/usr/bin/mcxdeblast is in mcl 1:14-137-1+b1.
This file is owned by root:root, with mode 0o755.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 | #!/usr/bin/perl -w
use Getopt::Long;
# (c) Copyright 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009 Stijn van Dongen
# (c) Copyright 2004 Jason Stajich (column output parsing)
#
# Other (C)ontributors;
# Dinakarpandian Deendayal (general comments)
# Abel Ureta-Vidal (general comments)
# Daniel Lundin (regexp tweak, warning)
#
# You can redistribute and/or modify this program under the terms of the GNU
# General Public License; either version 3 of the License or (at your option)
# any later version.
#
# TODO
#
# - Optionally read from STDIN
# - Require tab file for line-mode={123,packed}
#
# - Infer hsp_len from long output (?)
# - (Perhaps) enable section parsing ala tribe, for finer control.
# - $:: usage is arbitrary and ugly. pipe down.
# - Is the m9/seenlfgt combination correct?
# - Check whether m9 output state is correct if errors occur.
$^W = 1;
use strict;
$::mode_sort = 'o'; # a lphabetical
# o ccurrence
$::mode_score = 'e'; # e value
# b it
my $line_mode = ""; # default is raw mode, not line mode
$::name_out = '-';
$::bcut = 0;
$::ecut = 0;
$::rcut = 0;
my $blastfix = "";
my $addfix = "";
my $user_tabfile = "";
my %line_modes = qw ( abc 1 123 1);
my $obase = "";
my $stdhandler = 0;
my $help = 0;
my $m9 = 0;
my $abc = 0;
if
(! GetOptions
( "help" => \$help
, "apropos" => \$help
, "sort=s" => \$::mode_sort
, "ecut=f" => \$::ecut
, "bcut=f" => \$::bcut
, "rcut=f" => \$::rcut
, "score=s" => \$::mode_score
, "m9" => \$m9
, "tab=s" => \$user_tabfile
, "xo-dat=s" => \$addfix
, "xi-dat=s" => \$blastfix
, "base=s" => \$obase
, "stdhandler" => \$stdhandler
, "line-mode=s" => \$line_mode
, "out=s" => \$::name_out
)
)
{ print STDERR "option processing failed\n";
exit(1);
}
help() && exit(0) if $help;
die "unknown sort mode <$::mode_sort>"
unless $::mode_sort =~ /^[ao]$/;
die "unknown line mode <$line_mode>"
if ($line_mode && !defined($line_modes{$line_mode}));
die "unknown sort mode <$::mode_score>"
unless $::mode_score =~ /^[ebr]$/;
my $fname = shift || die "please submit name of blast file\n";
$obase = $fname unless $obase;
if ($blastfix) {
$obase = $fname;
if ($fname =~ /\Q.$blastfix\E$/) {
$obase =~ s/\Q.$blastfix\E$//;
}
else {
$fname .= ".$blastfix";
}
}
if ($addfix) {
$obase .= ".$addfix";
}
my ($gix, $giy);
$::seenlft = {};
$::seenrgt = {};
my $tagTocc = {};
my $me = "[$0] ";
my $lc = 0;
my $fhin = \*STDIN;
if ($fname ne '-') {
open(F_BLAST, "<$fname") || die "cannot open $fname\n";
$fhin = \*F_BLAST;
}
$::TAB_user = {};
if ($user_tabfile) {
read_tab($user_tabfile, $::TAB_user);
}
$::f_raw = undef;
my $f_err = undef;
if ($line_mode) {
if (!$::name_out || $::name_out eq '-') {
$::f_raw = \*STDOUT;
}
else {
open(F_RAW, ">$::name_out") || die "cannot open $::name_out";
$::f_raw = \*F_RAW;
}
$f_err = \*STDERR;
if ($line_mode eq 'abc') {
# print $::f_raw "#aa# (stream abc cookie)\n";
}
elsif ($line_mode eq '123') {
# print $::f_raw "#11# (stream abc cookie)\n";
}
}
else {
if ($stdhandler) {
$::f_raw = \*STDOUT;
$f_err = \*STDERR;
}
else {
open(F_RAW, ">$obase.raw") || die "cannot open $obase.raw\n";
$::f_raw = \*F_RAW;
open(F_ERR, ">$obase.err") || die "cannot open $obase.err\n";
$f_err = \*F_ERR;
}
}
$::ID = 0;
if ($m9) {
munge_linewise($fhin, $::f_raw, $line_mode);
}
else {
munge_long($fhin, $::f_raw, $line_mode);
}
close $::f_raw;
$::CT = scalar keys %$::seenrgt;
my $alnum = 0;
my $occTmisc = {};
if (!$user_tabfile && !$line_mode) {
open(F_HDR, ">$obase.hdr") || die "cannot open $obase.hdr\n"; # header
