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fasta36 #1

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db01e4e
updated code to support fasta36, and added help function to show help
HassanAmr Dec 19, 2016
8ef4cad
keeping the code from the current wip version
HassanAmr Dec 19, 2016
a5f303f
fixing whitespace to be the same as the current version
HassanAmr Dec 19, 2016
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32 changes: 28 additions & 4 deletions targetfinder.pl
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
#!/usr/bin/perl
#!/usr/bin/env perl
use strict;
use warnings;
use File::Temp qw(tempfile);
Expand All @@ -19,7 +19,7 @@
}

# Smith-Waterman alignment programs (with threads)
my $fasta = "ssearch35_t";
my $fasta = "ssearch36";

# Does the executable $fasta exist?
my $exists = which($fasta);
Expand Down Expand Up @@ -240,7 +240,7 @@ sub fasta {
my $input = shift;
my $db = shift;
my @output;
open FASTA, "$fasta -n -H -Q -f -16 -r +15/-10 -g -10 -w 100 -W 25 -E 100000 -i -U -T $threads $input $db 1 2> /dev/null |";
open FASTA, "$fasta -n -H -Q -f -16 -r +15/-10 -g -10 -w 100 -W 25 -E 100000 -i -U $input $db 1 2> /dev/null |";
while (<FASTA>) {
print LOG $_ if (DEBUG);
push (@output, $_);
Expand Down Expand Up @@ -686,7 +686,7 @@ sub print_json {
########################################
sub var_check {
if ($opt{'h'}) {
var_error();
show_help();
}
if ($opt{'s'}) {
$sRNA = $opt{'s'};
Expand Down Expand Up @@ -749,6 +749,30 @@ sub var_error {
exit 1;
}

########################################
# Function: show_help
# Error message/instructions to print
########################################
sub show_help {
print "\n\n";
print "TargetFinder: Plant small RNA target prediction tool.\n\n";
print "Usage: targetfinder.pl -s <sequence> -d <target database> [options]\n\n";
print "Options: -s <str> Small RNA sequence (RNA or DNA, 5'->3')\n";
print " -d <file> Target sequence database file (FASTA-format)\n";
print " -q <str> Query sequence name (DEFAULT = 'query')\n";
print " -c <float> Prediction score cutoff value (DEFAULT = 4)\n";
print " -t <int> Threads for parallel Smith-Waterman searches (DEFAULT = 1)\n";
print " -p <str> Output format for small RNA-target pairs (DEFAULT = 'classic')\n";
print " Available options: 'classic' (Original TargetFinder base-pairing format)\n";
print " 'gff' (Generic Feature Format)\n";
print " 'json' (JavaScript Object Notation)\n";
print " 'table' (Tab-deliminated Format)\n";
print " -r Search reverse strand for targets?. Use this option if the database is genomic DNA.\n";
print " -h Print this menu\n";
print "\n\n";
exit 0;
}

################################################################################
# End subroutines
################################################################################
27 changes: 25 additions & 2 deletions targetfinder_threads.pl
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
#!/usr/bin/perl
#!/usr/bin/env perl
use strict;
use warnings;
use Getopt::Std;
Expand Down Expand Up @@ -112,7 +112,7 @@ sub targetfinder {
########################################
sub var_check {
if ($opt{'h'}) {
var_error();
show_help();
}
if ($opt{'f'}) {
$file = $opt{'f'};
Expand Down Expand Up @@ -174,6 +174,29 @@ sub var_error {
exit 1;
}

########################################
# Function: show_help
# Error message/instructions to print
########################################
sub show_help {
print "\n\n";
print "TargetFinder: Plant small RNA target prediction tool.\n\n";
print "Usage: targetfinder.pl -s <sequence> -d <target database> [options]\n\n";
print "Options: -s <str> Small RNA sequence (RNA or DNA, 5'->3')\n";
print " -d <file> Target sequence database file (FASTA-format)\n";
print " -q <str> Query sequence name (DEFAULT = 'query')\n";
print " -c <float> Prediction score cutoff value (DEFAULT = 4)\n";
print " -t <int> Threads for parallel Smith-Waterman searches (DEFAULT = 1)\n";
print " -p <str> Output format for small RNA-target pairs (DEFAULT = 'classic')\n";
print " Available options: 'classic' (Original TargetFinder base-pairing format)\n";
print " 'gff' (Generic Feature Format)\n";
print " 'json' (JavaScript Object Notation)\n";
print " 'table' (Tab-deliminated Format)\n";
print " -r Search reverse strand for targets?. Use this option if the database is genomic DNA.\n";
print " -h Print this menu\n";
print "\n\n";
exit 0;
}
################################################################################
# End subroutines
################################################################################