 use Cwd; | |
| 7 #reading input arguments | |
| 8 &Getopt::Long::GetOptions( | |
| 9 'b|BLAT_OUT=s'=> \$blat_out, | |
| 10 'temp:s'=>\$dirtemp, | |
| 11 'f|FASTA=s'=>\$infast, | |
| 12 ); | |
| 13 $blat_out =~ s/\s|\t|\r|\n//g; | |
| 14 $dirtemp =~ s/\s|\t|\r|\n//g; | |
| 15 $infast =~ s/\s|\t|\r|\n//g; | |
| 16 $samtools=`which samtools`; | |
| 17 $samtools =~ s/\s|\t|\r|\n//g; | |
| 18 | |
| 19 if($blat_out eq "" || $infast eq "" ) | |
| 20 { | |
| 21 die "Try: perl blat_parse.pl -b <PSL FILE> -f <Contigs.fa> | |
| 22 -temp temporary file directory | |
| 23 \n"; | |
| 24 } | |
| 25 if (!(-e $samtools)) | |
| 26 { | |
| 27 die "samtools must be in your path\n"; | |
| 28 } | |
| 29 | |
| 30 if (!(-e $infast)) | |
| 31 { | |
| 32 die "input fasta file doesn't exit\n"; | |
| 33 } | |
| 34 unless(-d $dirtemp) | |
| 35 { | |
| 36 #system("mkdir -p $dirtemp"); | |
| 37 $dirtemp= getcwd; | |
| 38 } | |
| 39 #opening the blat output file | |
| 40 open(BUFF,$blat_out) or die "no file found $blat_out\n"; | |
| 41 open(WRBUFF,">$dirtemp/Temp_out.txt") or die "not able to write the file \n"; | |
| 42 #parsing throught he file | |
| 43 while(<BUFF>) | |
| 44 { | |
| 45 if($_ =~ m/^\d/) | |
| 46 { | |
| 47 print WRBUFF $_; | |
| 48 } | |
| 49 else | |
| 50 { | |
| 51 print "ignoring headers $.\n"; | |
| 52 } | |
| 53 } | |
| 54 close(WRBUFF); | |
| 55 system("sort -k10,10 -k18,18n $dirtemp/Temp_out.txt > $dirtemp/Temp_out1.txt"); | |
| 56 system("mv $dirtemp/Temp_out1.txt $dirtemp/Temp_out.txt"); | |
| 57 open(BUFF,"$dirtemp/Temp_out.txt") or die "no file found Temp_out.txt\n"; | |
| 58 open(WRBUFF,">$dirtemp/File1_out.txt") or die "not able to write the file \n"; | |
| 59 close(WRBUFF); | |
| 60 | |
| 61 $prev_contig_name=""; | |
| 62 my @temp; | |
| 63 #parsing throught he file | |
| 64 while(<BUFF>) | |
| 65 { | |
| 66 | |
| 67 chomp($_); | |
| 68 split "\t"; | |
| 69 if($_[9] ne $prev_contig_name) | |
| 70 { | |
| 71 if($prev_contig_name ne "") | |
| 72 { | |
| 73 #print @temp."\n"; | |
| 74 #print @temp."\n"; | |
| 75 &processing(@temp); | |
| 76 } | |
| 77 undef(@temp); | |
| 78 push(@temp,$_); | |
| 79 } | |
| 80 else | |
| 81 { | |
| 82 push(@temp,$_); | |
| 83 } | |
| 84 $prev_contig_name=$_[9]; | |
| 85 | |
| 86 | |
| 87 } | |
| 88 #processing last record | |
| 89 &processing(@temp); | |
| 90 #print @temp."\n"; | |
| 91 close(BUFF); | |
| 92 | |
| 93 | |
| 94 | |
| 95 | |
| 96 ##################SUBROUTINES###################### | |
| 97 #actual processing of each record in the temp array(same query name objects) | |
| 98 | |
| 99 sub processing { | |
| 100 open(WRBUFF,">>$dirtemp/File1_out.txt") or die "not able to write the file \n"; | |
| 101 open(BAD_CONTIG,">>$dirtemp/bad_contig.out.txt") or die "not able to write the file \n"; | |
