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Remove remaining references to $Bin .
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Thanks @DHatziioanou for reporting.
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@nsoranzo
nsoranzo committed Feb 9, 2016
1 parent 87d64d4 commit 2026946
Showing 1 changed file with 28 additions and 27 deletions.
55 changes: 28 additions & 27 deletions bin/ExtendOrFormatContigs.pl
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Original file line number Diff line number Diff line change
Expand Up @@ -24,11 +24,10 @@
my $min_base_ratio = $ARGV[7];
my $max_trim = $ARGV[8];
my $verbose = $ARGV[9];
my $minContigLength = $ARGV[11];
my $minContigLength = $ARGV[11];
my $libraryfile = $ARGV[12];
my $gaps = $ARGV[13];
my $threads = $ARGV[14];


my $log = $base_name . ".logfile.txt";
my $summaryfile = $base_name.".summaryfile.txt";
Expand All @@ -39,7 +38,7 @@
my ($bin);
if($extending == 1){

&ExtendContigs($base_name, $filecontig, $filenameOutExt, $Bin);
&ExtendContigs($base_name, $filecontig, $filenameOutExt);
print SUMFILE "\n" if($minContigLength > 0);
&FormatContigs() if($minContigLength > 0);
}else{
Expand All @@ -48,13 +47,13 @@

close SUMFILE;
close LOG;

mkpath('process_OK');
#--------------------------------------------------

###EXTEND CONTIGS WITH UNMAPPED READS
sub ExtendContigs{
my ($base_name, $filecontig, $filenameOutExt, $Bin) = @_;
my ($base_name, $filecontig, $filenameOutExt) = @_;
my ($seq);
#-------------------------------------------------NOW MAP SINGLE READS TO INITIAL CONTIGS FILE.
my $readfile = "reads/" . $filenameOutExt;
Expand All @@ -67,8 +66,8 @@ sub ExtendContigs{
#--------------------------------------------ASSEMBLY START

ASSEMBLY:
open(IN,$filecontig) || die "Can't open $filecontig -- fatal\n";
my ($exttig_count, $counter, $NCount, $orig_mer, $prevhead) = (0,0,0,0,'');
open(IN, $filecontig) || die "Can't open $filecontig -- fatal\n";
my ($exttig_count, $counter, $NCount, $orig_mer, $prevhead) = (0, 0, 0, 0, '');
while(<IN>){
s/\r\n/\n/;
chomp;
Expand All @@ -91,12 +90,12 @@ sub ExtendContigs{
my $reversetig = reverseComplement($seqrc); ### return to sequence, as inputted
if($leng > $orig_mer){ ### commented out: && $start_sequence ne $seqrc && $start_sequence ne $reversetig
my $cov = $total_bases / $leng;
printf TIG ">extcontig%i|size%i|read%i|cov%.2f|seed:$prevhead\n%s\n", ($counter,$leng,$reads_needed,$cov,$reversetig); #print contigs to file
printf TIG ">extcontig%i|size%i|read%i|cov%.2f|seed:$prevhead\n%s\n", ($counter, $leng, $reads_needed, $cov, $reversetig); #print contigs to file
$exttig_count++;
}else{
my $cov = $reads_needed = 0;
my $singlet_leng = length($start_sequence);
printf TIG ">contig%i|size%i|read%i|cov%.2f|seed:$prevhead\n%s\n", ($counter,$leng,$reads_needed,$cov,$reversetig); #print singlets to file
printf TIG ">contig%i|size%i|read%i|cov%.2f|seed:$prevhead\n%s\n", ($counter, $leng, $reads_needed, $cov, $reversetig); #print singlets to file
}
}
CounterPrint(++$counter);
Expand Down Expand Up @@ -124,8 +123,8 @@ sub ExtendContigs{
sub FormatContigs{
&printMessage("\n=>".getDate().": Storing contigs to format for scaffolding\n");
open (TIG, ">$contig") || die "Can't write to $contig -- fatal\n";
open(IN,$filecontig) || die "Can't open $filecontig -- fatal\n";
my ($counter, $seq, $prevhead, $step) = (0,'','', 100);
open(IN, $filecontig) || die "Can't open $filecontig -- fatal\n";
my ($counter, $seq, $prevhead, $step) = (0, '', '', 100);
while(<IN>){
s/\r\n/\n/;
chomp;
Expand All @@ -138,7 +137,7 @@ sub FormatContigs{
CounterPrint($counter);
$step = $step + 100;
}
printf TIG ">contig%i|size%i|read%i|cov%.2f|seed:$prevhead\n%s\n", ($counter,$length_seq,0,0.00,$seq);
printf TIG ">contig%i|size%i|read%i|cov%.2f|seed:$prevhead\n%s\n", ($counter, $length_seq, 0, 0.00, $seq);
}
$prevhead = $head;
$seq = '';
Expand All @@ -157,15 +156,15 @@ sub doExtension{
my ($direction, $orig_mer, $seq, $reads_needed, $total_bases, $min_overlap, $base_overlap, $min_base_ratio, $verbose, $tig_count, $max_trim) = @_;

my $previous = $seq;
my ($extended, $trim_ct) = (1,0);
my ($extended, $trim_ct) = (1, 0);

if($orig_mer > $MAX){$orig_mer=$MAX;} ### Deals with special cases where the seed sequences are different from the read set (and possibly very large) - goal here is not to increase sequence coverage of seed, but rather to extend it.

