/usr/bin/legacy_blast is in ncbi-blast+ 2.2.28-2.
This file is owned by root:root, with mode 0o755.
The actual contents of the file can be viewed below.
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# $Id: legacy_blast.pl 195935 2010-06-28 20:32:08Z camacho $
# ===========================================================================
#
# PUBLIC DOMAIN NOTICE
# National Center for Biotechnology Information
#
# This software/database is a "United States Government Work" under the
# terms of the United States Copyright Act. It was written as part of
# the author's official duties as a United States Government employee and
# thus cannot be copyrighted. This software/database is freely available
# to the public for use. The National Library of Medicine and the U.S.
# Government have not placed any restriction on its use or reproduction.
#
# Although all reasonable efforts have been taken to ensure the accuracy
# and reliability of the software and data, the NLM and the U.S.
# Government do not and cannot warrant the performance or results that
# may be obtained by using this software or data. The NLM and the U.S.
# Government disclaim all warranties, express or implied, including
# warranties of performance, merchantability or fitness for any particular
# purpose.
#
# Please cite the author in any work or product based on this material.
#
# ===========================================================================
#
# Author: Christiam Camacho
#
# File Description:
# Script to convert NCBI C toolkit command line program and arguments into
# NCBI C++ toolkit command line program and arguments for the BLAST suite of
# programs
#
# ===========================================================================
use strict;
use warnings;
use Getopt::Long qw(:config no_ignore_case bundling no_auto_abbrev);
use Pod::Usage;
use constant DEBUG => 0;
# Default PATH where binaries will be found
use constant DEFAULT_PATH => "/usr/bin";
pod2usage({-exitval => 1, -verbose => 2}) if (@ARGV == 0);
my $application = shift;
my $print_only = "0"; # Determines whether script prints or runs the command
# This array will contain file names to delete that are created with bl2seq's
# -A option
my @files2delete;
my $cmd;
if ($application eq "blastall") {
$cmd = &handle_blastall(\$print_only);
} elsif ($application eq "megablast") {
$cmd = &handle_megablast(\$print_only);
} elsif ($application eq "blastpgp") {
$cmd = &handle_blastpgp(\$print_only);
} elsif ($application eq "bl2seq") {
$cmd = &handle_bl2seq(\$print_only);
} elsif ($application eq "rpsblast") {
$cmd = &handle_rpsblast(\$print_only);
} elsif ($application eq "fastacmd") {
$cmd = &handle_fastacmd(\$print_only);
} elsif ($application eq "formatdb") {
$cmd = &handle_formatdb(\$print_only);
} elsif ($application eq "seedtop") {
$cmd = &handle_seedtop(\$print_only);
} elsif ($application =~ /version/) {
my $revision = '$Revision: 195935 $';
$revision =~ s/\$Revision: | \$//g;
print "$0 version $revision\n";
goto CLEAN_UP;
} elsif ($application =~ /help/) {
pod2usage({-exitval => 1, -verbose => 2});
} else {
die "Application: '$application' is not supported\n";
}
if ($print_only) {
print "$cmd\n";
} else {
print STDERR "$cmd\n" if (DEBUG);
my $rv = system($cmd);
unless ($rv == 0) {
die "Program failed, try executing the command manually.\n";
}
}
CLEAN_UP:
unlink foreach (@files2delete);
# Only add quotation marks in case there are spaces in the database argument
sub create_db_argument($)
{
my $arg = shift;
my $retval = "-db ";
$retval .= ( ($arg =~ /\s/) ? "\"$arg\" " : "$arg ");
return $retval;
}
# Converts floating point numbers to integers
sub convert_float_to_int($)
{
my $float_arg = shift;
my $retval = 0;
if ($float_arg =~ /(\d+)e([+-])(\d+)/) {
$retval = $1;
if ($2 eq "+") {
$retval *= 10**$3
} else {
$retval /= 10**$3
}
} else {
$retval = int($float_arg);
}
return $retval;
}
# Add the .exe extension for binaries if necessary on windows
sub add_exe_extension()
{
return ($^O =~ /mswin|cygwin/i) ? ".exe " : " ";
}
sub convert_sequence_locations($$)
{
my $arg = shift;
my $target = shift;
my $retval;
if (defined $arg) {
if ($target eq "query") {
$retval .= "-query_loc ";
} elsif ($target eq "range") {
$retval .= "-range ";
} else {
$retval .= "-subject_loc ";
}
my @fields = split(/[ ;,]/, $arg);
$retval .= "$fields[0]-$fields[1] ";
}
return $retval;
}
sub convert_filter_string($$)
{
my $filter_string = shift;
my $program = shift;
#print STDERR "Parsing '$filter_string'\n";
if ($filter_string =~ /F/) {
if ($program eq "blastp" or $program eq "tblastn" or
$program eq "blastx" or $program eq "tblastx") {
return "-seg no ";
} else {
return "-dust no ";
}
}
my $retval = "";
if ($filter_string =~ /S (\d+) (\S+) (\S+)/) {
$retval .= "-seg '$1 $2 $3' ";
}
if ($filter_string =~ /D (\d+) (\d+) (\d+)/) {
$retval .= "-dust '$1 $2 $3' ";
}
if ($filter_string =~ /R -d (\S+)/) {
$retval .= "-filtering_db $1 ";