open(F_MAP, ">$obase.map") || die "cannot open $obase.idx\n"; # map file
open(F_TAB, ">$obase.tab") || die "cannot open $obase.idx\n"; # indices
print F_TAB "#<mapped index> <tag>\n";
if ($::mode_sort eq 'o') {
print F_TAB "# sort mode is by occurrence\n";
}
elsif ($::mode_sort eq 'a') {
print F_TAB "# sort mode is alphabetical\n";
}
if ($::mode_sort eq 'a') {
for (sort {$::a cmp $::b; } keys %$tagTocc) {
print F_TAB "$alnum $_\n";
$occTmisc->{$tagTocc->{$_}} = [ $alnum, $_ ];
$alnum++;
}
print STDERR "Index [$obase.tab] is sorted by alphabetic order\n";
}
elsif ($::mode_sort eq 'o' || 1) {
for (sort {$tagTocc->{$::a} <=> $tagTocc->{$::b}; } keys %$tagTocc) {
print F_TAB "$alnum $_\n";
$occTmisc->{$tagTocc->{$_}} = [ $alnum, $_ ];
$alnum++;
}
print STDERR "Index [$obase.tab] is sorted by occurrence order\n";
print STDERR "Primary and secondary occurrences are considered equal\n";
}
my $ct = keys %$occTmisc;
print F_MAP "(mclheader\nmcltype matrix\ndimensions $ct", 'x',
"$ct\n)\n(mclmatrix\nbegin\n";
for (sort {$::a <=> $::b; } keys %$occTmisc) {
# print F_MAP "$_ ", $occTmisc->{$_}[0], " ", $occTmisc->{$_}[1], "\n";
print F_MAP "$_ $occTmisc->{$_}[0] \$\n";
}
print F_MAP ")\n";
print F_HDR "(mclheader\nmcltype matrix\ndimensions ";
print F_HDR $::ID . 'x' . $::ID;
print F_HDR "\n)\n";
close F_TAB;
close F_HDR;
close F_MAP;
}
my $n_err = 0;
for (sort keys %$::seenrgt) {
if (!$::seenlft->{$_}) {
print $f_err "secondary element $_ not seen as primary element\n";
print $f_err "emergency measure: added the element to the primary list\n";
$n_err++;
}
}
if ($n_err) {
print STDERR $me, "$n_err secondary elements not seen as primary element\n";
print STDERR $me, "I added all of them\n";
print STDERR $me, "There were $::CT elements in all\n";
}
else {
print STDERR $me,
"all secondary elements were also seen as primary elements (check ok)\n";
}
sub munge_linewise {
my ($fh_in, $fh_raw, $line_mode) = @_;
my $gix_prev = "";
while (<$fh_in>) {
next if /^#/;
chomp;
my $sc_abc = 0;
my ($gix, $giy, $percent_id, $hsp_len, $mismatches, $gapsm,
$qstart, $qend,$hstart, $hend, $e, $b)
=
split;
my $s = 0;
my $idx = getid($gix, 1);
next unless $idx >= 0;
if ($gix_prev ne $gix) {
if (!$line_mode) {
if ($gix_prev) {
print $fh_raw "\$\n";
}
if( $idx >= 0 ) {
print $fh_raw "$idx ";
}
}
}
my $idy = getid($giy, 0);
$s = getscore($e, $b, $hsp_len);
if ($idy >= 0) {
if (!$line_mode) {
print $fh_raw "$idy:$s ";
}
else {
print $fh_raw "$gix\t$giy\t$s\n";
}
}
$gix_prev = $gix;
}
if ($gix_prev) {
print $fh_raw "\$\n" if !$line_mode;
}
}
sub munge_long {
my ($fh_in, $fh_raw, $line_mode) = @_;
my $need_query = 1;
my $need_hits = 2;
my $need_gi = 3;
my $state = $need_query;
while (<$fh_in>) {
$lc++;
chomp;
if (/^Query=\s+gi\|(\d+(_\d+)?)/ || /^Query=\s+(\S+).*$/) {
# warn "STATE query $1\n";
if ($state != $need_query) {
print STDERR "Unexpected 'Query=' line\n";
}
$gix = $1;
my $idx = getid($gix, 1);
if ($idx >= 0) {
print $fh_raw "$idx " if !$line_mode;
}
$state = $need_hits;
}
elsif (/^Query=/) {
print STDERR "Query string not recognized: $_\n";
}
elsif
($state == $need_hits && /sequences producing significant alignments/i) {
$state = $need_gi;
# warn "STATE significant\n";
}
elsif ($state == $need_hits && /no hits found/i) {
print STDERR "no hits found for gi $gix\n";
print $fh_raw "\$\n" if !$line_mode;
$state = $need_query;
}
elsif
( $state == $need_gi
&& ! /^>/
&& (/^gi\|(\d+(_\d+)?)/ || /^(\S+)\s+.*$/)
)
{ $giy = $1;
my $idy = getid($giy, 0);
my ($s, $b, $e);
if (/(\S+)\s+(\S+)\s*$/) {
$b = +$1;
$e = +$2;
}
else {
print STDERR "no scores in line $lc [$_]!\n";
next;
}
$s = getscore($e, $b, 0);
if ($idy >= 0) { # fixme, void or explain.