| 102 | |
| 103 @temp = @_; | |
| 104 #if number of hits for a contig is one | |
| 105 if(@temp == 1) | |
| 106 { | |
| 107 $i=0; | |
| 108 #define blocksizes array | |
| 109 @row=split("\t",$temp[$i]); | |
| 110 $row[18] =~ s/,$//g; | |
| 111 @blockSizes=split(',',$row[18]); | |
| 112 #defining var | |
| 113 $qSize=$row[10]; | |
| 114 $qStart=$row[11]; | |
| 115 $qStop=$row[12]; | |
| 116 $tstart=$row[15]; | |
| 117 $tstop=$row[16]; | |
| 118 $Strand=$row[8]; | |
| 119 $coverage = $row[9]; | |
| 120 $coverage =~ s/\w+_//g; | |
| 121 #calculate match val | |
| 122 if(($qSize-($qStop-$qStart)) ==0) | |
| 123 { | |
| 124 $flag=1; | |
| 125 #these ara non informative | |
| 126 if (@blockSizes ==1) | |
| 127 { | |
| 128 print "ignoring one of the event $row[9] $i as the event is non informative \n"; | |
| 129 print BAD_CONTIG "$row[9]\n"; | |
| 130 } | |
| 131 #Ignoring when number of blocks are more than two | |
| 132 if(@blockSizes > 2) | |
| 133 { | |
| 134 print "ignoring event $row[9] $. AS BLOCK SIZE is greater than 2\n"; | |
| 135 } | |
| 136 #if number of blocks is equal to 2 | |
| 137 if(@blockSizes == 2) | |
| 138 { | |
| 139 $temp1=$tstart+$blockSizes[0]+1; | |
| 140 $temp2=$tstop-$blockSizes[1]-1; | |
| 141 | |
| 142 print WRBUFF "$row[9]\t$row[13]\t$temp1\t$Strand\t$row[13]\t$temp2\t$Strand\t$coverage\n"; | |
| 143 } | |
| 144 $i=@temp; | |
| 145 } | |
| 146 #later part missing | |
| 147 elsif($qStart ==0) | |
| 148 { | |
| 149 $temp1=$tstart+$blockSizes[0]+1; | |
| 150 $infast_chr=$infast; | |
| 151 $infast_chr=~ s/\.fa//g; | |
| 152 $infast_chr_start=$qStop+1; | |
| 153 $infast_chr_stop=$qSize; | |
| 154 $sys="$samtools faidx $infast $infast_chr:$infast_chr_start-$infast_chr_stop"; | |
| 155 | |
| 156 $sys = `$sys`; | |
| 157 chomp($sys); | |
| 158 @sys=split("\n",$sys); | |
| 159 $INSERTION=""; | |
| 160 for($i=1;$i<@sys;$i++) | |
| 161 { | |
| 162 $INSERTION=$INSERTION.$sys[$i]; | |
| 163 } | |
| 164 $INSERTION_LENGTH=length($INSERTION); | |
| 165 $temp1=$tstart+$blockSizes[0]+1; | |
| 166 print WRBUFF "$row[9]\t$row[13]\t$temp1\t$Strand\tUNKNOWN\tUNKNOWN\t$Strand\t$coverage\t$INSERTION\t$INSERTION_LENGTH\n"; | |
| 167 | |
| 168 } | |
| 169 #intial part missing | |
| 170 elsif($qStop == $qSize) | |
| 171 { | |
| 172 $temp1=$tstart; | |
| 173 $infast_chr=$infast; | |
| 174 $infast_chr=~ s/\.fa//g; | |
| 175 $infast_chr_start=0; | |
| 176 $infast_chr_stop=$qStart; | |
| 177 $sys ="$samtools faidx $infast $infast_chr:$infast_chr_start-$infast_chr_stop"; | |
| 178 #die "$sys\n"; | |
| 179 $sys = `$sys`; | |
| 180 #die "$sys\n"; | |
| 181 chomp($sys); | |
| 182 @sys=split("\n",$sys); | |
| 183 $INSERTION=""; | |
| 184 for( $i=1;$i<@sys;$i++) | |
| 185 { | |