TRIM:
while($trim_ct <= $max_trim){
while($extended){

my ($pos,$current_reads,$current_bases,$span) = (0,0,0,"");
my ($pos, $current_reads, $current_bases, $span) = (0, 0, 0, "");

### Added 19March08
if(length($seq) >= $MAX){ # $seq is length of contig being extended -- if larger than largest read, make sure the largest read could align and all subsequent rds.
Expand All @@ -177,10 +176,10 @@ sub doExtension{
my $overhang = {};
my @overlapping_reads = ();
for (my $x=1;$x <= ($orig_mer * 2);$x++){
($overhang->{$x}{'A'},$overhang->{$x}{'C'},$overhang->{$x}{'G'},$overhang->{$x}{'T'}) = (0,0,0,0);
($overhang->{$x}{'A'}, $overhang->{$x}{'C'}, $overhang->{$x}{'G'}, $overhang->{$x}{'T'}) = (0, 0, 0, 0);
}

### COLLECT SEQUENCES
### COLLECT SEQUENCES
while ($span >= $min_overlap){ # will slide the subseq, until the user-defined min overlap size

$pos = length($seq) - $span;
Expand All @@ -200,9 +199,9 @@ sub doExtension{

# Collect all overhangs
push @overlapping_reads, $pass; ### all overlapping reads
my @over = split(//,$dangle);
my @over = split(//, $dangle);
my $ct_oh = 0;

foreach my $bz(@over){
$ct_oh++; ### tracks overhang position passed the seed
$overhang->{$ct_oh}{$bz} += $bin->{$sub}{$pass};
Expand Down Expand Up @@ -242,7 +241,7 @@ sub doExtension{
last CONSENSUS;
}
}
$previous_bz = $bz;
$previous_bz = $bz;
$ct_dna++;
}
}
Expand All @@ -252,7 +251,7 @@ sub doExtension{
if($consensus ne ""){

print "Will extend $seq\nwith: $consensus\n\n" if($verbose);
my $temp_sequence = $seq . $consensus; ## this is the contig extension
my $temp_sequence = $seq . $consensus; ## this is the contig extension
my $integral = 0;
my $position = length($temp_sequence) - ($startspan + length($consensus));
my $temp_sequence_end = substr($temp_sequence, $position);
Expand Down Expand Up @@ -290,7 +289,7 @@ sub doExtension{
$extended = 1;
print "\n$direction prime EXTENSION ROUND $trim_ct COMPLETE UNTIL $max_trim nt TRIMMED OFF => TRIMMED SEQUENCE:$seq\n\n" if ($verbose);
}

}### while trimming within bounds

print "\n*** NOTHING ELSE TO BE DONE IN $direction prime- PERHAPS YOU COULD DECREASE THE MINIMUM OVERLAP -m (currently set to -m $min_overlap) ***\n\n" if ($verbose);
Expand All @@ -302,19 +301,19 @@ sub doExtension{
###DELETE READ DATA IF IT HAS BEEN USED FOR EXTENDING A CONTIG
sub deleteData {
my ($sequence) = @_;

my $subnor = substr($sequence, 0, 10);
my $comp_seq = reverseComplement($sequence);
my $subrv = substr($comp_seq, 0, 10);

#remove k-mer from hash table and prefix tree
delete $bin->{$subrv}{$comp_seq};
delete $bin->{$subnor}{$sequence};
}

sub getUnmappedReads{
my ($contigFile, $readfiles) = @_;
my ($library,$fnames) = ("start","");
my ($library, $fnames) = ("start", "");

#obtain sequences to map against the contigs
open(FILELIB, "< $libraryfile") || die "Can't open $libraryfile -- fatal\n";
Expand All @@ -330,9 +329,11 @@ sub getUnmappedReads{
close FILELIB;
my $unpaired = "reads/$base_name.singlereads.fasta";
$files->{$unpaired}++ if(-e $unpaired);
foreach my $f(keys %$files){ $fnames.="$f,";}
foreach my $f(keys %$files){
$fnames .= "$f,";
}
chop $fnames;

#build bowtie index of contigs and map reads to the index
my $bowtieout = $base_name . ".$library.bowtieIndex";
die "Contig file ($contigFile) not found. Exiting...\n" if(!(-e $contigFile));
Expand All @@ -344,7 +345,7 @@ sub getUnmappedReads{
#map reads with bowtie and obtain unmapped reads. Store the unmapped reads into a hash and use them for contig extension
open(IN, "$procline") || die "Can't open bowtie output -- fatal\n";
my ($counter, $step) = (0, 100000);
my ($orig, $rc, $subrv,$subnor, $orig_mer);
my ($orig, $rc, $subrv, $subnor, $orig_mer);
while(<IN>){
my @t = split(/\t/);
next if ($t[2] ne '*');
Expand Down

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