} elsif ($filter_string =~ /R\s*;/) {
$retval .= "-filtering_db repeat/repeat_9606 ";
}
if ($filter_string =~ /L|T|S|D/ and not ($retval =~ /seg|dust/)) {
if ($program eq "blastp" or $program eq "tblastn" or
$program eq "blastx") {
$retval .= "-seg yes ";
} else {
$retval .= "-dust yes ";
}
}
if ($filter_string =~ /m/) {
$retval .= "-soft_masking true ";
}
#print STDERR "returning '$retval'\n";
return $retval;
}
sub convert_strand($)
{
my $old_strand_arg = shift;
my $retval = "-strand ";
if ($old_strand_arg == 1) {
$retval .= "plus ";
} elsif ($old_strand_arg == 2) {
$retval .= "minus ";
} else {
$retval .= "both ";
}
return $retval;
}
# Handle the conversion from blastall arguments to the corresponding C++
# binaries
sub handle_blastall($)
{
my $print_only = shift;
my $path = DEFAULT_PATH;
my ($opt_A, $opt_B, $opt_C, $opt_D, $opt_E, $opt_F, $opt_G, $opt_I, $opt_J,
$opt_K, $opt_L, $opt_M, $opt_O, $opt_P, $opt_Q, $opt_R, $opt_S, $opt_T,
$opt_U, $opt_V, $opt_W, $opt_X, $opt_Y, $opt_Z, $opt_a, $opt_b, $opt_d,
$opt_e, $opt_f, $opt_g, $opt_i, $opt_l, $opt_m, $opt_n, $opt_o, $opt_p,
$opt_q, $opt_r, $opt_s, $opt_t, $opt_v, $opt_w, $opt_y, $opt_z);
GetOptions("<>" => sub { $application = shift; },
"print_only!" => $print_only,
"path=s" => \$path,
"A=i" => \$opt_A,
"B=i" => \$opt_B, # not handled, not applicable
"C=s" => \$opt_C,
"D=i" => \$opt_D,
"E=i" => \$opt_E,
"F=s" => \$opt_F,
"G=i" => \$opt_G,
"I:s" => \$opt_I,
"J:s" => \$opt_J,
"K=i" => \$opt_K,
"L=s" => \$opt_L,
"M=s" => \$opt_M,
"O=s" => \$opt_O,
"P=i" => \$opt_P,
"Q=i" => \$opt_Q,
"R=s" => \$opt_R,
"S=i" => \$opt_S,
"T:s" => \$opt_T,
"U:s" => \$opt_U,
"V:s" => \$opt_V, # not handled, not applicable
"W=i" => \$opt_W,
"X=i" => \$opt_X,
"Y=f" => \$opt_Y,
"Z=i" => \$opt_Z,
"a=i" => \$opt_a,
"b=i" => \$opt_b,
"d=s" => \$opt_d,
"e=f" => \$opt_e,
"f=i" => \$opt_f,
"g:s" => \$opt_g,
"i=s" => \$opt_i,
"l=s" => \$opt_l,
"m=i" => \$opt_m,
"n:s" => \$opt_n,
"o=s" => \$opt_o,
"p=s" => \$opt_p,
"q=i" => \$opt_q,
"r=i" => \$opt_r,
"s:s" => \$opt_s,
"t=i" => \$opt_t,
"v=i" => \$opt_v,
"w=i" => \$opt_w,
"y=f" => \$opt_y,
"z=f" => \$opt_z,
);
unless (defined $opt_p) {
die "-p must be provided\n";
}
my $retval = $path;
if (defined $opt_p) {
if (defined $opt_R) {
$retval .= "/tblastn";
$retval .= &add_exe_extension();
$retval .= "-in_pssm $opt_R ";
} elsif (defined $opt_n and $opt_n =~ /t/i) {
$retval .= "/blastn";
$retval .= &add_exe_extension();
$retval .= "-task megablast ";
} else {
$retval .= "/$opt_p";
$retval .= &add_exe_extension();
$retval .= "-task blastn " if ($opt_p eq "blastn");
}
}
$retval .= &create_db_argument($opt_d) if (defined $opt_d);
unless (($retval =~ /\/tblastn/) and defined $opt_R) {
$retval .= "-query $opt_i " if (defined $opt_i);
}
$retval .= "-gilist $opt_l " if (defined $opt_l);
$retval .= "-dbsize $opt_z " if (defined $opt_z);
$retval .= "-matrix $opt_M " if (defined $opt_M);
$retval .= "-evalue $opt_e " if (defined $opt_e);
$retval .= "-gapopen $opt_G " if (defined $opt_G);
$retval .= "-gapextend $opt_E " if (defined $opt_E);
$retval .= "-xdrop_ungap $opt_y " if (defined $opt_y);
$retval .= "-xdrop_gap $opt_X " if (defined $opt_X);
$retval .= "-xdrop_gap_final $opt_Z " if (defined $opt_Z);
$retval .= "-num_threads $opt_a " if (defined $opt_a);
if (defined $opt_A) {
if (defined $opt_P and $opt_P ne "0") {
print STDERR "Warning: ignoring -P because window size is set\n";
}
$retval .= "-window_size $opt_A "
}
if (defined $opt_P and $opt_P eq "1" and (not defined $opt_A)) {
$retval .= "-window_size 0 ";
}
$retval .= "-word_size $opt_W " if (defined $opt_W);
if (defined $opt_Y) {
$retval .= "-searchsp " . &convert_float_to_int($opt_Y) . " ";
}
if (defined $opt_f) {
unless ($opt_p eq "blastn") {
$retval .= "-min_word_score $opt_f "
} else {
print STDERR "Warning: -f is not supported for blastn\n";
}
}
if (defined $opt_I and (length($opt_I) == 0 or $opt_I =~ /t/i)) {
$retval .= "-show_gis ";
}
$retval .= "-num_descriptions $opt_v " if (defined $opt_v);
$retval .= "-num_alignments $opt_b " if (defined $opt_b);
$retval .= "-query_gencode $opt_Q " if (defined $opt_Q);
$retval .= "-db_gencode $opt_D " if (defined $opt_D);
$retval .= "-penalty $opt_q " if (defined $opt_q);
$retval .= "-reward $opt_r " if (defined $opt_r);
$retval .= "-culling_limit $opt_K " if (defined $opt_K);
$retval .= "-max_intron_length $opt_t " if (defined $opt_t);
$retval .= "-frame_shift_penalty $opt_w " if (defined $opt_w);
$retval .= "-comp_based_stats $opt_C " if (defined $opt_C);
$retval .= "-out $opt_o " if (defined $opt_o);
if (defined $opt_m) {
if ($opt_m == 5 or $opt_m == 6) {
print STDERR "Warning: -m5 or -m6 formatting options ";
print STDERR "are not supported!\n";
}
$opt_m -= 2 if ($opt_m >= 7);
$retval .= "-outfmt $opt_m "
}
if (defined $opt_O) {
unless ($retval =~ s/-out \S+ /-out $opt_O /) {
$retval .= "-out $opt_O ";
}
unless ($retval =~ s/-outfmt \d+/-outfmt 8/) {
$retval .= "-outfmt 8 ";
} else {
