├── LICENSE ├── README.md ├── Sort ├── Naturally.pm └── Topological.pm ├── check-disorder.pl └── gff3sort.pl /LICENSE: -------------------------------------------------------------------------------- 1 | GNU GENERAL PUBLIC LICENSE 2 | Version 3, 29 June 2007 3 | 4 | Copyright (C) 2007 Free Software Foundation, Inc. 5 | Everyone is permitted to copy and distribute verbatim copies 6 | of this license document, but changing it is not allowed. 7 | 8 | Preamble 9 | 10 | The GNU General Public License is a free, copyleft license for 11 | software and other kinds of works. 12 | 13 | The licenses for most software and other practical works are designed 14 | to take away your freedom to share and change the works. By contrast, 15 | the GNU General Public License is intended to guarantee your freedom to 16 | share and change all versions of a program--to make sure it remains free 17 | software for all its users. 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It is safest 630 | to attach them to the start of each source file to most effectively 631 | state the exclusion of warranty; and each file should have at least 632 | the "copyright" line and a pointer to where the full notice is found. 633 | 634 | {one line to give the program's name and a brief idea of what it does.} 635 | Copyright (C) {year} {name of author} 636 | 637 | This program is free software: you can redistribute it and/or modify 638 | it under the terms of the GNU General Public License as published by 639 | the Free Software Foundation, either version 3 of the License, or 640 | (at your option) any later version. 641 | 642 | This program is distributed in the hope that it will be useful, 643 | but WITHOUT ANY WARRANTY; without even the implied warranty of 644 | MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 645 | GNU General Public License for more details. 646 | 647 | You should have received a copy of the GNU General Public License 648 | along with this program. If not, see . 649 | 650 | Also add information on how to contact you by electronic and paper mail. 651 | 652 | If the program does terminal interaction, make it output a short 653 | notice like this when it starts in an interactive mode: 654 | 655 | {project} Copyright (C) {year} {fullname} 656 | This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. 657 | This is free software, and you are welcome to redistribute it 658 | under certain conditions; type `show c' for details. 659 | 660 | The hypothetical commands `show w' and `show c' should show the appropriate 661 | parts of the General Public License. Of course, your program's commands 662 | might be different; for a GUI interface, you would use an "about box". 663 | 664 | You should also get your employer (if you work as a programmer) or school, 665 | if any, to sign a "copyright disclaimer" for the program, if necessary. 666 | For more information on this, and how to apply and follow the GNU GPL, see 667 | . 668 | 669 | The GNU General Public License does not permit incorporating your program 670 | into proprietary programs. If your program is a subroutine library, you 671 | may consider it more useful to permit linking proprietary applications with 672 | the library. If this is what you want to do, use the GNU Lesser General 673 | Public License instead of this License. But first, please read 674 | . 675 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | # GFF3sort 2 | A Perl Script to sort gff3 files and produce suitable results for tabix tools 3 | 4 | ## Usage 5 | ``` 6 | gff3sort.pl [input GFF3 file] >output.sort.gff3 7 | Optional Parameters: 8 | --precise Run in precise mode, about 2X~3X slower than the default mode. 9 | Only needed to be used if your original GFF3 files have parent 10 | features appearing behind their children features. 11 | 12 | --chr_order Select how the chromosome IDs should be sorted. 13 | Acceptable values are: alphabet, natural, original 14 | [Default: alphabet] 15 | 16 | --extract_FASTA If the input GFF3 file contains FASTA sequence at the end, use this 17 | option to extract the FASTA sequence and place in a separate file 18 | with the extention '.fasta'. By default, the FASTA sequences would be 19 | discarded. 20 | ``` 21 | 22 | ## Publication 23 | ``` 24 | Zhu T, Liang C, Meng Z, Guo S, Zhang R: GFF3sort: A novel tool to sort GFF3 files for tabix indexing. BMC Bioinformatics 2017, 18:482, https://doi.org/10.1186/s12859-017-1930-3 25 | ``` 26 | 27 | 28 | ## Background 29 | The tabix tool from [htslib](https://github.com/samtools/htslib) requires files sorted by their chromosomes and positions. For GFF3 files, they would be [sorted](http://gmod.org/wiki/JBrowse_FAQ#How_do_I_create_a_Tabix_indexed_GFF) by column 1 (chromosomes) and 4 (start positions) as: 30 | ``` 31 | sort -k1,1 -k4,4n myfile.gff > myfile.sorted.gff 32 | (OR) 33 | gt gff3 -sortlines -tidy -retainids myfile.gff > myfile.sorted.gff 34 | ``` 35 | Then, the sorted GFF3 file could be indexed by: 36 | ``` 37 | bgzip myfile.sorted.gff 38 | tabix -p gff myfile.sorted.gff.gz 39 | ``` 40 | 41 | However, either the GNU sort or the gt tool has a bug: Lines with the same chromosomes and start positions would be placed randomly. Therefore, parent feature lines might sometimes be placed after their children lines. For example, the following features: 42 | ``` 43 | ##gff-version 3 44 | ### 45 | A01 Cufflinks mRNA 473 6154 . - . ID=XLOC_001154.41;description=Novel: Intergenic transcript 46 | A01 Cufflinks exon 473 814 . - . Parent=XLOC_001154.41 47 | A01 Cufflinks exon 1626 2574 . - . Parent=XLOC_001154.41 48 | A01 Cufflinks exon 2695 2721 . - . Parent=XLOC_001154.41 49 | A01 Cufflinks exon 3637 3726 . - . Parent=XLOC_001154.41 50 | A01 Cufflinks exon 5329 5408 . - . Parent=XLOC_001154.41 51 | A01 Cufflinks exon 5994 6154 . - . Parent=XLOC_001154.41 52 | ### 53 | A01 Cufflinks mRNA 473 6386 . - . ID=XLOC_001154.42;description=Novel: Intergenic transcript 54 | A01 Cufflinks exon 473 2024 . - . Parent=XLOC_001154.42 55 | A01 Cufflinks exon 2615 2721 . - . Parent=XLOC_001154.42 56 | A01 Cufflinks exon 3637 3726 . - . Parent=XLOC_001154.42 57 | A01 Cufflinks exon 5329 6386 . - . Parent=XLOC_001154.42 