| 186 $INSERTION=$INSERTION.$sys[$i]; | |
| 187 } | |
| 188 $INSERTION_LENGTH=length($INSERTION); | |
| 189 $temp1=$tstart+1; | |
| 190 print WRBUFF "$row[9]\tUNKNOWN\tUNKNOWN\t$Strand\t$row[13]\t$temp1\t$Strand\t$coverage\n"; | |
| 191 | |
| 192 } | |
| 193 else | |
| 194 { | |
| 195 print "ignoring one of the event $row[9] $i as the event is non informative \n"; | |
| 196 } | |
| 197 | |
| 198 } | |
| 199 #if number of hits for a contig is greater than one | |
| 200 else | |
| 201 { | |
| 202 #this flag is used to see if perfect hit not found (match val =0) | |
| 203 $flag1 = 0; | |
| 204 for(my $i=0;$i<@temp;$i++) | |
| 205 { | |
| 206 | |
| 207 #define blocksizes array | |
| 208 @row=split("\t",$temp[$i]); | |
| 209 $row[18] =~ s/,$//g; | |
| 210 @blockSizes=split(',',$row[18]); | |
| 211 #defining var | |
| 212 $qSize=$row[10]; | |
| 213 $qStart=$row[11]; | |
| 214 $qStop=$row[12]; | |
| 215 $tstart=$row[15]; | |
| 216 $tstop=$row[16]; | |
| 217 $Strand=$row[8]; | |
| 218 $coverage = $row[9]; | |
| 219 $coverage =~ s/\w+_//g; | |
| 220 #calculate match val | |
| 221 if(($qSize-($qStop-$qStart)) ==0) | |
| 222 { | |
| 223 $flag1=1; | |
| 224 #these ara non informative | |
| 225 if (@blockSizes ==1) | |
| 226 { | |
| 227 print "ignoring one of the event $row[9] $i as the event is non informative \n"; | |
| 228 print BAD_CONTIG "$row[9]\n"; | |
| 229 } | |
| 230 #Ignoring when number of blocks are more than two | |
| 231 if(@blockSizes > 2) | |
| 232 { | |
| 233 print "ignoring event $row[9] $. AS BLOCK SIZE is greater than 2\n"; | |
| 234 } | |
| 235 if(@blockSizes == 2) | |
| 236 { | |
| 237 $temp1=$tstart+$blockSizes[0]+1; | |
| 238 $temp2=$tstop-$blockSizes[1]-1; | |
| 239 | |
| 240 print WRBUFF "$row[9]\t$row[13]\t$temp1\t$Strand\t$row[13]\t$temp2\t$Strand\t$coverage\n"; | |
| 241 } | |
| 242 $i=@temp; | |
| 243 } | |
| 244 } | |
| 245 #as flag value not changed proceed to see next step | |
| 246 if($flag1 == 0) | |
| 247 { | |
| 248 undef(@initial); | |
| 249 my @initial; | |
| 250 for(my $i=0;$i<@temp;$i++) | |
| 251 { | |
| 252 @row=split("\t",$temp[$i]); | |
| 253 #print "@row\n"; | |
| 254 unshift(@initial,[@row]); | |
| 255 } | |
| 256 #sortin the hits according to qstart & qend | |
| 257 @initial = sort {$a->[11] <=> $b->[11] || $b->[12] <=> $a->[12]} @initial; | |
| 258 #print "$row[9]\t@initial\n"; | |
| 259 #if($row[9] eq "NODE_5_length_149_cov_12.395973") | |
| 260 #{ | |
| 261 # for($i=0;$i<@initial;$i++) | |
| 262 # { | |
| 263 # print "@{$initial[$i]}\n"; | |
| 264 # } | |
| 265 #} | |
| 266 $start = ""; | |
| 267 $stop = ""; | |
| 268 $start_len=0; | |
| 269 $stop_len=0; | |
| 270 #this super flag is used to skip processing of remaining uncessary hits | |
| 271 $super_flag = 0; | |