print STDERR "Warning: overriding output format\n";
}
}
if (defined $opt_T and (length($opt_T) == 0 or $opt_T =~ /t/i)) {
$retval .= "-html "
}
$retval .= &convert_sequence_locations($opt_L, "query") if ($opt_L);
if (defined $opt_U and (length($opt_U) == 0 or $opt_U =~ /t/i)) {
$retval .= "-lcase_masking ";
}
if (defined $opt_g and $opt_g =~ /f/i) {
$retval .= "-ungapped ";
}
if (defined $opt_J and (length($opt_J) == 0 or $opt_J =~ /t/i)) {
$retval .= "-parse_deflines ";
}
$retval .= &convert_strand($opt_S) if (defined $opt_S and not
($opt_p ne "blastp" or
$opt_p ne "tblastn"));
if (defined $opt_s and (length($opt_s) == 0 or $opt_s =~ /t/i)) {
$retval .= "-use_sw_tback ";
}
if (defined $opt_F) {
$retval .= &convert_filter_string($opt_F, $opt_p);
} elsif (not defined $opt_F and $opt_p eq "blastp") {
$retval .= &convert_filter_string("T", $opt_p);
}
return $retval;
}
sub handle_seedtop($)
{
my $print_only = shift;
my $path = DEFAULT_PATH;
my ($opt_C, $opt_D, $opt_E, $opt_F, $opt_G, $opt_I, $opt_J, $opt_K, $opt_M,
$opt_O, $opt_S, $opt_X, $opt_d, $opt_e, $opt_f, $opt_i, $opt_k, $opt_o,
$opt_p, $opt_q, $opt_r);
GetOptions("<>" => sub { $application = shift; },
"print_only!" => $print_only,
"path=s" => \$path,
"C=i" => \$opt_C,
"D=i" => \$opt_D,
"E=i" => \$opt_E,
"F:s" => \$opt_F,
"G=i" => \$opt_G,
"I:s" => \$opt_I,
"J:s" => \$opt_J,
"K=i" => \$opt_K,
"M=s" => \$opt_M,
"O=s" => \$opt_O,
"S=i" => \$opt_S,
"X=i" => \$opt_X,
"d=s" => \$opt_d,
"e=f" => \$opt_e,
"f:s" => \$opt_f,
"i=s" => \$opt_i,
"k=s" => \$opt_k,
"o=s" => \$opt_o,
"p=s" => \$opt_p,
"q=i" => \$opt_q,
"r=i" => \$opt_r
);
my $retval = $path;
$retval .= "/psiblast";
$retval .= &add_exe_extension();
$retval .= "-query $opt_i " if (defined $opt_i);
$retval .= "-phi_pattern $opt_k " if (defined $opt_k);
$retval .= &create_db_argument($opt_d) if (defined $opt_d);
$retval .= "-gapopen $opt_G " if (defined $opt_G);
$retval .= "-gapextend $opt_E " if (defined $opt_E);
$retval .= "-out $opt_o " if (defined $opt_o);
if (defined $opt_O) {
unless ($retval =~ s/-out \S+ /-out $opt_O /) {
$retval .= "-out $opt_O ";
}
unless ($retval =~ s/-outfmt \d+/-outfmt 8/) {
$retval .= "-outfmt 8 ";
} else {
print STDERR "Warning: overriding output format\n";
}
}
if (defined $opt_I and (length($opt_I) == 0 or $opt_I =~ /t/i)) {
$retval .= "-show_gis ";
}
if (defined $opt_J and (length($opt_J) == 0 or $opt_J =~ /t/i)) {
$retval .= "-parse_deflines ";
}
$retval .= "-xdrop_gap $opt_X " if (defined $opt_X);
$retval .= "-evalue $opt_e " if (defined $opt_e);
$retval .= "-matrix $opt_M " if (defined $opt_M);
my $query_is_protein = "1";
if (defined $opt_p) {
unless ($opt_p eq "patseedp") {
die "Only patseedp program is supported\n";
}
# Change query_is_protein if other programs are supported
} else {
die "Program must be specified\n";
}
if (defined $opt_F) {
$retval .= &convert_filter_string($opt_F,
($query_is_protein eq "1")
? "blastp" : "blastn");
}
# Unsupported options
if (defined $opt_D) {
print STDERR "Warning: -D option is not supported!\n";
}
if (defined $opt_S) {
print STDERR "Warning: -S option is not supported!\n";
}
if (defined $opt_C) {
print STDERR "Warning: -C option is not supported!\n";
}
if (defined $opt_q) {
print STDERR "Warning: -q option is not supported!\n";
}
if (defined $opt_r) {
print STDERR "Warning: -r option is not supported!\n";
}
if (defined $opt_f) {
print STDERR "Warning: -f option is not supported!\n";
}
if (defined $opt_K) {
print STDERR "Warning: -K option is not supported!\n";
}
return $retval;
}
sub handle_megablast($)
{
my $print_only = shift;
my $path = DEFAULT_PATH;
my ($opt_A, $opt_D, $opt_E, $opt_F, $opt_G, $opt_H, $opt_I, $opt_J,
$opt_L, $opt_M, $opt_N, $opt_O, $opt_P, $opt_Q, $opt_R, $opt_S,
$opt_T, $opt_U, $opt_V, $opt_W, $opt_X, $opt_Y, $opt_Z, $opt_a,
$opt_b, $opt_d, $opt_e, $opt_f, $opt_g, $opt_i, $opt_l, $opt_m,
$opt_n, $opt_o, $opt_p, $opt_q, $opt_r, $opt_s, $opt_t, $opt_v,
$opt_y, $opt_z);
GetOptions("<>" => sub { $application = shift; },
"print_only!" => $print_only,
"path=s" => \$path,
"A=i" => \$opt_A,
"D=i" => \$opt_D,
"E=i" => \$opt_E,
"F=s" => \$opt_F,
"G=i" => \$opt_G,
"H=i" => \$opt_H,
"I:s" => \$opt_I,
"J:s" => \$opt_J,
"L=s" => \$opt_L,
"M=i" => \$opt_M,
"N=i" => \$opt_N,
"O=s" => \$opt_O,
"P=i" => \$opt_P, # no equivalent in new engine
"Q=s" => \$opt_Q,
"R:s" => \$opt_R,
"S=i" => \$opt_S,
"T:s" => \$opt_T,
"U:s" => \$opt_U,
"V:s" => \$opt_V, # not handled, not applicable
"W=i" => \$opt_W,
"X=i" => \$opt_X,
"Y=f" => \$opt_Y,
"Z=i" => \$opt_Z,
"a=i" => \$opt_a,
"b=i" => \$opt_b,
"d=s" => \$opt_d,
"e=f" => \$opt_e,
"f:s" => \$opt_f,
"g:s" => \$opt_g,
"i=s" => \$opt_i,
"l=s" => \$opt_l,
"m=i" => \$opt_m,
"n:s" => \$opt_n,
"o=s" => \$opt_o,
"p=f" => \$opt_p,
"q=i" => \$opt_q,
"r=i" => \$opt_r,
"s=i" => \$opt_s,
"t=i" => \$opt_t,
"v=i" => \$opt_v,
"y=i" => \$opt_y,
"z=f" => \$opt_z
);
my $retval = $path;
$retval .= "/blastn";
$retval .= &add_exe_extension();