58 | ``` 59 | 60 | would be sorted as: 61 | ``` 62 | ##gff-version 3 63 | ##sequence-region A01 473 6386 64 | A01 Cufflinks exon 473 814 . - . Parent=XLOC_001154.41 65 | A01 Cufflinks exon 473 2024 . - . Parent=XLOC_001154.42 66 | A01 Cufflinks mRNA 473 6154 . - . ID=XLOC_001154.41;description=Novel: Intergenic transcript 67 | A01 Cufflinks mRNA 473 6386 . - . ID=XLOC_001154.42;description=Novel: Intergenic transcript 68 | A01 Cufflinks exon 1626 2574 . - . Parent=XLOC_001154.41 69 | A01 Cufflinks exon 2615 2721 . - . Parent=XLOC_001154.42 70 | A01 Cufflinks exon 2695 2721 . - . Parent=XLOC_001154.41 71 | A01 Cufflinks exon 3637 3726 . - . Parent=XLOC_001154.42 72 | A01 Cufflinks exon 3637 3726 . - . Parent=XLOC_001154.41 73 | A01 Cufflinks exon 5329 5408 . - . Parent=XLOC_001154.41 74 | A01 Cufflinks exon 5329 6386 . - . Parent=XLOC_001154.42 75 | A01 Cufflinks exon 5994 6154 . - . Parent=XLOC_001154.41 76 | ### 77 | ``` 78 | 79 | That is, the two `mRNA` lines start with pos `473` would be "randomly" placed after the two `exon` lines which also start with pos `473`. These would encount bugs such as https://github.com/GMOD/jbrowse/issues/780 80 | 81 | This script would adjust lines with the same start positions. It would move lines with `"Parent="` attributes (case insensitive) behind lines without `"Parent="` attributes. The result would be: 82 | 83 | ``` 84 | A01 Cufflinks mRNA 473 6386 . - . ID=XLOC_001154.42;description=Novel: Intergenic transcript 85 | A01 Cufflinks mRNA 473 6154 . - . ID=XLOC_001154.41;description=Novel: Intergenic transcript 86 | A01 Cufflinks exon 473 814 . - . Parent=XLOC_001154.41 87 | A01 Cufflinks exon 473 2024 . - . Parent=XLOC_001154.42 88 | A01 Cufflinks exon 1626 2574 . - . Parent=XLOC_001154.41 89 | A01 Cufflinks exon 2615 2721 . - . Parent=XLOC_001154.42 90 | A01 Cufflinks exon 2695 2721 . - . Parent=XLOC_001154.41 91 | A01 Cufflinks exon 3637 3726 . - . Parent=XLOC_001154.41 92 | A01 Cufflinks exon 3637 3726 . - . Parent=XLOC_001154.42 93 | A01 Cufflinks exon 5329 5408 . - . Parent=XLOC_001154.41 94 | A01 Cufflinks exon 5329 6386 . - . Parent=XLOC_001154.42 95 | A01 Cufflinks exon 5994 6154 . - . Parent=XLOC_001154.41 96 | ``` 97 | 98 | 99 | -------------------------------------------------------------------------------- /Sort/Naturally.pm: -------------------------------------------------------------------------------- 1 | 2 | require 5; 3 | package Sort::Naturally; # Time-stamp: "2004-12-29 18:30:03 AST" 4 | $VERSION = '1.03'; 5 | @EXPORT = ('nsort', 'ncmp'); 6 | require Exporter; 7 | @ISA = ('Exporter'); 8 | 9 | use strict; 10 | use locale; 11 | use integer; 12 | 13 | #----------------------------------------------------------------------------- 14 | # constants: 15 | BEGIN { *DEBUG = sub () {0} unless defined &DEBUG } 16 | 17 | use Config (); 18 | BEGIN { 19 | # Make a constant such that if a whole-number string is that long 20 | # or shorter, we KNOW it's treatable as an integer 21 | no integer; 22 | my $x = length(256 ** $Config::Config{'intsize'} / 2) - 1; 23 | die "Crazy intsize: <$Config::Config{'intsize'}>" if $x < 4; 24 | eval 'sub MAX_INT_SIZE () {' . $x . '}'; 25 | die $@ if $@; 26 | print "intsize $Config::Config{'intsize'} => MAX_INT_SIZE $x\n" if DEBUG; 27 | } 28 | 29 | sub X_FIRST () {-1} 30 | sub Y_FIRST () { 1} 31 | 32 | my @ORD = ('same', 'swap', 'asis'); 33 | 34 | #----------------------------------------------------------------------------- 35 | # For lack of a preprocessor: 36 | 37 | my($code, $guts); 38 | $guts = <<'EOGUTS'; # This is the guts of both ncmp and nsort: 39 | 40 | if($x eq $y) { 41 | # trap this expensive case first, and then fall thru to tiebreaker 42 | $rv = 0; 43 | 44 | # Convoluted hack to get numerics to sort first, at string start: 45 | } elsif($x =~ m/^\d/s) { 46 | if($y =~ m/^\d/s) { 47 | $rv = 0; # fall thru to normal comparison for the two numbers 48 | } else { 49 | $rv = X_FIRST; 50 | DEBUG > 1 and print "Numeric-initial $x trumps letter-initial $y\n"; 51 | } 52 | } elsif($y =~ m/^\d/s) { 53 | $rv = Y_FIRST; 54 | DEBUG > 1 and print "Numeric-initial $y trumps letter-initial $x\n"; 55 | } else { 56 | $rv = 0; 57 | } 58 | 59 | unless($rv) { 60 | # Normal case: 61 | $rv = 0; 62 | DEBUG and print "<$x> and <$y> compared...\n"; 63 | 64 | Consideration: 65 | while(length $x and length $y) { 66 | 67 | DEBUG > 2 and print " <$x> and <$y>...\n"; 68 | 69 | # First, non-numeric comparison: 70 | $x2 = ($x =~ m/^(\D+)/s) ? length($1) : 0; 71 | $y2 = ($y =~ m/^(\D+)/s) ? length($1) : 0; 72 | # Now make x2 the min length of the two: 73 | $x2 = $y2 if $x2 > $y2; 74 | if($x2) { 75 | DEBUG > 1 and printf " <%s> and <%s> lexically for length $x2...\n", 76 | substr($x,0,$x2), substr($y,0,$x2); 77 | do { 78 | my $i = substr($x,0,$x2); 79 | my $j = substr($y,0,$x2); 80 | my $sv = $i cmp $j; 81 | print "SCREAM! on <$i><$j> -- $sv != $rv \n" unless $rv == $sv; 82 | last; 83 | } 84 | 85 | 86 | if $rv = 87 | # The ''. things here force a copy that seems to work around a 88 | # mysterious intermittent bug that 'use locale' provokes in 89 | # many versions of Perl. 90 | $cmp 91 | ? $cmp->(substr($x,0,$x2) . '', 92 | substr($y,0,$x2) . '', 93 | ) 94 | : 95 | scalar(( substr($x,0,$x2) . '' ) cmp 96 | ( substr($y,0,$x2) . '' ) 97 | ) 98 | ; 99 | # otherwise trim and keep going: 100 | substr($x,0,$x2) = ''; 101 | substr($y,0,$x2) = ''; 102 | } 103 | 104 | # Now numeric: 105 | # (actually just using $x2 and $y2 as scratch) 106 | 107 | if( $x =~ s/^(\d+)//s ) { 108 | $x2 = $1; 109 | if( $y =~ s/^(\d+)//s ) { 110 | # We have two numbers here. 111 | DEBUG > 1 and print " <$x2> and <$1> numerically\n"; 112 | if(length($x2) < MAX_INT_SIZE and length($1) < MAX_INT_SIZE) { 113 | # small numbers: we can compare happily 114 | last if $rv = $x2 <=> $1; 115 | } else { 116 | # ARBITRARILY large integers! 117 | 118 | # This saves on loss of precision that could happen 119 | # with actual stringification. 