| 272 for($i=0;$i<@initial && $super_flag == 0;$i++) | |
| 273 { | |
| 274 $flag = 0; | |
| 275 #print "@{$initial[$i]}\n"; | |
| 276 $initial[$i][18] =~ s/,$//g; | |
| 277 @blockSizes1=split(',',$initial[$i][18]); | |
| 278 #defining var | |
| 279 $qSize1=$initial[$i][10]; | |
| 280 $qStart1=$initial[$i][11]; | |
| 281 $qStop1=$initial[$i][12]; | |
| 282 $tstart1=$initial[$i][15]; | |
| 283 $tstop1=$initial[$i][16]; | |
| 284 $Strand1=$initial[$i][8]; | |
| 285 $Chr1 = $initial[$i][13]; | |
| 286 $coverage1 = $initial[$i][9]; | |
| 287 $coverage1 =~ s/\w+_//g; | |
| 288 #die "$qSize1\t$qStart1\t$qStop1\t$tstart1\t$tstop1\t$Strand1\t$Chr1\t$coverage1\n"; | |
| 289 #if a hit qstart = 0 then set flag =1 | |
| 290 if($qStart1 == 0) | |
| 291 { | |
| 292 $flag =1; | |
| 293 } | |
| 294 #if a hit qstop = 0 then set flag =2 | |
| 295 if($qStop1 == $qSize1) | |
| 296 { | |
| 297 $flag =2; | |
| 298 } | |
| 299 #if($row[9] eq "NODE_5_length_149_cov_12.395973") | |
| 300 #{ | |
| 301 # print "$flag \n"; | |
| 302 #} | |
| 303 if(@blockSizes1 == 1) | |
| 304 { | |
| 305 if($flag == 1 ) | |
| 306 { | |
| 307 for($j=0;$j<@initial;$j++) | |
| 308 { | |
| 309 #both hits should not be the same | |
| 310 if($i != $j) | |
| 311 { | |
| 312 #print "@{$initial[$i]}\n"; | |
| 313 $initial[$j][18] =~ s/,$//g; | |
| 314 @blockSizes2=split(',',$initial[$j][18]); | |
| 315 #defining var | |
| 316 $qSize2=$initial[$j][10]; | |
| 317 $qStart2=$initial[$j][11]; | |
| 318 $qStop2=$initial[$j][12]; | |
| 319 $tstart2=$initial[$j][15]; | |
| 320 $tstop2=$initial[$j][16]; | |
| 321 $Strand2=$initial[$j][8]; | |
| 322 $coverage2 = $initial[$j][9]; | |
| 323 $Chr2 = $initial[$j][13]; | |
| 324 $coverage2 =~ s/\w+_//g; | |
| 325 #making sure both hits are not over lapping | |
| 326 if($qStart2 > $qStart1) | |
| 327 { #allowing +-2 bases as the this hit is immediate next continous hit | |
| 328 if($qStop1 >= $qStart2 -2 && $qStop1 <= $qStart2 +2 ) | |
| 329 { | |
| 330 #perfect match | |
| 331 if($qStop2 == $qSize2) | |
| 332 { | |
| 333 if($Strand1 eq "+") | |
| 334 { | |
| 335 $tmp1 = $tstart1+$blockSizes1[0]+1; | |
| 336 $tmp2 = $tstart2+$blockSizes2[0]; | |
| 337 print WRBUFF "$initial[$i][9]\t$Chr1\t$tmp1\t$Strand1\t$Chr2\t$tmp2\t$Strand2\t$coverage1\n"; | |
| 338 } | |
| 339 else | |
| 340 { | |
| 341 $tmp1 = $tstart1+1; | |
| 342 $tmp2 = $tstart2+1; | |
| 343 print WRBUFF "$initial[$i][9]\t$Chr1\t$tmp1\t$Strand1\t$Chr2\t$tmp2\t$Strand2\t$coverage1\n"; | |
| 344 | |
| 345 } | |
| 346 $super_flag = 1; | |
| 347 $j = @initial+1; | |
| 348 } | |
| 349 #some part is missing after the second hit | |
| 350 else | |
| 351 { | |
| 352 $tmp1 = $tstart1+$blockSizes1[0]; | |
| 353 $tmp2 = $tstart2+$blockSizes2[0]; | |
| 354 $INSERTION=""; | |
| 355 $infast_chr=$infast; | |