$retval .= "-query $opt_i " if (defined $opt_i);
$retval .= &create_db_argument($opt_d) if (defined $opt_d);
$retval .= "-evalue $opt_e " if (defined $opt_e);
$retval .= "-xdrop_gap $opt_X " if (defined $opt_X);
$retval .= "-gilist $opt_l " if (defined $opt_l);
$retval .= "-penalty $opt_q " if (defined $opt_q);
$retval .= "-reward $opt_r " if (defined $opt_r);
$retval .= "-gapopen $opt_G " if (defined $opt_G);
$retval .= "-gapextend $opt_E " if (defined $opt_E);
$retval .= "-out $opt_o " if (defined $opt_o);
if (defined $opt_m) {
if ($opt_m == 5 or $opt_m == 6) {
print STDERR "Warning: -m5 or -m6 formatting options ";
print STDERR "are not supported!\n";
}
$opt_m -= 2 if ($opt_m >= 7);
$retval .= "-outfmt $opt_m "
}
if (defined $opt_O) {
unless ($retval =~ s/-out \S+ /-out $opt_O /) {
$retval .= "-out $opt_O ";
}
unless ($retval =~ s/-outfmt \d+/-outfmt 8/) {
$retval .= "-outfmt 8 ";
} else {
print STDERR "Warning: overriding output format\n";
}
}
if (defined $opt_T and (length($opt_T) == 0 or $opt_T =~ /t/i)) {
$retval .= "-html "
}
$retval .= "-num_descriptions $opt_v " if (defined $opt_v);
$retval .= "-num_alignments $opt_b " if (defined $opt_b);
$retval .= "-num_threads $opt_a " if (defined $opt_a);
$retval .= "-word_size $opt_W " if (defined $opt_W);
$retval .= "-dbsize $opt_z " if (defined $opt_z);
if (defined $opt_Y) {
$retval .= "-searchsp " . &convert_float_to_int($opt_Y) . " ";
}
$retval .= "-xdrop_ungap $opt_y " if (defined $opt_y);
$retval .= "-xdrop_gap_final $opt_Z " if (defined $opt_Z);
if (defined $opt_t) {
$retval .= "-template_length $opt_t ";
# Set the template type to the default value in megablast if not
# provided, as blastn requires it
$opt_N = 0 unless (defined $opt_N);
}
$retval .= "-window_size $opt_A " if (defined $opt_A);
if (defined $opt_N) {
$retval .= "-template_type coding " if ($opt_N == 0);
$retval .= "-template_type optimal " if ($opt_N == 1);
$retval .= "-template_type coding_and_optimal " if ($opt_N == 2);
}
if (defined $opt_F) {
$retval .= &convert_filter_string($opt_F, "blastn");
}
if (defined $opt_J and (length($opt_J) == 0 or $opt_J =~ /t/i)) {
$retval .= "-parse_deflines ";
}
$retval .= "-perc_identity $opt_p " if (defined $opt_p);
$retval .= "-min_raw_gapped_score $opt_s " if (defined $opt_s);
$retval .= &convert_strand($opt_S) if (defined $opt_S);
$retval .= &convert_sequence_locations($opt_L, "query") if ($opt_L);
if (defined $opt_U and (length($opt_U) == 0 or $opt_U =~ /t/i)) {
$retval .= "-lcase_masking ";
}
if (defined $opt_n and (length($opt_n) == 0 or $opt_n =~ /t/i)) {
$retval .= "-no_greedy ";
}
# Unsupported options
# This option can be safely ignored
#if (defined $opt_M) {
# print STDERR "Warning: -M option is ignored\n";
#}
my $tab_with_acc =
"-outfmt \"7 qacc sseqid pident length mismatch gapopen qstart qend " .
"sstart send evalue bitscore\" ";
# Here are some combinations of options and their equivalent conversion to
# the -outfmt option:
# NOTE: only in the last case we use sgi as the user explicitely requests
# the GIs to be shown (via -I), thus we assume the database/subjects will
# have GIs. We don't do the same for accessions, because if these are not
# available, an ordinal ID gets printed.
# -J -D3 -R -fF = -outfmt "7 qacc sseqid pident length mismatch gapopen
# qstart qend sstart send evalue bitscore"
# -J -D3 -R -fT = -outfmt "7 qseqid sseqid pident length mismatch gapopen
# qstart qend sstart send evalue bitscore"
# -J -D3 -R -fT -I = -outfmt "7 qgi sgi pident length mismatch gapopen
# qstart qend sstart send evalue bitscore"
if (defined $opt_D) {
if ($opt_D == 3) { # tabular output
unless ($retval =~ s/-outfmt \d+/$tab_with_acc/) {
$retval .= "$tab_with_acc ";
} else {
print STDERR "Warning: overriding output format\n";
}
} elsif ($opt_D == 2) { # traditional BLAST output
unless ($retval =~ s/-outfmt \d+/-outfmt 0/) {
$retval .= "-outfmt 0 ";
} else {
print STDERR "Warning: overriding output format\n";
}
} elsif ($opt_D == 4) { # text ASN.1
unless ($retval =~ s/-outfmt \d+/-outfmt 8/) {
$retval .= "-outfmt 8 ";
} else {
print STDERR "Warning: overriding output format\n";
}
} elsif ($opt_D == 5) { # binary ASN.1
unless ($retval =~ s/-outfmt \d+/-outfmt 9/) {
$retval .= "-outfmt 9 ";
} else {
print STDERR "Warning: overriding output format\n";
}
} else {
print STDERR "Warning: -D option with value $opt_D is not " .
"supported!\n";
}
}
if (defined $opt_I and (length($opt_I) == 0 or $opt_I =~ /t/i)) {
$retval .= "-show_gis ";
$retval =~ s/qacc/qgi/;
$retval =~ s/sseqid/sgi/;
}
# -fF is the default, if -f or -fT is specified, we assume that's what's
# desired and we apply a modification to the previously set output format
# (we can safely assume this b/c -f only works with -D3)
if (defined $opt_f and (length($opt_f) == 0 or $opt_f =~ /t/i)) {
$retval =~ s/qacc/qseqid/;
}
if (defined $opt_R and not ($retval =~ /-outfmt.*7/)) {
print STDERR "Warning: -R option is deprecated, please rely on the ".