120 | # Also, I sense that very large numbers aren't too 121 | # terribly common in sort data. 122 | 123 | # trim leading 0's: 124 | ($y2 = $1) =~ s/^0+//s; 125 | $x2 =~ s/^0+//s; 126 | print " Treating $x2 and $y2 as bigint\n" if DEBUG; 127 | 128 | no locale; # we want the dumb cmp back. 129 | last if $rv = ( 130 | # works only for non-negative whole numbers: 131 | length($x2) <=> length($y2) 132 | # the longer the numeral, the larger the value 133 | or $x2 cmp $y2 134 | # between equals, compare lexically!! amazing but true. 135 | ); 136 | } 137 | } else { 138 | # X is numeric but Y isn't 139 | $rv = Y_FIRST; 140 | last; 141 | } 142 | } elsif( $y =~ s/^\d+//s ) { # we don't need to capture the substring 143 | $rv = X_FIRST; 144 | last; 145 | } 146 | # else one of them is 0-length. 147 | 148 | # end-while 149 | } 150 | } 151 | EOGUTS 152 | 153 | sub maker { 154 | my $code = $_[0]; 155 | $code =~ s/~COMPARATOR~/$guts/g || die "Can't find ~COMPARATOR~"; 156 | eval $code; 157 | die $@ if $@; 158 | } 159 | 160 | ############################################################################## 161 | 162 | maker(<<'EONSORT'); 163 | sub nsort { 164 | # get options: 165 | my($cmp, $lc); 166 | ($cmp,$lc) = @{shift @_} if @_ and ref($_[0]) eq 'ARRAY'; 167 | 168 | return @_ unless @_ > 1 or wantarray; # be clever 169 | 170 | my($x, $x2, $y, $y2, $rv); # scratch vars 171 | 172 | # We use a Schwartzian xform to memoize the lc'ing and \W-removal 173 | 174 | map $_->[0], 175 | sort { 176 | if($a->[0] eq $b->[0]) { 0 } # trap this expensive case 177 | else { 178 | 179 | $x = $a->[1]; 180 | $y = $b->[1]; 181 | 182 | ~COMPARATOR~ 183 | 184 | # Tiebreakers... 185 | DEBUG > 1 and print " -<${$a}[0]> cmp <${$b}[0]> is $rv ($ORD[$rv])\n"; 186 | $rv ||= (length($x) <=> length($y)) # shorter is always first 187 | || ($cmp and $cmp->($x,$y) || $cmp->($a->[0], $b->[0])) 188 | || ($x cmp $y ) 189 | || ($a->[0] cmp $b->[0]) 190 | ; 191 | 192 | DEBUG > 1 and print " <${$a}[0]> cmp <${$b}[0]> is $rv ($ORD[$rv])\n"; 193 | $rv; 194 | }} 195 | 196 | map {; 197 | $x = $lc ? $lc->($_) : lc($_); # x as scratch 198 | $x =~ s/\W+//s; 199 | [$_, $x]; 200 | } 201 | @_ 202 | } 203 | EONSORT 204 | 205 | #----------------------------------------------------------------------------- 206 | maker(<<'EONCMP'); 207 | sub ncmp { 208 | # The guts are basically the same as above... 209 | 210 | # get options: 211 | my($cmp, $lc); 212 | ($cmp,$lc) = @{shift @_} if @_ and ref($_[0]) eq 'ARRAY'; 213 | 214 | if(@_ == 0) { 215 | @_ = ($a, $b); # bit of a hack! 216 | DEBUG > 1 and print "Hacking in <$a><$b>\n"; 217 | } elsif(@_ != 2) { 218 | require Carp; 219 | Carp::croak("Not enough options to ncmp!"); 220 | } 221 | my($a,$b) = @_; 222 | my($x, $x2, $y, $y2, $rv); # scratch vars 223 | 224 | DEBUG > 1 and print "ncmp args <$a><$b>\n"; 225 | if($a eq $b) { # trap this expensive case 226 | 0; 227 | } else { 228 | $x = ($lc ? $lc->($a) : lc($a)); 229 | $x =~ s/\W+//s; 230 | $y = ($lc ? $lc->($b) : lc($b)); 231 | $y =~ s/\W+//s; 232 | 233 | ~COMPARATOR~ 234 | 235 | 236 | # Tiebreakers... 237 | DEBUG > 1 and print " -<$a> cmp <$b> is $rv ($ORD[$rv])\n"; 238 | $rv ||= (length($x) <=> length($y)) # shorter is always first 239 | || ($cmp and $cmp->($x,$y) || $cmp->($a,$b)) 240 | || ($x cmp $y) 241 | || ($a cmp $b) 242 | ; 243 | 244 | DEBUG > 1 and print " <$a> cmp <$b> is $rv\n"; 245 | $rv; 246 | } 247 | } 248 | EONCMP 249 | 250 | # clean up: 251 | undef $guts; 252 | undef &maker; 253 | 254 | #----------------------------------------------------------------------------- 255 | 1; 256 | 257 | ############### END OF MAIN SOURCE ########################################### 258 | __END__ 259 | 260 | =head1 NAME 261 | 262 | Sort::Naturally -- sort lexically, but sort numeral parts numerically 263 | 264 | =head1 SYNOPSIS 265 | 266 | @them = nsort(qw( 267 | foo12a foo12z foo13a foo 14 9x foo12 fooa foolio Foolio Foo12a 268 | )); 269 | print join(' ', @them), "\n"; 270 | 271 | Prints: 272 | 273 | 9x 14 foo fooa foolio Foolio foo12 foo12a Foo12a foo12z foo13a 274 | 275 | (Or "foo12a" + "Foo12a" and "foolio" + "Foolio" and might be 276 | switched, depending on your locale.) 277 | 278 | =head1 DESCRIPTION 279 | 280 | This module exports two functions, C and C; they are used 281 | in implementing my idea of a "natural sorting" algorithm. Under natural 282 | sorting, numeric substrings are compared numerically, and other 283 | word-characters are compared lexically. 284 | 285 | This is the way I define natural sorting: 286 | 287 | =over 288 | 289 | =item * 290 | 291 | Non-numeric word-character substrings are sorted lexically, 292 | case-insensitively: "Foo" comes between "fish" and "fowl". 293 | 294 | =item * 295 | 296 | Numeric substrings are sorted numerically: 297 | "100" comes after "20", not before. 298 | 299 | =item * 300 | 301 | \W substrings (neither words-characters nor digits) are I. 302 | 303 | =item * 304 | 305 | Our use of \w, \d, \D, and \W is locale-sensitive: Sort::Naturally 306 | uses a C statement. 307 | 308 | =item * 309 | 310 | When comparing two strings, where a numeric substring in one 311 | place is I up against a numeric substring in another, 312 | the non-numeric always comes first. This is fudged by 313 | reading pretending that the lack of a number substring has 314 | the value -1, like so: 315 | 316 | foo => "foo", -1 317 | foobar => "foo", -1, "bar" 318 | foo13 => "foo", 13, 319 | foo13xyz => "foo", 13, "xyz" 320 | 321 | That's so that "foo" will come before "foo13", which will come 322 | before "foobar". 323 | 324 | =item * 325 | 326 | The start of a string is exceptional: leading non-\W (non-word, 327 | non-digit) 328 | components are are ignored, and numbers come I letters. 329 | 330 | =item * 331 | 332 | I define "numeric substring" just as sequences matching m/\d+/ -- 333 | scientific notation, commas, decimals, etc., are not seen. If 334 | your data has thousands separators in numbers 335 | ("20,000 Leagues Under The Sea" or "20.000 lieues sous les mers"), 336 | consider stripping them before feeding them to C or 337 | C. 338 | 339 | =back 340 | 341 | =head2 The nsort function 342 | 343 | This function takes a list of strings, and returns a copy of the list, 344 | sorted. 345 | 346 | This is what most people will want to use: 347 | 348 | @stuff = nsort(...list...); 349 | 350 | When nsort needs to compare non-numeric substrings, it 351 | uses Perl's C function in scope of a . 