| 356 $infast_chr=~ s/\.fa//g; | |
| 357 $infast_chr_start=$qStop1+1; | |
| 358 $infast_chr_stop=$qStart2-1; | |
| 359 $sys ="$samtools faidx $infast $infast_chr:$infast_chr_start-$infast_chr_stop"; | |
| 360 #die "$sys\n"; | |
| 361 $sys = `$sys`; | |
| 362 #die "$sys\n"; | |
| 363 chomp($sys); | |
| 364 @sys=split("\n",$sys); | |
| 365 for( $i=1;$i<@sys;$i++) | |
| 366 { | |
| 367 $INSERTION=$INSERTION.$sys[$i]; | |
| 368 } | |
| 369 $INSERTION_LENGTH=length($INSERTION); | |
| 370 print WRBUFF "$initial[$i][9]\t$Chr1\t$tmp1\t$Strand1\t$Chr2\t$tmp2\t$Strand2\t$coverage1\n"; | |
| 371 $super_flag = 1; | |
| 372 $j = @initial+1; | |
| 373 } | |
| 374 | |
| 375 } | |
| 376 #if there are some insertion between two hits | |
| 377 elsif($qStop2 == $qSize2) | |
| 378 { | |
| 379 $tmp1 = $tstart1+$blockSizes1[0]; | |
| 380 $tmp2 = $tstart2+$blockSizes2[0]; | |
| 381 $INSERTION=""; | |
| 382 $infast_chr=$infast; | |
| 383 $infast_chr=~ s/\.fa//g; | |
| 384 $infast_chr_start=$qStop2+1; | |
| 385 $infast_chr_stop=$qSize; | |
| 386 $sys ="$samtools faidx $infast $infast_chr:$infast_chr_start-$infast_chr_stop"; | |
| 387 #die "$sys\n"; | |
| 388 $sys = `$sys`; | |
| 389 #die "$sys\n"; | |
| 390 chomp($sys); | |
| 391 @sys=split("\n",$sys); | |
| 392 for( $i=1;$i<@sys;$i++) | |
| 393 { | |
| 394 $INSERTION=$INSERTION.$sys[$i]; | |
| 395 } | |
| 396 $INSERTION_LENGTH=length($INSERTION); | |
| 397 print WRBUFF "$initial[$i][9]\t$Chr1\t$tmp1\t$Strand1\t$Chr2\t$tmp2\t$Strand2\t$coverage1\n"; | |
| 398 $super_flag = 1; | |
| 399 $j = @initial+1; | |
| 400 } | |
| 401 | |
| 402 } | |
| 403 | |
| 404 } | |
| 405 } | |
| 406 #if none worked with other reads then only process that read | |
| 407 if($j == @initial) | |
| 408 { | |
| 409 #die "success\n"; | |
| 410 $temp1=$tstart1+$blockSizes1[0]+1; | |
| 411 #print WRBUFF "$Chr1\t$temp1\t$Strand1\tUNKNOWN\tUNKNOWN\t$Strand\t$coverage\n"; | |
| 412 $infast_chr=$infast; | |
| 413 $infast_chr=~ s/\.fa//g; | |
| 414 $infast_chr_start=$qStop1+1; | |
| 415 $infast_chr_stop=$qSize1; | |
| 416 $sys ="$samtools faidx $infast $infast_chr:$infast_chr_start-$infast_chr_stop"; | |
| 417 #die "$sys\n"; | |
| 418 $sys = `$sys`; | |
| 419 #die "$sys\n"; | |
| 420 chomp($sys); | |
| 421 @sys=split("\n",$sys); | |
| 422 $INSERTION=""; | |
| 423 for( $i=1;$i<@sys;$i++) | |
| 424 { | |
| 425 $INSERTION=$INSERTION.$sys[$i]; | |
| 426 } | |
| 427 $INSERTION_LENGTH=length($INSERTION); | |
| 428 print WRBUFF "$initial[$i][9]\t$Chr1\t$temp1\t$Strand1\tUNKNOWN\tUNKNOWN\t$Strand1\t$coverage1\n"; | |
| 429 $super_flag = 1; | |
| 430 } | |
| 431 } | |
| 432 #if query end is matched to query size | |
| 433 elsif($flag == 2) | |
| 434 { | |
| 435 #going through other hits | |
| 436 for($j=0;$j<@initial;$j++) | |