"application's exit code to determine its success or failure.\n" .
"0 means success, non-zero means failure\n";
}
# Deprecated options
if (defined $opt_g and $opt_g =~ /f/i) {
print STDERR "Warning: -g option is not supported!\n";
}
if (defined $opt_H) {
print STDERR "Warning -H option is not supported!\n";
}
if (defined $opt_Q) {
print STDERR "Warning: -Q option is deprecated\n";
}
if (defined $opt_P) {
print STDERR "Warning: -P option is deprecated\n";
}
return $retval;
}
sub handle_blastpgp($)
{
my $print_only = shift;
my $path = DEFAULT_PATH;
my ($opt_A, $opt_B, $opt_C, $opt_E, $opt_F, $opt_G, $opt_H, $opt_I,
$opt_J, $opt_K, $opt_L, $opt_M, $opt_N, $opt_O, $opt_P, $opt_Q,
$opt_R, $opt_S, $opt_T, $opt_U, $opt_W, $opt_X, $opt_Y, $opt_Z,
$opt_a, $opt_b, $opt_c, $opt_d, $opt_e, $opt_f, $opt_h, $opt_i,
$opt_j, $opt_k, $opt_l, $opt_m, $opt_o, $opt_p, $opt_q, $opt_s,
$opt_t, $opt_u, $opt_v, $opt_y, $opt_z);
GetOptions("<>" => sub { $application = shift; },
"print_only!" => $print_only,
"path=s" => \$path,
"A=i" => \$opt_A,
"B=s" => \$opt_B,
"C=s" => \$opt_C,
"E=i" => \$opt_E,
"F=s" => \$opt_F,
"G=i" => \$opt_G,
"H=i" => \$opt_H,
"I:s" => \$opt_I,
"J:s" => \$opt_J,
"K=i" => \$opt_K,
"L=i" => \$opt_L,
"M=s" => \$opt_M,
"N=f" => \$opt_N,
"O=s" => \$opt_O,
"P=i" => \$opt_P,
"Q=s" => \$opt_Q,
"R=s" => \$opt_R,
"S=i" => \$opt_S,
"T:s" => \$opt_T,
"U:s" => \$opt_U,
"W=i" => \$opt_W,
"X=i" => \$opt_X,
"Y=f" => \$opt_Y,
"Z=i" => \$opt_Z,
"a=i" => \$opt_a,
"b=i" => \$opt_b,
"c=i" => \$opt_c,
"d=s" => \$opt_d,
"e=f" => \$opt_e,
"f=i" => \$opt_f,
"h=f" => \$opt_h,
"i=s" => \$opt_i,
"j=i" => \$opt_j,
"k=s" => \$opt_k,
"l=s" => \$opt_l,
"m=i" => \$opt_m,
"o=s" => \$opt_o,
"p=s" => \$opt_p,
"q=i" => \$opt_q,
"s:s" => \$opt_s,
"t=s" => \$opt_t,
"u=i" => \$opt_u,
"v=i" => \$opt_v,
"y=f" => \$opt_y,
"z=f" => \$opt_z
);
my $retval = $path . "/psiblast";
$retval .= &add_exe_extension();
my $query_is_protein = "1";
if (defined $opt_p and not ($opt_p ne "blastpgp" or
$opt_p ne "patseedp")) {
die "Program '$opt_p' not implemented\n";
}
$retval .= &create_db_argument($opt_d) if (defined $opt_d);
$retval .= "-query $opt_i " if (defined $opt_i);
$retval .= "-gilist $opt_l " if (defined $opt_l);
$retval .= "-gap_trigger $opt_N " if (defined $opt_N);
$retval .= "-matrix $opt_M " if (defined $opt_M);
$retval .= "-num_iterations $opt_j " if (defined $opt_j);
$retval .= "-min_word_score $opt_f " if (defined $opt_f);
$retval .= "-evalue $opt_e " if (defined $opt_e);
$retval .= "-gapopen $opt_G " if (defined $opt_G);
$retval .= "-gapextend $opt_E " if (defined $opt_E);
$retval .= "-num_threads $opt_a " if (defined $opt_a);
$retval .= "-dbsize $opt_z " if (defined $opt_z);
if (defined $opt_Y) {
$retval .= "-searchsp " . &convert_float_to_int($opt_Y) . " ";
}
$retval .= "-pseudocount $opt_c " if (defined $opt_c);
$retval .= "-inclusion_ethresh $opt_h " if (defined $opt_h);
if (defined $opt_A) {
if (defined $opt_P and $opt_P ne "0") {
print STDERR "Warning: ignoring -P because window size is set\n";
}
$retval .= "-window_size $opt_A "
}
if (defined $opt_P and $opt_P eq "1" and (not defined $opt_A)) {
$retval .= "-window_size 0 ";
}
$retval .= "-word_size $opt_W " if (defined $opt_W);
$retval .= "-xdrop_ungap $opt_y " if (defined $opt_y);
$retval .= "-xdrop_gap $opt_X " if (defined $opt_X);
$retval .= "-xdrop_gap_final $opt_Z " if (defined $opt_Z);
$retval .= "-num_descriptions $opt_v " if (defined $opt_v);
$retval .= "-num_alignments $opt_b " if (defined $opt_b);
$retval .= "-culling_limit $opt_K " if (defined $opt_K);
$retval .= "-comp_based_stats $opt_t " if (defined $opt_t);
$retval .= "-phi_pattern $opt_k " if (defined $opt_k);
$retval .= "-out $opt_o " if (defined $opt_o);
$retval .= "-out_ascii_pssm $opt_Q " if (defined $opt_Q);
$retval .= "-in_msa $opt_B " if (defined $opt_B);
if (defined $opt_m) {
if ($opt_m == 5 or $opt_m == 6) {
print STDERR "Warning: -m5 or -m6 formatting options ";
print STDERR "are not supported!\n";
}
$opt_m -= 2 if ($opt_m >= 7);
$retval .= "-outfmt $opt_m "
}
if (defined $opt_O) {
unless ($retval =~ s/-out \S+ /-out $opt_O /) {
$retval .= "-out $opt_O ";
}
unless ($retval =~ s/-outfmt \d+/-outfmt 8/) {
$retval .= "-outfmt 8 ";
} else {
print STDERR "Warning: overriding output format\n";
}
}
if (defined $opt_T and (length($opt_T) == 0 or $opt_T =~ /t/i)) {
$retval .= "-html "
}
if (defined $opt_I and (length($opt_I) == 0 or $opt_I =~ /t/i)) {
$retval .= "-show_gis ";
}
if (defined $opt_J and (length($opt_J) == 0 or $opt_J =~ /t/i)) {
$retval .= "-parse_deflines ";
}
if (defined $opt_s and (length($opt_s) == 0 or $opt_s =~ /t/i)) {
$retval .= "-use_sw_tback ";
}
if (defined $opt_U and (length($opt_U) == 0 or $opt_U =~ /t/i)) {
$retval .= "-lcase_masking ";
}
if (defined $opt_F) {
$retval .= &convert_filter_string($opt_F,
($query_is_protein eq "1")
? "blastp" : "blastn");
}
my $location = "";
$location .= $opt_S if (defined $opt_S);
if (defined $opt_H) {
if ($location eq "") {
$location = "0,$opt_H";
} else {
$location .= ",$opt_H";
}
}
if ($location ne "") {
$location .= ",-1" unless (defined $opt_H);
$retval .= &convert_sequence_locations($location, "query");
}
# Checkpoint file recovery
if (defined $opt_R) {
if (defined $opt_q and $opt_q ne "0") {
$retval .= "-in_pssm $opt_R "
} else {
die "ERROR: recovery from C toolkit checkpoint " .