352 | And when nsort needs to lowercase things, it uses Perl's 353 | C function in scope of a . If you want nsort 354 | to use other functions instead, you can specify them in 355 | an arrayref as the first argument to nsort: 356 | 357 | @stuff = nsort( [ 358 | \&string_comparator, # optional 359 | \&lowercaser_function # optional 360 | ], 361 | ...list... 362 | ); 363 | 364 | If you want to specify a string comparator but no lowercaser, 365 | then the options list is C<[\&comparator, '']> or 366 | C<[\&comparator]>. If you want to specify no string comparator 367 | but a lowercaser, then the options list is 368 | C<['', \&lowercaser]>. 369 | 370 | Any comparator you specify is called as 371 | C<$comparator-E($left, $right)>, 372 | and, like a normal Perl C replacement, must return 373 | -1, 0, or 1 depending on whether the left argument is stringwise 374 | less than, equal to, or greater than the right argument. 375 | 376 | Any lowercaser function you specify is called as 377 | C<$lowercased = $lowercaser-E($original)>. The routine 378 | must not modify its C<$_[0]>. 379 | 380 | =head2 The ncmp function 381 | 382 | Often, when sorting non-string values like this: 383 | 384 | @objects_sorted = sort { $a->tag cmp $b->tag } @objects; 385 | 386 | ...or even in a Schwartzian transform, like this: 387 | 388 | @strings = 389 | map $_->[0] 390 | sort { $a->[1] cmp $b->[1] } 391 | map { [$_, make_a_sort_key_from($_) ] 392 | @_ 393 | ; 394 | 395 | ...you wight want something that replaces not C, but C. 396 | That's what Sort::Naturally's C function is for. Call it with 397 | the syntax C instead of C<$left cmp $right>, 398 | but otherwise it's a fine replacement: 399 | 400 | @objects_sorted = sort { ncmp($a->tag,$b->tag) } @objects; 401 | 402 | @strings = 403 | map $_->[0] 404 | sort { ncmp($a->[1], $b->[1]) } 405 | map { [$_, make_a_sort_key_from($_) ] 406 | @_ 407 | ; 408 | 409 | Just as with C can take different a string-comparator 410 | and/or lowercaser, you can do the same with C, by passing 411 | an arrayref as the first argument: 412 | 413 | ncmp( [ 414 | \&string_comparator, # optional 415 | \&lowercaser_function # optional 416 | ], 417 | $left, $right 418 | ) 419 | 420 | You might get string comparators from L. 421 | 422 | =head1 NOTES 423 | 424 | =over 425 | 426 | =item * 427 | 428 | This module is not a substitute for 429 | L! If 430 | you just need proper version sorting, use I 431 | 432 | =item * 433 | 434 | If you need something that works I like this module's 435 | functions, but not quite the same, consider scouting thru this 436 | module's source code, and adapting what you see. Besides 437 | the functions that actually compile in this module, after the POD, 438 | there's several alternate attempts of mine at natural sorting 439 | routines, which are not compiled as part of the module, but which you 440 | might find useful. They should all be I implementations of 441 | slightly different algorithms 442 | (all of them based on Martin Pool's C) which I eventually 443 | discarded in favor of my algorithm. If you are having to 444 | naturally-sort I data sets, and sorting is getting 445 | ridiculously slow, you might consider trying one of those 446 | discarded functions -- I have a feeling they might be faster on 447 | large data sets. Benchmark them on your data and see. (Unless 448 | you I the speed, don't bother. Hint: substitute C 449 | for C in your code, and unless your program speeds up 450 | drastically, it's not the sorting that's slowing things down. 451 | But if it I C that's slowing things down, consider 452 | just: 453 | 454 | if(@set >= SOME_VERY_BIG_NUMBER) { 455 | no locale; # vroom vroom 456 | @sorted = sort(@set); # feh, good enough 457 | } elsif(@set >= SOME_BIG_NUMBER) { 458 | use locale; 459 | @sorted = sort(@set); # feh, good enough 460 | } else { 461 | # but keep it pretty for normal cases 462 | @sorted = nsort(@set); 463 | } 464 | 465 | =item * 466 | 467 | If you do adapt the routines in this module, email me; I'd 468 | just be interested in hearing about it. 469 | 470 | =item * 471 | 472 | Thanks to the EFNet #perl people for encouraging this module, 473 | especially magister and a-mused. 474 | 475 | =back 476 | 477 | =head1 COPYRIGHT AND DISCLAIMER 478 | 479 | Copyright 2001, Sean M. Burke C, all rights 480 | reserved. This program is free software; you can redistribute it 481 | and/or modify it under the same terms as Perl itself. 482 | 483 | This program is distributed in the hope that it will be useful, but 484 | without any warranty; without even the implied warranty of 485 | merchantability or fitness for a particular purpose. 486 | 487 | =head1 AUTHOR 488 | 489 | Sean M. Burke C 490 | 491 | =cut 492 | 493 | ############ END OF DOCS ############ 494 | 495 | ############################################################################ 496 | ############################################################################ 497 | 498 | ############ BEGIN OLD STUFF ############ 499 | 500 | # We can't have "use integer;", or else (5 <=> 5.1) comes out "0" ! 501 | 502 | #----------------------------------------------------------------------------- 503 | sub nsort { 504 | my($cmp, $lc); 505 | return @_ if @_ < 2; # Just to be CLEVER. 506 | 507 | my($x, $i); # scratch vars 508 | 509 | # And now, the GREAT BIG Schwartzian transform: 510 | 511 | map 512 | $_->[0], 513 | 514 | sort { 515 | # Uses $i as the index variable, $x as the result. 516 | $x = 0; 517 | $i = 1; 518 | DEBUG and print "\nComparing ", map("{$_}", @$a), 519 | ' : ', map("{$_}", @$b), , "...\n"; 520 | 521 | while($i < @$a and $i < @$b) { 522 | DEBUG and print " comparing $i: {$a->[$i]} cmp {$b->[$i]} => ", 523 | $a->[$i] cmp $b->[$i], "\n"; 524 | last if ($x = ($a->[$i] cmp $b->[$i])); # lexicographic 525 | ++$i; 526 | 527 | DEBUG and print " comparing $i: {$a->[$i]} <=> {$b->[$i]} => ", 528 | $a->[$i] <=> $b->[$i], "\n"; 529 | last if ($x = ($a->[$i] <=> $b->[$i])); # numeric 530 | ++$i; 531 | } 532 | 533 | DEBUG and print "{$a->[0]} : {$b->[0]} is ", 534 | $x || (@$a <=> @$b) || 0 535 | ,"\n" 536 | ; 537 | $x || (@$a <=> @$b) || ($a->[0] cmp $b->[0]); 538 | # unless we found a result for $x in the while loop, 539 | # use length as a tiebreaker, otherwise use cmp 540 | # on the original string as a fallback tiebreaker. 