Skip to content

Commit

Permalink
Update and rename NOVOPlasty2.5.8.pl to NOVOPlasty2.5.9.pl
Browse files Browse the repository at this point in the history
  • Loading branch information
@ndierckx
ndierckx authored May 4, 2017
1 parent 80380ad commit 566f578
Showing 1 changed file with 91 additions and 5 deletions.
96 changes: 91 additions & 5 deletions NOVOPlasty2.5.8.pl → NOVOPlasty2.5.9.pl
View file
Original file line number Diff line number Diff line change
Expand Up @@ -341,12 +341,12 @@

print "\n\n-----------------------------------------------";
print "\nNOVOPlasty: The Organelle Assembler\n";
print "Version 2.5.8\n";
print "Version 2.5.9\n";
print "Author: Nicolas Dierckxsens, (c) 2015-2016\n";
print "-----------------------------------------------\n\n";
print OUTPUT4 "\n\n-----------------------------------------------";
print OUTPUT4 "\nNOVOPlasty: The Organelle Assembler\n";
print OUTPUT4 "Version 2.5.8\n";
print OUTPUT4 "Version 2.5.9\n";
print OUTPUT4 "Author: Nicolas Dierckxsens, (c) 2015-2016\n";
print OUTPUT4 "-----------------------------------------------\n\n";

Expand Down Expand Up @@ -1531,6 +1531,7 @@ sub correct
my $no_quality_score = substr $thirdLine, 0, 1;
my $type_of_file;
my $code_before_end = substr $firstLine, -2,1;
my $SRA = "";
if ($code_before_end eq "/" && $firstLine_reverse ne $firstLine)
{
$type_of_file = '-1';
Expand All @@ -1551,9 +1552,23 @@ sub correct
{
$type_of_file = -length($2)-1;
}
elsif($firstLine =~ m/.*\.(1)(\s(\d+)\s.*)$/ && $firstLine_reverse ne $firstLine)
elsif($firstLine =~ m/\S*\.(1)(\s(\d+)\s.*)$/ && $firstLine_reverse ne $firstLine)
{
$type_of_file = -length($2)-1;
my $test1 = $3;
if($fifthLine =~ m/\S*\.(1)(\s(\d+)(\s.*))$/ && $firstLine_reverse ne $firstLine)
{
my $test2 = $3;
if ($test2 eq $test1)
{
$type_of_file = -length($2)-1;
}
else
{
$type_of_file = -length($4);
$SRA = "yes";
}
}
print "TEST\n";
}
elsif($fifthLine =~ m/.*\.(1)(\s(.+)\s.+)$/ && $firstLine_reverse ne $firstLine)
{
Expand Down Expand Up @@ -1607,7 +1622,7 @@ sub correct

print OUTPUT4 "\n\n-----------------------------------------------";
print OUTPUT4 "\nNOVOPlasty: The Organelle Assembler\n";
print OUTPUT4 "Version 2.5.8\n";
print OUTPUT4 "Version 2.5.9\n";
print OUTPUT4 "Author: Nicolas Dierckxsens, (c) 2015-2016\n";
print OUTPUT4 "-----------------------------------------------\n\n";

Expand Down Expand Up @@ -1755,6 +1770,15 @@ sub correct
}
my $code2 = $code;
my $code_end = substr $code2, $type_of_file,1;
my $code0_SRA;

if ($SRA eq "yes")
{
my $code_SRA = substr $code2, 0, $type_of_file;
my @code_SRA = split / /, $code_SRA;
$code0_SRA = $code_SRA[0];
$code_end = substr $code0_SRA, -1, 1, "";
}

if ($type_of_file eq "identical")
{
Expand All @@ -1778,6 +1802,10 @@ sub correct
if ($code_end eq "1" && $out_of_memory ne "yes")
{
my $code0 = substr $code2, 0, $type_of_file;
if ($SRA eq "yes")
{
$code0 = $code0_SRA;
}

if ($type_of_file eq "identical")
{
Expand All @@ -1804,6 +1832,10 @@ sub correct
if ($code_end eq "2" )
{
my $code1 = substr $code2, 0, $type_of_file;
if ($SRA eq "yes")
{
$code1 = $code0_SRA;
}

if ($type_of_file eq "identical")
{
Expand Down Expand Up @@ -7197,6 +7229,19 @@ sub correct
$filter_before4_pair{$search} = $found_tmp;
$before4B{$search} = $found_tmp;
}
if ($save_reads eq "yes")
{
my $add_read = $search_tmp;
print OUTPUT10 ">".$add_read."\/1\n";
print OUTPUT11 ">".$add_read."\/2\n";
if (exists($hash{$add_read}))
{
my @add_read = split /,/,$hash{$add_read};
print OUTPUT10 $add_read[0]."\n";
print OUTPUT11 $add_read[1]."\n";
}
}

}
}
}
Expand Down Expand Up @@ -7337,6 +7382,19 @@ sub correct
my $found_rev2 = reverse($found_rev);
$repetitive_pair{$found_rev2} = $search_rev;
}
if ($save_reads eq "yes")
{
my $add_read = $search_tmp;
print OUTPUT10 ">".$add_read."\/1\n";
print OUTPUT11 ">".$add_read."\/2\n";
if (exists($hash{$add_read}))
{
my @add_read = split /,/,$hash{$add_read};
print OUTPUT10 $add_read[0]."\n";
print OUTPUT11 $add_read[1]."\n";
}
}

}
}
}
Expand Down Expand Up @@ -8952,6 +9010,7 @@ sub correct
$best_extension = "";
goto BACK;
}
$noforward{$id} = "stop";
}
}

Expand Down Expand Up @@ -9773,6 +9832,7 @@ sub correct
delete $yuyu_option{$id.'C'};
delete $yuyu_option{$id.'T'};
delete $yuyu_option{$id.'G'};
delete $before_shorter_skip{$id};
}
$use_regex = "";
if ($SNR_read ne "" && $last_chance eq "yes")
Expand Down Expand Up @@ -12084,6 +12144,18 @@ sub correct
}
$before4B{$search} = $found_reverse;
}
if ($save_reads eq "yes")
{
my $add_read = $search_tmp;
print OUTPUT10 ">".$add_read."\/1\n";
print OUTPUT11 ">".$add_read."\/2\n";
if (exists($hash{$add_read}))
{
my @add_read = split /,/,$hash{$add_read};
print OUTPUT10 $add_read[0]."\n";
print OUTPUT11 $add_read[1]."\n";
}
}
}
}
}
Expand Down Expand Up @@ -12207,6 +12279,19 @@ sub correct
$filter_before4_pair{$search} = $found_new;
$before4F{$search} = $found_new;
}
if ($save_reads eq "yes")
{
my $add_read = $search_tmp;
print OUTPUT10 ">".$add_read."\/1\n";
print OUTPUT11 ">".$add_read."\/2\n";
if (exists($hash{$add_read}))
{
my @add_read = split /,/,$hash{$add_read};
print OUTPUT10 $add_read[0]."\n";
print OUTPUT11 $add_read[1]."\n";
}
}

}
}
}
Expand Down Expand Up @@ -13739,6 +13824,7 @@ sub correct
delete $yuyu_option_back{$id.'C'};
delete $yuyu_option_back{$id.'T'};
delete $yuyu_option_back{$id.'G'};
delete $before_shorter_skip_back{$id};
}
if ($split eq "")
{
Expand Down

0 comments on commit 566f578

Please sign in to comment.