"file format not supported\n";
}
}
# Checkpoint file saving
if (defined $opt_C) {
if (defined $opt_C and $opt_u ne "0") {
$retval .= "-out_pssm $opt_C "
} else {
die "ERROR: saving PSSM to C toolkit checkpoint " .
"file format not supported\n";
}
}
return $retval;
}
# Tested: all conversions should work
sub handle_bl2seq
{
use File::Temp qw(:POSIX); # for tmpnam
my $print_only = shift;
my $path = DEFAULT_PATH;
my ($opt_A, $opt_D, $opt_E, $opt_F, $opt_G, $opt_I, $opt_J, $opt_M,
$opt_S, $opt_T, $opt_U, $opt_V, $opt_W, $opt_X, $opt_Y, $opt_a,
$opt_d, $opt_e, $opt_g, $opt_i, $opt_j, $opt_m, $opt_o, $opt_p,
$opt_q, $opt_r, $opt_t);
GetOptions("<>" => sub { $application = shift; },
"print_only!" => $print_only,
"path=s" => \$path,
"A:s" => \$opt_A,
"D=i" => \$opt_D,
"E=i" => \$opt_E,
"F=s" => \$opt_F,
"G=i" => \$opt_G,
"I=s" => \$opt_I,
"J=s" => \$opt_J,
"M=s" => \$opt_M,
"S=i" => \$opt_S,
"T:s" => \$opt_T,
"U:s" => \$opt_U,
"V:s" => \$opt_V, # not handled, not applicable
"W=i" => \$opt_W,
"X=i" => \$opt_X,
"Y=f" => \$opt_Y,
"a=s" => \$opt_a,
"d=f" => \$opt_d,
"e=f" => \$opt_e,
"g:s" => \$opt_g,
"i=s" => \$opt_i,
"j=s" => \$opt_j,
"m:s" => \$opt_m,
"o=s" => \$opt_o,
"p=s" => \$opt_p,
"q=i" => \$opt_q,
"r=i" => \$opt_r,
"t=i" => \$opt_t
);
my $retval = $path;
unless (defined $opt_i and defined $opt_j) {
die "-i and -j are required in bl2seq\n";
}
if (defined $opt_p) {
$retval .= "/$opt_p";
$retval .= &add_exe_extension();
} else {
die "Program must be specified via the -p option\n";
}
unless (defined $opt_A) {
$retval .= "-query $opt_i " if (defined $opt_i);
$retval .= "-subject $opt_j " if (defined $opt_j);
} else {
# The -A option is not supported, so we create temporary files to
# simulate it (example input: bl2seq -i129295 -j104501 -pblastp -A)
my $query_fname = tmpnam();
open(Q, ">$query_fname") or die "Failed to open $query_fname: $!\n";
print Q "$opt_i" and close(Q);
push @files2delete, $query_fname;
my $subj_fname = tmpnam();
open(S, ">$subj_fname") or die "Failed to open $subj_fname: $!\n";
print S "$opt_j" and close(S);
push @files2delete, $subj_fname;
if (DEBUG) {
print STDERR "Created temp. files $query_fname and $subj_fname\n";
}
$retval .= "-query $query_fname -subject $subj_fname ";
if ($$print_only) {
print STDERR "Warning: arguments to -query and -subject must be ";
print STDERR "files containing the\narguments to bl2seq's -i and ";
print STDERR "-j arguments respectively.\n";
}
}
$retval .= "-out $opt_o " if (defined $opt_o);
if (defined $opt_a) {
unless ($retval =~ s/-out \S+ /-out $opt_a /) {
$retval .= "-out $opt_a ";
}
unless ($retval =~ s/-outfmt \d+/-outfmt 8/) {
$retval .= "-outfmt 8 ";
} else {
print STDERR "Warning: overriding output format\n";
}
}
if (defined $opt_D and $opt_D =~ /1/) {
if ($retval =~ s/-outfmt \d+/-outfmt 7/) {
print STDERR "Warning: overriding output format\n";
} else {
$retval .= "-outfmt 7 ";
}
}
if (defined $opt_T and (length($opt_T) == 0 or $opt_T =~ /t/i)) {
$retval .= "-html "
}
$retval .= "-evalue $opt_e " if (defined $opt_e);
$retval .= "-gapopen $opt_G " if (defined $opt_G);
$retval .= "-gapextend $opt_E " if (defined $opt_E);
$retval .= "-word_size $opt_W " if (defined $opt_W);
$retval .= "-matrix $opt_M " if (defined $opt_M);
$retval .= "-penalty $opt_q " if (defined $opt_q);
$retval .= "-reward $opt_r " if (defined $opt_r);
$retval .= &convert_strand($opt_S) if (defined $opt_S);
$retval .= "-max_intron_length $opt_t " if (defined $opt_t);
$retval .= "-dbsize $opt_d " if (defined $opt_d);
$retval .= "-xdrop_gap $opt_X " if (defined $opt_X);
if (defined $opt_Y) {
$retval .= "-searchsp " . &convert_float_to_int($opt_Y) . " ";
}
if (defined $opt_U and (length($opt_U) == 0 or $opt_U =~ /t/i)) {
$retval .= "-lcase_masking ";
}
if (defined $opt_m and (length($opt_m) == 0 or $opt_m =~ /t/i)) {
$retval .= "-task megablast ";
}
if (defined $opt_g and $opt_g =~ /f/i) {
$retval .= "-ungapped ";
}
$retval .= &convert_sequence_locations($opt_I, "query") if ($opt_I);
$retval .= &convert_sequence_locations($opt_J, "subject") if ($opt_J);
if (defined $opt_F) {
$retval .= &convert_filter_string($opt_F, $opt_p);
}
return $retval;
}
sub handle_rpsblast
{
my $print_only = shift;
my $path = DEFAULT_PATH;
my ($opt_F, $opt_I, $opt_J, $opt_L, $opt_N, $opt_O, $opt_P, $opt_T,