541 | } 542 | 543 | map { 544 | my @bit = ($x = defined($_) ? $_ : ''); 545 | 546 | if($x =~ m/^[+-]?(?=\d|\.\d)\d*(?:\.\d*)?(?:[Ee](?:[+-]?\d+))?\z/s) { 547 | # It's entirely purely numeric, so treat it specially: 548 | push @bit, '', $x; 549 | } else { 550 | # Consume the string. 551 | while(length $x) { 552 | push @bit, ($x =~ s/^(\D+)//s) ? lc($1) : ''; 553 | push @bit, ($x =~ s/^(\d+)//s) ? $1 : 0; 554 | } 555 | } 556 | DEBUG and print "$bit[0] => ", map("{$_} ", @bit), "\n"; 557 | 558 | # End result: [original bit , (text, number), (text, number), ...] 559 | # Minimally: [0-length original bit,] 560 | # Examples: 561 | # ['10' => '' , 10, ] 562 | # ['fo900' => 'fo' , 900, ] 563 | # ['foo10' => 'foo', 10, ] 564 | # ['foo9.pl' => 'foo', 9, , '.pl', 0 ] 565 | # ['foo32.pl' => 'foo', 32, , '.pl', 0 ] 566 | # ['foo325.pl' => 'foo', 325, , '.pl', 0 ] 567 | # Yes, always an ODD number of elements. 568 | 569 | \@bit; 570 | } 571 | @_; 572 | } 573 | 574 | #----------------------------------------------------------------------------- 575 | # Same as before, except without the pure-number trap. 576 | 577 | sub nsorts { 578 | return @_ if @_ < 2; # Just to be CLEVER. 579 | 580 | my($x, $i); # scratch vars 581 | 582 | # And now, the GREAT BIG Schwartzian transform: 583 | 584 | map 585 | $_->[0], 586 | 587 | sort { 588 | # Uses $i as the index variable, $x as the result. 589 | $x = 0; 590 | $i = 1; 591 | DEBUG and print "\nComparing ", map("{$_}", @$a), 592 | ' : ', map("{$_}", @$b), , "...\n"; 593 | 594 | while($i < @$a and $i < @$b) { 595 | DEBUG and print " comparing $i: {$a->[$i]} cmp {$b->[$i]} => ", 596 | $a->[$i] cmp $b->[$i], "\n"; 597 | last if ($x = ($a->[$i] cmp $b->[$i])); # lexicographic 598 | ++$i; 599 | 600 | DEBUG and print " comparing $i: {$a->[$i]} <=> {$b->[$i]} => ", 601 | $a->[$i] <=> $b->[$i], "\n"; 602 | last if ($x = ($a->[$i] <=> $b->[$i])); # numeric 603 | ++$i; 604 | } 605 | 606 | DEBUG and print "{$a->[0]} : {$b->[0]} is ", 607 | $x || (@$a <=> @$b) || 0 608 | ,"\n" 609 | ; 610 | $x || (@$a <=> @$b) || ($a->[0] cmp $b->[0]); 611 | # unless we found a result for $x in the while loop, 612 | # use length as a tiebreaker, otherwise use cmp 613 | # on the original string as a fallback tiebreaker. 614 | } 615 | 616 | map { 617 | my @bit = ($x = defined($_) ? $_ : ''); 618 | 619 | while(length $x) { 620 | push @bit, ($x =~ s/^(\D+)//s) ? lc($1) : ''; 621 | push @bit, ($x =~ s/^(\d+)//s) ? $1 : 0; 622 | } 623 | DEBUG and print "$bit[0] => ", map("{$_} ", @bit), "\n"; 624 | 625 | # End result: [original bit , (text, number), (text, number), ...] 626 | # Minimally: [0-length original bit,] 627 | # Examples: 628 | # ['10' => '' , 10, ] 629 | # ['fo900' => 'fo' , 900, ] 630 | # ['foo10' => 'foo', 10, ] 631 | # ['foo9.pl' => 'foo', 9, , '.pl', 0 ] 632 | # ['foo32.pl' => 'foo', 32, , '.pl', 0 ] 633 | # ['foo325.pl' => 'foo', 325, , '.pl', 0 ] 634 | # Yes, always an ODD number of elements. 635 | 636 | \@bit; 637 | } 638 | @_; 639 | } 640 | 641 | #----------------------------------------------------------------------------- 642 | # Same as before, except for the sort-key-making 643 | 644 | sub nsort0 { 645 | return @_ if @_ < 2; # Just to be CLEVER. 646 | 647 | my($x, $i); # scratch vars 648 | 649 | # And now, the GREAT BIG Schwartzian transform: 650 | 651 | map 652 | $_->[0], 653 | 654 | sort { 655 | # Uses $i as the index variable, $x as the result. 656 | $x = 0; 657 | $i = 1; 658 | DEBUG and print "\nComparing ", map("{$_}", @$a), 659 | ' : ', map("{$_}", @$b), , "...\n"; 660 | 661 | while($i < @$a and $i < @$b) { 662 | DEBUG and print " comparing $i: {$a->[$i]} cmp {$b->[$i]} => ", 663 | $a->[$i] cmp $b->[$i], "\n"; 664 | last if ($x = ($a->[$i] cmp $b->[$i])); # lexicographic 665 | ++$i; 666 | 667 | DEBUG and print " comparing $i: {$a->[$i]} <=> {$b->[$i]} => ", 668 | $a->[$i] <=> $b->[$i], "\n"; 669 | last if ($x = ($a->[$i] <=> $b->[$i])); # numeric 670 | ++$i; 671 | } 672 | 673 | DEBUG and print "{$a->[0]} : {$b->[0]} is ", 674 | $x || (@$a <=> @$b) || 0 675 | ,"\n" 676 | ; 677 | $x || (@$a <=> @$b) || ($a->[0] cmp $b->[0]); 678 | # unless we found a result for $x in the while loop, 679 | # use length as a tiebreaker, otherwise use cmp 680 | # on the original string as a fallback tiebreaker. 681 | } 682 | 683 | map { 684 | my @bit = ($x = defined($_) ? $_ : ''); 685 | 686 | if($x =~ m/^[+-]?(?=\d|\.\d)\d*(?:\.\d*)?(?:[Ee](?:[+-]?\d+))?\z/s) { 687 | # It's entirely purely numeric, so treat it specially: 688 | push @bit, '', $x; 689 | } else { 690 | # Consume the string. 691 | while(length $x) { 692 | push @bit, ($x =~ s/^(\D+)//s) ? lc($1) : ''; 693 | # Secret sauce: 694 | if($x =~ s/^(\d+)//s) { 695 | if(substr($1,0,1) eq '0' and $1 != 0) { 696 | push @bit, $1 / (10 ** length($1)); 697 | } else { 698 | push @bit, $1; 699 | } 700 | } else { 701 | push @bit, 0; 702 | } 703 | } 704 | } 705 | DEBUG and print "$bit[0] => ", map("{$_} ", @bit), "\n"; 706 | 707 | \@bit; 708 | } 709 | @_; 710 | } 711 | 712 | #----------------------------------------------------------------------------- 713 | # Like nsort0, but WITHOUT pure number handling, and WITH special treatment 714 | # of pulling off extensions and version numbers. 715 | 716 | sub nsortf { 717 | return @_ if @_ < 2; # Just to be CLEVER. 718 | 719 | my($x, $i); # scratch vars 720 | 721 | # And now, the GREAT BIG Schwartzian transform: 722 | 723 | map 724 | $_->[0], 725 | 726 | sort { 727 | # Uses $i as the index variable, $x as the result. 728 | $x = 0; 729 | $i = 3; 730 | DEBUG and print "\nComparing ", map("{$_}", @$a), 731 | ' : ', map("{$_}", @$b), , "...