| 437 { | |
| 438 #hits should not be same | |
| 439 if($i != $j && $qStop2) | |
| 440 { | |
| 441 #print "@{$initial[$i]}\n"; | |
| 442 $initial[$j][18] =~ s/,$//g; | |
| 443 @blockSizes2=split(',',$initial[$j][18]); | |
| 444 #defining var | |
| 445 $qSize2=$initial[$j][10]; | |
| 446 $qStart2=$initial[$j][11]; | |
| 447 $qStop2=$initial[$j][12]; | |
| 448 $tstart2=$initial[$j][15]; | |
| 449 $tstop2=$initial[$j][16]; | |
| 450 $Strand2=$initial[$j][8]; | |
| 451 $coverage2 = $initial[$j][9]; | |
| 452 $Chr2 = $initial[$j][13]; | |
| 453 $coverage2 =~ s/\w+_//g; | |
| 454 #if | |
| 455 if($qStop2 < $qStop1) | |
| 456 { | |
| 457 if($qStart1 >= $qStop2 -2 && $qStart1 <= $qStop2 +2 ) | |
| 458 { | |
| 459 #die "$qStart1 <= $qStop2 \n"; | |
| 460 $tmp1 = $tstart1+$blockSizes1[0]; | |
| 461 $tmp2 = $tstart2+$blockSizes2[0]; | |
| 462 $INSERTION=""; | |
| 463 $infast_chr=$infast; | |
| 464 $infast_chr=~ s/\.fa//g; | |
| 465 $infast_chr_start=0; | |
| 466 $infast_chr_stop=$qStart1-1; | |
| 467 $sys ="$samtools faidx $infast $infast_chr:$infast_chr_start-$infast_chr_stop"; | |
| 468 #die "test $sys\n"; | |
| 469 $sys = `$sys`; | |
| 470 #die "$sys\n"; | |
| 471 chomp($sys); | |
| 472 @sys=split("\n",$sys); | |
| 473 for( $i=1;$i<@sys;$i++) | |
| 474 { | |
| 475 $INSERTION=$INSERTION.$sys[$i]; | |
| 476 } | |
| 477 $INSERTION_LENGTH=length($INSERTION); | |
| 478 print WRBUFF "$initial[$i][9]\t$Chr2\t$tmp2\t$Strand2\t$Chr1\t$tmp1\t$Strand1\t$coverage1\n"; | |
| 479 $super_flag = 1; | |
| 480 $j = @initial+1; | |
| 481 | |
| 482 } | |
| 483 | |
| 484 } | |
| 485 } | |
| 486 } | |
| 487 if($j == @initial) | |
| 488 { | |
| 489 $infast_chr=$infast; | |
| 490 $infast_chr=~ s/\.fa//g; | |
| 491 $infast_chr_start=0; | |
| 492 $infast_chr_stop=$qStart1; | |
| 493 $sys ="$samtools faidx $infast $infast_chr:$infast_chr_start-$infast_chr_stop"; | |
| 494 #die "test $sys\n"; | |
| 495 $sys = `$sys`; | |
| 496 #die "$sys\n"; | |
| 497 chomp($sys); | |
| 498 @sys=split("\n",$sys); | |
| 499 $INSERTION=""; | |
| 500 for( $i=1;$i<@sys;$i++) | |
| 501 { | |
| 502 $INSERTION=$INSERTION.$sys[$i]; | |
| 503 } | |
| 504 $INSERTION_LENGTH=length($INSERTION); | |
| 505 $tmp = $tstart1+1; | |
| 506 print WRBUFF "$initial[$i][9]\tUNKNOWN\tUNKNOWN\t$Strand1\t$Chr1\t$tmp\t$Strand1\t$coverage1\n"; | |
| 507 $super_flag = 1; | |
| 508 } | |
| 509 } | |
| 510 } | |
| 511 elsif(@blockSizes == 2) | |
| 512 { | |
| 513 $temp1=$tstart1+$blockSizes[0]+1; | |
| 514 $temp2=$tstop1-$blockSizes[1]-1; | |
| 515 print WRBUFF "$initial[$i][9]\t$Chr1\t$temp1\t$Strand1\t$Chr1\t$temp2\t$Strand1\t$coverage1\n"; | |
| 516 | |
| 517 } | |
| 518 } | |
| 519 } | |
| 520 | |
| 521 } | |
| 522 close(WRBUFF); | |
| 523 | |
| 524 undef(@temp); | |
| 525 } | |
| 526 |