$opt_U, $opt_V, $opt_X, $opt_Y, $opt_Z, $opt_a, $opt_b, $opt_d,
$opt_e, $opt_i, $opt_l, $opt_m, $opt_o, $opt_p, $opt_v, $opt_y,
$opt_z);
GetOptions("<>" => sub { $application = shift; },
"print_only!" => $print_only,
"path=s" => \$path,
"F=s" => \$opt_F,
"I:s" => \$opt_I,
"J:s" => \$opt_J,
"L=s" => \$opt_L,
"N=f" => \$opt_N,
"O=s" => \$opt_O,
"P=i" => \$opt_P,
"T:s" => \$opt_T,
"U:s" => \$opt_U,
"V=s" => \$opt_V,
"X=i" => \$opt_X,
"Y=f" => \$opt_Y,
"Z=i" => \$opt_Z,
"a=i" => \$opt_a,
"b=i" => \$opt_b,
"d=s" => \$opt_d,
"e=f" => \$opt_e,
"i=s" => \$opt_i,
"l=s" => \$opt_l,
"m=i" => \$opt_m,
"o=s" => \$opt_o,
"p:s" => \$opt_p,
"v=i" => \$opt_v,
"y=f" => \$opt_y,
"z=f" => \$opt_z
);
my $retval = $path;
if (defined $opt_p and $opt_p =~ /f/i) {
$retval .= "/rpstblastn";
} else {
$retval .= "/rpsblast+";
}
$retval .= &add_exe_extension();
$retval .= "-query $opt_i " if (defined $opt_i);
$retval .= &create_db_argument($opt_d) if (defined $opt_d);
$retval .= "-evalue $opt_e " if (defined $opt_e);
$retval .= "-out $opt_o " if (defined $opt_o);
$retval .= "-xdrop_ungap $opt_y " if (defined $opt_y);
$retval .= "-xdrop_gap $opt_X " if (defined $opt_X);
$retval .= "-min_raw_gapped_score $opt_N " if (defined $opt_N);
$retval .= "-num_threads $opt_a " if (defined $opt_a);
$retval .= "-num_descriptions $opt_v " if (defined $opt_v);
$retval .= "-num_alignments $opt_b " if (defined $opt_b);
$retval .= "-dbsize $opt_z " if (defined $opt_z);
if (defined $opt_Y) {
$retval .= "-searchsp " . &convert_float_to_int($opt_Y) . " ";
}
$retval .= "-xdrop_gap_final $opt_Z " if (defined $opt_Z);
if (defined $opt_m) {
if ($opt_m == 5 or $opt_m == 6) {
print STDERR "Warning: -m5 or -m6 formatting options ";
print STDERR "are not supported!\n";
}
$opt_m -= 2 if ($opt_m >= 7);
$retval .= "-outfmt $opt_m "
}
if (defined $opt_O) {
unless ($retval =~ s/-out \S+ /-out $opt_O /) {
$retval .= "-out $opt_O ";
}
unless ($retval =~ s/-outfmt \d+/-outfmt 8/) {
$retval .= "-outfmt 8 ";
} else {
print STDERR "Warning: overriding output format\n";
}
}
if (defined $opt_T and (length($opt_T) == 0 or $opt_T =~ /t/i)) {
$retval .= "-html "
}
if (defined $opt_P and $opt_P eq "1") {
$retval .= "-window_size 0 ";
}
if (defined $opt_F) {
$retval .= &convert_filter_string($opt_F, "blastp");
}
if (defined $opt_I and (length($opt_I) == 0 or $opt_I =~ /t/i)) {
$retval .= "-show_gis ";
}
if (defined $opt_J and (length($opt_J) == 0 or $opt_J =~ /t/i)) {
$retval .= "-parse_deflines ";
}
if (defined $opt_U and (length($opt_U) == 0 or $opt_U =~ /t/i)) {
$retval .= "-lcase_masking ";
}
$retval .= &convert_sequence_locations($opt_L, "query") if ($opt_L);
return $retval;
}
sub handle_fastacmd
{
my $print_only = shift;
my $path = DEFAULT_PATH;
my ($opt_d, $opt_p, $opt_s, $opt_i, $opt_a, $opt_l, $opt_t, $opt_o,
$opt_c, $opt_D, $opt_L, $opt_S, $opt_T, $opt_I, $opt_P);
GetOptions("<>" => sub { $application = shift; },
"print_only!" => $print_only,
"path=s" => \$path,
"D=i" => \$opt_D,
"I:s" => \$opt_I,
"L=s" => \$opt_L,
"P=i" => \$opt_P,
"S=i" => \$opt_S,
"T:s" => \$opt_T,
"a:s" => \$opt_a,
"c:s" => \$opt_c,
"d=s" => \$opt_d,
"i=s" => \$opt_i,
"l=i" => \$opt_l,
"o=s" => \$opt_o,
"p=s" => \$opt_p,
"s=s" => \$opt_s,
"t:s" => \$opt_t
);
my $retval = $path . "/blastdbcmd";
$retval .= &add_exe_extension();
$retval .= &create_db_argument($opt_d) if (defined $opt_d);
if (defined $opt_p) {
$retval .= "-dbtype ";
if ($opt_p =~ /p/i) {
$retval .= "prot ";
} elsif ($opt_p =~ /f/i) {
$retval .= "nucl ";
} else {
$retval .= "guess ";
}
}
$retval .= "-entry $opt_s " if (defined $opt_s);
$retval .= "-entry_batch $opt_i " if (defined $opt_i);
$retval .= "-line_length $opt_l " if (defined $opt_l);
$retval .= "-out $opt_o " if (defined $opt_o);
$retval .= "-pig $opt_P " if (defined $opt_P);
if (defined $opt_D) {
$retval .= "-entry all -outfmt ";
if ($opt_D eq '1') {
$retval .= "\%f ";
} elsif ($opt_D eq '2') {
$retval .= "\%g ";
} elsif ($opt_D eq '3') {
$retval .= "\%a ";
} else {
die "Invalid argument to -D\n";
}
}
$retval .= &convert_sequence_locations($opt_L, "range") if ($opt_L);
$retval .= &convert_strand($opt_S) if (defined $opt_S);
if (defined $opt_T) {
#print STDERR "Warning: -T option is not supported, please use " .