\n"; 732 | 733 | while($i < @$a and $i < @$b) { 734 | DEBUG and print " comparing $i: {$a->[$i]} cmp {$b->[$i]} => ", 735 | $a->[$i] cmp $b->[$i], "\n"; 736 | last if ($x = ($a->[$i] cmp $b->[$i])); # lexicographic 737 | ++$i; 738 | 739 | DEBUG and print " comparing $i: {$a->[$i]} <=> {$b->[$i]} => ", 740 | $a->[$i] <=> $b->[$i], "\n"; 741 | last if ($x = ($a->[$i] <=> $b->[$i])); # numeric 742 | ++$i; 743 | } 744 | 745 | DEBUG and print "{$a->[0]} : {$b->[0]} is ", 746 | $x || (@$a <=> @$b) || 0 747 | ,"\n" 748 | ; 749 | $x || (@$a <=> @$b ) || ($a->[1] cmp $b->[1]) 750 | || ($a->[2] <=> $b->[2]) || ($a->[0] cmp $b->[0]); 751 | # unless we found a result for $x in the while loop, 752 | # use length as a tiebreaker, otherwise use the 753 | # lc'd extension, otherwise the verison, otherwise use 754 | # the original string as a fallback tiebreaker. 755 | } 756 | 757 | map { 758 | my @bit = ( ($x = defined($_) ? $_ : ''), '',0 ); 759 | 760 | { 761 | # Consume the string. 762 | 763 | # First, pull off any VAX-style version 764 | $bit[2] = $1 if $x =~ s/;(\d+)$//; 765 | 766 | # Then pull off any apparent extension 767 | if( $x !~ m/^\.+$/s and # don't mangle ".", "..", or "..." 768 | $x =~ s/(\.[^\.\;]*)$//sg 769 | # We could try to avoid catching all-digit extensions, 770 | # but I think that's getting /too/ clever. 771 | ) { 772 | $i = $1; 773 | if($x =~ m<[^\\\://]$>s) { 774 | # We didn't take the whole basename. 775 | $bit[1] = lc $i; 776 | DEBUG and print "Consuming extension \"$1\"\n"; 777 | } else { 778 | # We DID take the whole basename. Fix it. 779 | $x = $1; # Repair it. 780 | } 781 | } 782 | 783 | push @bit, '', -1 if $x =~ m/^\./s; 784 | # A hack to make .-initial filenames sort first, regardless of locale. 785 | # And -1 is always a sort-firster, since in the code below, there's 786 | # no allowance for filenames containing negative numbers: -1.dat 787 | # will be read as string '-' followed by number 1. 788 | 789 | while(length $x) { 790 | push @bit, ($x =~ s/^(\D+)//s) ? lc($1) : ''; 791 | # Secret sauce: 792 | if($x =~ s/^(\d+)//s) { 793 | if(substr($1,0,1) eq '0' and $1 != 0) { 794 | push @bit, $1 / (10 ** length($1)); 795 | } else { 796 | push @bit, $1; 797 | } 798 | } else { 799 | push @bit, 0; 800 | } 801 | } 802 | } 803 | 804 | DEBUG and print "$bit[0] => ", map("{$_} ", @bit), "\n"; 805 | 806 | \@bit; 807 | } 808 | @_; 809 | } 810 | 811 | # yowza yowza yowza. 812 | 813 | -------------------------------------------------------------------------------- /Sort/Topological.pm: -------------------------------------------------------------------------------- 1 | package Sort::Topological; 2 | 3 | ######################################################################### 4 | 5 | =head1 NAME 6 | 7 | Sort::Topological - Topological Sort 8 | 9 | =head1 SYNOPSIS 10 | 11 | use Sort::Topological qw(toposort); 12 | my @result = toposort($item_direct_sub, @items); 13 | 14 | =head1 DESCRIPTION 15 | 16 | Sort::Topological does a topological sort of an acyclical directed graph. 17 | 18 | =head1 EXAMPLE 19 | 20 | my %children = ( 21 | 'a' => [ 'b', 'c' ], 22 | 'c' => [ 'x' ], 23 | 'b' => [ 'x' ], 24 | 'x' => [ 'y' ], 25 | 'y' => [ 'z' ], 26 | 'z' => [ ], 27 | ); 28 | sub children { @{$children{$_[0]} || []}; } 29 | my @unsorted = ( 'z', 'a', 'x', 'c', 'b', 'y' ); 30 | my @sorted = toposort(\&children, \@unsorted); 31 | 32 | 33 | In the above example C<%children> is the graph, C<&children($x)> returns a list of targets of the directed graph from C<$x>. 34 | 35 | C<@sorted> is sorted such that: 36 | 37 | =over 4 38 | 39 | for any C<$x> in C<@sorted>: 40 | 41 | =over 4 42 | C<$x> is not reachable through the directed graph of anything after C<$x> in C<@sorted>. 43 | 44 | =back 45 | 46 | i.e.: 'y' is not reachable by 'z', 'x' is not reachable by 'y' or 'z', and so on. 47 | 48 | =back 49 | 50 | =head1 CAVEATS 51 | 52 | =over 4 53 | 54 | =item * 55 | 56 | Does not handle cyclical graphs. 57 | 58 | =back 59 | 60 | =head1 STATUS 61 | 62 | If you find this to be useful please contact the author. This is alpha software; all APIs, semantics and behavors are subject to change. 63 | 64 | =head1 INTERFACE 65 | 66 | This section describes the external interface of this module. 67 | 68 | 69 | =cut 70 | 71 | 72 | ######################################################################### 73 | 74 | 75 | use strict; 76 | use warnings; 77 | 78 | our $VERSION = '0.02'; 79 | our $REVISION = do { my @r = (q$Revision: 1.2 $ =~ /\d+/g); sprintf "%d." . "%02d" x $#r, @r }; 80 | 81 | our $PACKAGE = __PACKAGE__; 82 | 83 | use Exporter; 84 | our @ISA = qw(Exporter); 85 | our @EXPORT = qw(); 86 | our @EXPORT_OK = qw(toposort); 87 | our %EXPORT_TAGS = ( 88 | 'all' => \@EXPORT_OK, 89 | ); 90 | 91 | 92 | sub toposort 93 | { 94 | my ($deps, $in) = @_; 95 | 96 | # Assign the depth of traversal. 97 | my %depth; 98 | { 99 | # Assign a base depth of traversal for the input. 100 | my @stack = reverse map([ $_, 1 ], @$in); 101 | 102 | # While there are still items to traverse, 103 | while ( @stack ) { 104 | # Pop the top item and the current traversal depth. 105 | my $q = pop @stack; 106 | my $x = $q->[0]; 107 | my $d = $q->[1]; 108 | 109 | # Remember current depth. 110 | if ( (! defined $depth{$x}) || $depth{$x} < $d ) { 111 | $depth{$x} = $d; 112 | # warn "$x depth = $d"; 113 | } 114 | 115 | # Push the next items along the graph, remembering the depth they were found at. 116 | if ( 1 ) { 117 | my @depa = $deps->($x); 118 | unshift(@stack, reverse map([ $_, $d + 1 ], @depa)); 119 | } 120 | } 121 | } 122 | 123 | # print STDERR 'depth = ', join(', ', %depth), "\n"; 124 | 125 | # Create a depth tie-breaker map based on order of appearance of list. 126 | my %order; 127 | { 128 | my $i = 0; 129 | %order = map(($_, ++ $i), @$in); 130 | } 131 | 132 | # Sort by depth and input order. 