MD5 file list checker

This program reads a file with filenames with correct path and MD5 values separated by a tab character and checks if the MD5 is correct or not.

#!/usr/bin/perl
use strict;
use Digest::MD5 qw(md5_base64);

open MD5, $ARGV[0] or die $!;
my $line="";
while($line = ){
chomp $line;
my @files=split(/[ \t]+/,$line);
open(FILE, $files[1]) or die "Can't find file $files[1]\n";
my $digobj = Digest::MD5->new;
$digobj->addfile(*FILE);
$digest = $digobj->hexdigest;
close(FILE);
if($digest!~m/$files[0]/){print "Md5 does not match for file:" . $files[1];}
else{
print "Md5 match for file:$files[1]\n";
print $digest ."\n" . $files[0] . "\n";
}
}

It would make sense to have MD5 checks integrated into the OS and have a MD5 list in each folder. May be it will get added into the code of various programs like ftp, sftp or even ordinary copy and mv.

Sort fasta file

Many programs like GATK require the fasta files to be sorted before use. Here is a rather simple script for the job:

 #!/usr/bin/perl  
 open FASTA, $ARGV[0] or die $!;  
 my $temp="";  
 my $seqs = {SEQ =>my $fheader};  
 my $sortemp="";  
 while($line = <FASTA> ){  
 if($line=~ /^>/){  
 if($header){$seqs{$header}{SEQ}=$temp;}  
 chomp $line;  
 $header="";  
 $line =~ s/[\s]/_/g;  
 $header=$line;  
 $temp="";  
 }  
 else{$line =~ s/[\n\t\f\r_0-9\s]//g;$temp .= $line;}  
 }#end of while loop  
 if($header){$seqs{$header}{SEQ}=$temp;}  
 close FASTA;  
 foreach $sortemp (sort keys %seqs) {  
 print "$sortemp\n";  
 print "$seqs{$sortemp}{SEQ}\n";  
 }  

However, you can find more elegant solutions that use Bioperl at Wolf/Takebayashi lab.

Why you cannot give Feedback to the LS?

The recent Anna Hazare movement has been opposed by many. Intellectuals like Nandan Nilekani among many others wanted the use better ways to comment or provide feedback to the parliament.

I wonder if Mr Nilekani has ever tried using the feedback form on the parliament of India website. The website which is designed and hosted by National Informatics Centre has a very interesting feature indeed :)

It has excellent code which makes sure that feedback can never be submitted. If you don't believe me you can try it yourself. As soon as you type anything in the feedback form the javascript onkey event calls the validate function. This function is supposed to replace all special characters. However, the brilliant person who designed this included the ^ (caret) character in the "myC" array that lists all special characters. This results in all possible characters being matched by the Regular expression. Hence, anything thats typed into the feedback form gets deleted.

If this is the situation in a website that can be easily verified by anybody with access to the internet. We can only imagine what happens to the feedback which actually manages to reach the Politicians after manging to escape the caret.

English? Inglish? Or watever this is!!

Recently, i found this(See picture) stamped on a bill from westside. It says, "No Exchange on Sale Merchandise". My first thought was it meant "No Exchange on Sold Merchandise". Would this qualify for Inglish? May be the BBC would find it interesting enough to publish? A similar collection of images about chinglish was published few years ago.

The English may find that their language is being ruined. But is that the price that must be paid to be an international language? How much can a language be stretched and modified before it stops being itself?

After further thought, it seemed that it actually meant "No Exchange on merchandise which is on 'Sale(Being sold at a lower price)' ". May be it is self evident as a measure to save on print space.

Hyperboloids of wondrous Light

" Hyperboloids of wondrous Light

Rolling for aye through Space and Time

Harbour those Waves which somehow Might

Play out God's holy pantomime”

This is what it says on the gravestone of Alan Turing, the code breaker who was involved in breaking the Enigma's cryptic codes. I like to think of these hyperboloids as the very essence of the universe. An explanation for the existence of our universe and development of intelligent life.

Many would agree that the "genome" is indeed God's holy pantomime. It will not be surprising that it plays out not just in the living world but also in most things in the universe. A mathematical explanation for the way things happen. How probable is the development of intelligent life? Is the universe bound by rules that direct the formation of intelligent life? These are some questions that could shed light on the oldest questions that man has sought answers to.

Turing does feature on the list of atheists, although its not clear when and what changed his thoughts. However, its probably worth noting that the "God" here would most likely not refer to a god associated with any religious denomination. A spiritual god cannot be ruled out, but most likely refers to a mathematical god, one of  physical principles.

The problem with walls

It is very common to have walls surrounding most buildings in tropical countries. However, walls are rare and fences are more common in the colder(LOL) countries. Is it just a question of style or does it have anything to do with the climate?