# "the -outfmt option to blastdbcmd with \%T, \%L, or \%S as an " .
# "argument\n";
$retval .= "-outfmt \"NCBI Taxonomy id: \%T; Common name: \%L; ";
$retval .= "Scientific name: \%S\" ";
}
if (defined $opt_I and (length($opt_I) == 0 or $opt_I =~ /t/i)) {
$retval .= "-info ";
}
if (defined $opt_a and (length($opt_a) == 0 or $opt_a =~ /t/i)) {
$retval .= "-get_dups ";
}
if (defined $opt_t and (length($opt_t) == 0 or $opt_t =~ /t/i)) {
$retval .= "-target_only ";
}
if (defined $opt_c and (length($opt_c) == 0 or $opt_c =~ /t/i)) {
$retval .= "-ctrl_a ";
}
return $retval;
}
sub handle_formatdb
{
my $print_only = shift;
my $path = DEFAULT_PATH;
my ($opt_B, $opt_F, $opt_L, $opt_T, $opt_V, $opt_a, $opt_b, $opt_e, $opt_i,
$opt_l, $opt_n, $opt_o, $opt_p, $opt_s, $opt_t, $opt_v);
GetOptions("<>" => sub { $application = shift; },
"print_only!" => $print_only,
"path=s" => \$path,
"B=s" => \$opt_B,
"F=s" => \$opt_F,
"L=s" => \$opt_L,
"T=s" => \$opt_T,
"V:s" => \$opt_V,
"a:s" => \$opt_a,
"b:s" => \$opt_b,
"e:s" => \$opt_e,
"i=s" => \$opt_i,
"l=s" => \$opt_l,
"n=s" => \$opt_n,
"o:s" => \$opt_o,
"p:s" => \$opt_p,
"s:s" => \$opt_s,
"t=s" => \$opt_t,
"v=i" => \$opt_v
);
my $retval = $path;
if (defined $opt_L) {
$retval .= "/blastdb_aliastool";
die "-i is required\n" unless (defined $opt_i);
die "-F is required\n" unless (defined $opt_F);
} else {
$retval .= "/makeblastdb";
}
$retval .= &add_exe_extension();
if (defined $opt_B) {
die "-F option must be specified with -B\n" unless (defined $opt_F);
$retval = $path . "/blastdb_aliastool";
$retval .= &add_exe_extension();
$retval .= "-gi_file_in $opt_F -gi_file_out $opt_B";
return $retval;
}
$retval .= "-title \"$opt_t\" " if (defined $opt_t);
if (defined $opt_p) {
$retval .= "-dbtype ";
if ((length($opt_p) == 0 or $opt_p =~ /t/i)) {
$retval .= "prot ";
} else {
$retval .= "nucl ";
}
}
if ($retval =~ /blastdb_aliastool/) {
$retval .= "-out $opt_L " if (defined $opt_L);
if (defined $opt_i and not defined $opt_n) {
$retval .= &create_db_argument($opt_i);
}
# there's no -n in blastdb_aliastool, as we copy the argument value
# verbatim into the DBLIST field of the alias file, so we make
# formatdb's -n option tool override -i
$retval .= &create_db_argument($opt_n) if (defined $opt_n);
} else {
$retval .= "-out $opt_n " if (defined $opt_n);
$retval .= "-in $opt_i " if (defined $opt_i);
}
$retval .= "-gilist $opt_F " if (defined $opt_F);
$retval .= "-logfile $opt_l " if (defined $opt_l);
$retval .= "-taxid-map $opt_T " if (defined $opt_T);
if (defined $opt_o and (length($opt_o) == 0 or $opt_o =~ /t/i)) {
$retval .= "-parse_seqids ";
}
if (defined $opt_a) {
print STDERR "Warning: -a option is not supported\n";
}
if (defined $opt_b) {
print STDERR "Warning: -b option is not supported\n";
}
if (defined $opt_e) {
print STDERR "Warning: -e option is not supported\n";
}
if (defined $opt_s) {
print STDERR "Warning: -s option is not supported\n";
}
if (defined $opt_V) {
print STDERR "Warning: -V option is not supported\n";
}
if (defined $opt_v) {
print STDERR "Warning: -v option is not supported, please use " .
"the -max_file_sz option to makeblastdb\n";
}
return $retval;
}
__END__
=head1 NAME
B<legacy_blast.pl> - Convert BLAST command line invocations from NCBI C
toolkit's implementation to NCBI C++ toolkit's implementation.
=head1 SYNOPSIS
legacy_blast.pl <C toolkit command line program and arguments> [--print_only]
[--path /path/to/binaries]
legacy_blast.pl [--version]
legacy_blast.pl [--help]
=head1 OPTIONS
=over 2
=item B<--path>
Use the provided path as the location of the BLAST binaries to execute/print
(default: /usr/bin).
=item B<--print_only>
Print the equivalent command line option instead of running the command
(default: false).
=item B<--version>
Prints this script's version. Must be invoked as the first and only argument to
this script.
=back
=head1 DESCRIPTION
This script converts and runs the equivalent NCBI C toolkit command line BLAST
program and arguments provided to it (whenever possible) to NCBI C++ tookit
BLAST programs. Note that to specify options to this script they B<MUST> use 2
dashes to prefix the options B<AND> be listed at the end of the command line
invocation to convert.
=head1 EXIT CODES
This script returns 0 on success and a non-zero value on errors.
=head1 BUGS
Please report them to <blast-help@ncbi.nlm.nih.gov>
=head1 COPYRIGHT
See PUBLIC DOMAIN NOTICE included at the top of this script.
=cut
|