133 | my @out = sort { 134 | $depth{$a} <=> $depth{$b} || 135 | $order{$a} <=> $order{$b} 136 | } @$in; 137 | 138 | # Return array or array ref. 139 | wantarray ? @out : \@out; 140 | } 141 | 142 | 143 | sub deep_deps 144 | { 145 | my ($deps, @x) = @_; 146 | 147 | my @out; 148 | 149 | @x = map($deps->($_), @x); 150 | 151 | while ( @x ) { 152 | my $x = shift @x; 153 | push(@out, $x); 154 | push(@x, $deps->($x)); 155 | } 156 | 157 | @out; 158 | } 159 | 160 | 161 | sub validate_sorted 162 | { 163 | my ($dep, @sorted) = @_; 164 | my $ok = 1; 165 | 166 | my @after = @sorted; 167 | my @before; 168 | while ( @after ) { 169 | my $x = shift @after; 170 | my @deep_deps = deep_deps($dep, @after); 171 | # warn " @deep_deps"; 172 | # each $x is not a dep of anything after it. 173 | if ( grep($_ eq $x, @deep_deps) ) { 174 | warn "found $x in @deep_deps"; 175 | $ok = 0; 176 | } 177 | push(@before, $x); 178 | } 179 | 180 | $ok 181 | } 182 | 183 | 184 | sub UNIT_TEST 185 | { 186 | print STDERR "VERSION = $VERSION, PACKAGE = $PACKAGE\n"; 187 | my %children = ( 188 | 'a' => [ 'b', 'c' ], 189 | 'b' => [ 'd' ], 190 | 'c' => [ 'e', 'y' ], 191 | 'd' => [ 'x' ], 192 | 'e' => [ 'y', 'z' ], 193 | 'f' => [ 'z' ], 194 | 'x' => [ 'y' ], 195 | 'y' => [ 'z' ], 196 | 'z' => [ ], 197 | ); 198 | 199 | my $passes = 20; 200 | my $verbose = 0; 201 | 202 | for my $pass ( 1 .. $passes ) { 203 | my @unsorted = ( 'a', 'b', 'c', 'd', 'e', 'f', 'x', 'y', 'z' ); 204 | for my $i ( 0 .. $#unsorted ) { 205 | my $j = rand($#unsorted); 206 | ($unsorted[$i], $unsorted[$j]) = ($unsorted[$j], $unsorted[$i]); 207 | } 208 | my $children = sub { @{$children{$_[0]} || []} }; 209 | 210 | $DB::single = 1; 211 | my @sorted = toposort($children, \@unsorted); 212 | 213 | print 'unsorted = ', join(', ', @unsorted), "\n" if $verbose; 214 | print ' sorted = ', join(', ', @sorted), "\n" if $verbose; 215 | validate_sorted($children, @sorted); 216 | } 217 | } 218 | 219 | 220 | # UNIT_TEST(@ARGV); 221 | 222 | ######################################################################### 223 | 224 | =head1 VERSION 225 | 226 | Version 0.01, $Revision: 1.2 $. 227 | 228 | =head1 AUTHOR 229 | 230 | Kurt A. Stephens 231 | 232 | =head1 COPYRIGHT 233 | 234 | Copyright (c) 2001, 2002, Kurt A. Stephens and ION, INC. 235 | 236 | =head1 SEE ALSO 237 | 238 | >. 239 | 240 | =cut 241 | 242 | ################################################## 243 | 244 | 1; 245 | 246 | ### Keep these comments at end of file: kurtstephens@acm.org 2001/12/28 ### 247 | ### Local Variables: ### 248 | ### mode:perl ### 249 | ### perl-indent-level:2 ### 250 | ### perl-continued-statement-offset:0 ### 251 | ### perl-brace-offset:0 ### 252 | ### perl-label-offset:0 ### 253 | ### End: ### 254 | 255 | -------------------------------------------------------------------------------- /check-disorder.pl: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env perl 2 | 3 | use 5.010; 4 | use strict; 5 | use warnings; 6 | use Fatal qw/open close chdir/; 7 | use Getopt::Long; 8 | 9 | my $usage = <<"END_USAGE"; 10 | usage: $0 [input GFF3 file] 11 | Optional Parameters: 12 | --list list all IDs that have children features appearing in front of themselves 13 | END_USAGE 14 | 15 | ############ Usage ############ 16 | my $help; 17 | my $list; 18 | GetOptions( 19 | 'help' => \$help, 20 | 'list' => \$list, 21 | ); 22 | if ($help or @ARGV!=1) { 23 | print "$usage"; 24 | exit(0); 25 | } 26 | 27 | my %line_rank; 28 | my %is_error_parent; 29 | my %all_parent; 30 | while (<>) { 31 | chomp; 32 | next if (/^#/); 33 | my $line_rank = $.; 34 | my ($chr, $pos, $note) = (split /\t/, $_)[0,3,-1]; 35 | my ($id) = $note=~/ID=([^;]+);/; 36 | my ($parent) = $note=~/Parent=([^;]+);/; 37 | if ($id && !$line_rank{$id}) { 38 | $line_rank{$id} = $line_rank; 39 | } 40 | if ($parent) { 41 | $all_parent{$parent} = 1; 42 | } 43 | if ($parent && !$line_rank{$parent}) { 44 | $is_error_parent{$parent} = 1; 45 | } 46 | } 47 | 48 | if ($list) { 49 | for my $id (keys %is_error_parent) { 50 | print "$id\n"; 51 | } 52 | } 53 | 54 | my $all_num = keys %all_parent; 55 | my $error_num = keys %is_error_parent; 56 | 57 | print "Number of all parent features: $all_num\nNumber of disordered parent features: $error_num\n"; 58 | -------------------------------------------------------------------------------- /gff3sort.pl: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env perl 2 | 3 | use 5.010_001; 4 | use strict; 5 | use warnings; 6 | use Fatal qw/open close chdir/; 7 | use Getopt::Long; 8 | use FindBin qw($Bin); 9 | use lib "$Bin"; 10 | use Sort::Naturally qw/nsort/; ###### https://metacpan.org/pod/Sort::Naturally 11 | use Sort::Topological qw/toposort/; ###### https://metacpan.org/pod/Sort::Topological 12 | use Pod::Usage; 13 | no if ($] >= 5.018), 'warnings' => 'experimental'; 14 | 15 | ############ Usage ############ 16 | my $help; 17 | my $precise; 18 | my $chr_order = 'alphabet'; 19 | my $extract_FASTA; 20 | GetOptions( 21 | 'help' => \$help, 22 | 'precise' => \$precise, 23 | 'chr_order=s' => \$chr_order, 24 | 'extract_FASTA' => \$extract_FASTA, 25 | ); 26 | if ($help or @ARGV!=1) { 27 | pod2usage(-verbose => 2); 28 | } 29 | if ($chr_order !~ /(alphabet)|(natural)|(original)/i) { 30 | die "Unknown option: --chr_order=$chr_order. Only [alphabet] [natural] [original] are allowed\n"; 31 | exit(0); 32 | } 33 | $chr_order = lc($chr_order); 34 | 35 | ############################ 36 | # %gff: sort by: chr, start pos, lines in their original order (default mode, very fast) 37 | # OR in Topological order of parent-children relationships (precise mode, a little slower) 38 | ############################ 39 | 40 | my %gff; 41 | my @chromosomes; # Store the order of chromosomes 42 | my $encounter_FASTA = 0; 43 | my $FASTA_str; 44 | my $input = shift; 45 | open my $in_fh, "<", $input; 46 | while (<$in_fh>) { 47 | chomp; 48 | 49 | # deal with ##FASTA pragma, as tabix does not allow such blocks 50 | if ($_ eq '##FASTA') { 51 | $encounter_FASTA = 1; 52 | } 53 | 54 | # If we have not encountered the ##FASTA pragma, collect annotation lines to our hash %gff 55 | if (!$encounter_FASTA) { 56 | if ($_ =~ /^#/) { 57 | if ($_ !~ /[^#]/) { # lines with pure # chars are separators. As GFF3sort 58 | # generates results for tabix indexing instead of human reading, these separators 59 | # are not so necessary 60 | next; 61 | } 62 | else { # lines start with # and contains other non # chars are pragma lines, keep them 63 | print "$_\n"; 64 | next; 65 | } 66 | } 67 | my ($chr, $pos) = (split /\t/, $_)[0,3]; 68 | push @{$gff{$chr}{$pos}}, $_; 69 | push @chromosomes, $chr unless ($chr~~@chromosomes); 70 | } 71 | # If we have encountered the ##FASTA pragma, we should stop collect lines 72 | # If users have chosen to extract_FASTA, 73 | # Then extract FASTA here (excluding the ##FASTA pragma it self) 74 | else { 75 | if ($extract_FASTA && $_ ne '##FASTA') { 76 | $FASTA_str .