if (!$line_mode) {
print $fh_raw "$idy:$s ";
}
else {
print $fh_raw "$giy\t$gix\t$s\n";
}
}
}
elsif (/^\s*$/) {
# paragraph skip does not change state, including the $need_gi case.
}
elsif (/(Statistics|Parameters):/) {
$state = $need_query;
# this provides WU-blast compatibility.
}
elsif ($state == $need_gi) {
print $fh_raw "\$\n" if !$line_mode;
$state = $need_query;
}
}
if ($state == $need_gi) {
print $f_err "run ended while expecting more secondary scores\n";
print STDERR "run ended while expecting more secondary scores\n";
print $fh_raw "\$\n" if !$line_mode;
}
}
sub read_tab {
my $file = shift;
my $tab = shift;
open (U_TAB, "<$file") || die "cannot open $file\n";
while (<U_TAB>) {
if (/^\s*#/) {
next;
}
else {
if (/^(\d+)\s+(.*)/) {
$tab->{$2} = $1;
}
else {
print STDERR "___ cannot parse line: $_";
}
}
}
}
sub getscore {
my ($e, $b, $hl) = @_;
my $s = 0;
if ($::mode_score eq 'e') {
$e = "1$e" if $e =~ /^e/;
$s = $e > 0 ? -log($e)/log(10) : 200;
if ($s > 200) {
$s = 200;
}
$s = $s > $::ecut ? $s : 0;
}
elsif ($::mode_score eq 'b') {
$s = $b > $::bcut ? $b : 0;
}
elsif ($::mode_score eq 'r' && $hl) {
$s = $b / $hl;
$s = $s > $::rcut ? $s : 0;
}
return $s;
}
sub getid {
my ($gi, $is_a_query) = @_;
my $id = -1;
if ($user_tabfile) {
if (defined($::TAB_user->{$gi})) {
$id = $::TAB_user->{$gi};
}
else {
print STDERR "___ no user tab entry for label <$gi>\n";
return -1;
}
}
else {
if (!exists($tagTocc->{$gi})) {
# warn "$is_a_query $gi <-> $::ID\n";
$tagTocc->{$gi} = $::ID++;
}
$id = $tagTocc->{$gi};
}
$::seenrgt->{$id}++;
if ($is_a_query) {
$::seenlft->{$id}++;
}
return $id;
}
sub help {
print <<_help_;
Usage: mcxdeblast <options> file-name
where file-name is in BLAST NCBI format.
mcxdeblast will create
base.hdr [to be read by mcxassemble]
base.raw [to be read by mcxassemble]
base.map [to be read by mcxassemble]
base.tab [to be read by clmformat]
base.err [error log]
where base is derived from or equal to file-name
Options:
--m9 Expect column (-m 9) input.
--line-mode=abc Output simple ID1 ID2 SCORE format.
--score=<b|e|r> Use bit scores, E-values,
or bit scores normalized by hsp-length
--sort=<a|o> Use alphabetic sorting (default) or occurrence.
--tab=<fname> Use user-supplied tab file.
--xi-dat=<suf> Strip <suf> from file-name to create output base name.
--xo-dat=<suf> Add <suf> to base name.
--bcut=<val> Ignore hits below bit score <val>
--ecut=<val> Ignore hits below E-value <val>
--rcut=<val> Ignore hits below raw value <val>
--out=<fname> Output file name ('-' for STDOUT)
_help_
}
|