Walls would make it easier for the snow to pileup around a building making it inaccessible. Removal of snow would also be complicated by the presence of solid structures hidden below layers of snow. Such obstructions would have to be properly marked, if heavy machinery is to be used for clearing the snow. Moreover, as the snow melts, walls without proper drainage could cause the formation of puddles and stagnation of water. These seem reasonable enough to have fences instead of walls.

Forts had walls to act as a barrier to invading armies. With the advent of modern warfare, walls have lost their significance as defenses against human armies. Cattle and wild animals can be contained within or outside walls.

Break scaffolds into Mate pairs

Could not find any programs that can merge a set of scaffolds. Hence, decided to break the scaffolds into mate pairs and use those for scaffolding. Below is a simple perl script to break scaffolds into all possible mate pairs in a format suitable for SSPACE (a hierarchical scaffolder). It can easily be modified to work for BAMBUS or any other scaffolder or assembler.


#!/usr/bin/perl

#AUTHOR
# Nagarjun Vijay (c) 2011
# mate maker.pl - program to break scaffolds into mate pairs
#

#DATE
# 3rd March 2011
#

use strict;

my $scafile=$ARGV[0];

#reading the scaffold sequences
open SCAF, "<",$scafile or die $!;

#open contigs file
open CONTIG, ">>",$scafile . ".contigs.fa" or die $!;


#open contigs file
open LIB, ">>",$scafile . ".lib" or die $!;

my ($scaffoldcount,$seqst_temp,$contigcount,$notscaffoldcount,$z,$head,$i,$j,$libcount);
$scaffoldcount=0,$seqst_temp="",$contigcount=0,$notscaffoldcount=0,$libcount=0;
my $header = ;#reading the first header

while($z = ){
if($z=~ />/)
{
#split scaffold into contigs
if($seqst_temp=~ m/[N]+/){#is really a scaffold
$scaffoldcount++;
$contigcount +=SplitScaffold($seqst_temp);
}#end of scaffold check if
else{#not a scaffold - so not writing into breaker file
$head=">unbreak";
$notscaffoldcount++;
print CONTIG $head . "" . $notscaffoldcount ."\n";
print CONTIG "$seqst_temp\n";
}#end of scaffold check else

#next sequence
$seqst_temp="";
}
else
{
$z =~ s/[\n\t\f\r_0-9\s]//g;
$seqst_temp .= $z;
}
}#end of File while loop

if($seqst_temp=~ m/[N]+/){#is really a scaffold
$scaffoldcount++;
$contigcount +=SplitScaffold($seqst_temp);
}#end of scaffold check if
else{#not a scaffold - so not writing into breaker file
$head=">unbreak";
$notscaffoldcount++;
print CONTIG $head . "" . $notscaffoldcount ."\n";
print CONTIG "$seqst_temp\n";
}#end of scaffold check else
close SCAF;
close CONTIG;

#Split scaffolds, write contigs and breaker file
sub SplitScaffold{
my $seq = shift;
my ($head,$num,$contigs,$n);
$head=">breaker$scaffoldcount";
$num=1,$contigs=1;
my @values=split(/([N]+)/,$seq);
my $vallen= scalar (@values);
for($i=0;$i<$vallen;$i++) {
my $val=$values[$i];
if(($num % 2) == 0){
$n = length $val;
}
else{
print CONTIG $head . "" . $contigs ."\n";
print CONTIG "$val\n";
$contigs++;
my $matedist=(length $values[$i])+(length $values[$i+1])+(length $values[$i+2]);
for($j=$i+2;$j<$vallen;$j=$j+2){
print LIB "lib".$libcount." l".$libcount."s".$scaffoldcount."b".$i.".fasta l".$libcount."s".$scaffoldcount."b".$j.".fasta ".$matedist." 0.75 0\n";
$matedist=$matedist+(length $values[$j+1])+(length $values[$j+2]);
open READ1, ">>","l".$libcount."s".$scaffoldcount."b".$i.".fasta" or die $!;
open READ2, ">>","l".$libcount."s".$scaffoldcount."b".$j.".fasta" or die $!;
print READ1 ">l".$libcount."s".$scaffoldcount."b".$i."\n";
print READ1 $values[$i]."\n";
print READ2 ">l".$libcount."s".$scaffoldcount."b".$j."\n";
print READ2 reverseComplement($values[$j])."\n";
close READ1;
close READ2;
$libcount++;
}

}
$num++;
}

return $contigs;
}
#reverse complement a sequence
sub reverseComplement{
$_ = shift;
tr/ATGC/TACG/;
return (reverse());
}
#end of Breaker