= "$_\n"; 77 | } 78 | } 79 | } 80 | close $in_fh; 81 | 82 | # If the users have chosen to extract_FASTA, and there exisis FASTA sequences in the GFF file, print them 83 | if ($extract_FASTA && $FASTA_str) { 84 | open my $out_fh, ">", "$input.fasta"; 85 | print {$out_fh} $FASTA_str; 86 | close $out_fh; 87 | warn "The inline FASTA sequences were extracted to file $input.fasta\n"; 88 | } 89 | 90 | 91 | ###### Define the order of chromosomes based on users' option 92 | if ($chr_order eq 'alphabet') { 93 | @chromosomes = sort @chromosomes; 94 | } 95 | elsif ($chr_order eq 'natural') { 96 | @chromosomes = nsort(@chromosomes); 97 | } 98 | else { 99 | 1; # the original chromosome order is kept 100 | } 101 | 102 | ###### Begin Sorting 103 | 104 | for my $chr (@chromosomes) { 105 | for my $pos (sort {$a<=>$b} keys %{$gff{$chr}}) { 106 | my @lines = @{$gff{$chr}{$pos}}; 107 | ###### Only one feature line under this chromosome and position: Do not need to sort 108 | if (@lines==1) { 109 | print "$lines[0]\n"; 110 | } 111 | ###### Precise mode: do Topological Sort 112 | elsif ($precise) { 113 | my %parent2children = (); # This hash is used to do Topological Sort in precise mode 114 | my %id2line = (); # This hash maps a ID to its full feature line 115 | for my $line (@lines) { 116 | my ($note) = (split /\t/, $line)[-1]; 117 | my ($id) = $note=~/ID=([^;]+)/; # Using the semicolon as the separator can deal with any IDs even with blanks. 118 | my ($parents) = $note=~/Parent=([^;]+)/; # Attribute names are case sensitive. "Parent" is not the same as "parent". 119 | 120 | ##### Begin to fill the hash %id2line 121 | if (defined($id)) { 122 | $id2line{$id} = $line; 123 | } 124 | else { # These lines has no ID attributes (but possibly have Parent attributes, 125 | # i.e they are the least-level features with no children 126 | $id2line{$line} = $line; 127 | } 128 | ##### Finished filling the hash %id2line 129 | 130 | ##### Begin to fill the hash %parent2children 131 | if (defined($parents)) { 132 | my @parents = split /,/, $parents; # Parent can have multiple values separated by comma 133 | for my $parent (@parents) { 134 | if (defined($id)) { 135 | push @{ $parent2children{$parent} }, $id; 136 | } 137 | else { # These lines has no ID attributes (but possibly have Parent attributes, 138 | # i.e they are the least-level features with no children 139 | push @{ $parent2children{$parent} }, $line; 140 | } 141 | } 142 | } 143 | ##### Finished filling the hash %parent2children 144 | } 145 | my @unsorted_ids = keys %id2line; 146 | my @sorted_ids = toposort(\&{sub {my $i = shift @_; return @{$parent2children{$i} || []}}}, \@unsorted_ids); 147 | for my $id (@sorted_ids) { 148 | print "$id2line{$id}\n"; 149 | } 150 | } 151 | ###### Default mode: keep lines in their original order 152 | else { 153 | print join("\n", @lines), "\n"; 154 | } 155 | } 156 | } 157 | 158 | __END__ 159 | 160 | =head1 NAME 161 | 162 | gff3sort.pl - Sort GFF3 file for tabix indexing 163 | 164 | =head1 SYNOPSIS 165 | 166 | gff3sort.pl [OPTIONS] input.file.gff3 >output.sort.gff3 167 | 168 | =head1 COMMAND-LINE OPTIONS 169 | 170 | These optional options could be placed either before or after the I/O files in the 171 | commandline 172 | 173 | --precise Run in precise mode, about 2X~3X slower than the default mode. 174 | Only needed to be used if your original GFF3 files have parent 175 | features appearing behind their children features. 176 | 177 | --chr_order Select how the chromosome IDs should be sorted. 178 | Acceptable values are: alphabet, natural, original 179 | [Default: alphabet] 180 | 181 | --extract_FASTA If the input GFF3 file contains FASTA sequence at the end, use this 182 | option to extract the FASTA sequence and place in a separate file 183 | with the extention '.fasta'. By default, the FASTA sequences would be 184 | discarded. 185 | 186 | =head1 DESCRIPTION 187 | 188 | The tabix tool requires GFF3 files to be sorted by chromosomes and positions, which could be 189 | performed in the GNU sort program or the GenomeTools package. However, when dealing with feature 190 | lines in the same chromosome and position, both of the tools would sort them in an ambiguous 191 | way that usually results in parent features being placed behind their children. This would cause erroneous 192 | in some genome browsers such as JBrowse. GFF3sort can properly deal with the order of features 193 | that have the same chromosome and start position, therefore generating suitable results for JBrowse display. 194 | 195 | =head2 Precise mode 196 | 197 | In most situations, the original GFF3 annotations produced by genome annotation projects have already placed 198 | parent features before their children. Therefore, GFF3sort would remember their original order and placed them accordingly 199 | within the same chromosome and start position block, which is the default behavior. 200 | 201 | Sometimes the order in the input file has already been disturbed (for example, by GNU sort or GenomeTools). 202 | In this situation, GFF3sort would sort them according to the parent-child topology using the sorting algorithm of 203 | directed acyclic graph (https://metacpan.org/pod/Sort::Topological), which is the most precise behavior but 2X~3X 204 | slower than the default mode. 205 | 206 | =head2 The chromosome order 207 | 208 | In default, chromosomes are sorted alphabetly. Users can choose to sort naturally (see https://metacpan.org/pod/Sort::Naturally) 209 | or keep their original orders. 210 | 211 | Therefore, chromosomes "Chr7 Chr1 Chr10 Chr2 Chr1" would be sorted as: 212 | 213 | By alphabet (default): Chr1 Chr10 Chr2 Chr7 214 | 215 | By natural: Chr1 Chr2 Chr7 Chr10 216 | 217 | Kepp original: Chr7 Chr1 Chr10 Chr2 (Note: tabix requires continuous chromosome blocks. Therefore the same chromosomes 218 | such as Chr1 must be grouped together) 219 | 220 | =head1 AUTHOR 221 | 222 | Tao Zhu Ezhutao@caas.cnE 223 | 224 | Copyright (c) 2017 225 | 226 | This script is free software; you can redistribute it and/or modify 227 | it under the same terms as Perl itself. 228 | 229 | =cut 230 | --------------------------------------------------------------------------------