Friday, December 29, 2006

Code to get GenBank file using Bioperl

#!/usr/local/bin/perl -w # Modified by using # "How to retrieve GenBank entries over the Web" # by Jason Stajich # Downloads E. dispar WGS sequence from
# AANV01000001:AANV01018095 # and invadens: AANW01000001:AANW01015173 # Just for Info:
# Histolytica: AAFB01000001:AAFB01001819 # Avoiding get_Stream_by_batch so that
# individual file can be written use Bio::DB::GenBank; use Bio::SeqIO; use strict; #for dispar getGB(1,18095,"AANV010"); #for invadens getGB(1,15173,"AANW010"); sub getGB{ my $start=shift; my $end=shift; my $common=shift;
for(my $c=start;$c<=$end;$c++){
$c=sprintf('%05d', $c); my $accession_no=$common.$c; my $fname=$accession_no.".gbk"; print "Writing $fname\t"; my $seqout = new Bio::SeqIO( -file => ">$fname", -format=>'GenBank');
my $getseq = new Bio::DB::GenBank;
my $seq = $getseq->get_Seq_by_acc($accession_no);
} }

Thursday, May 11, 2006

Song Ik Onkar from Rang De Basanti ( ) Simply amazing... you can feel the words creating a matrix around you... Music: A R Rehman Vocals: Harshdeep Kaur ek onkar satnam kartapurakh nirmoh nirvair akaal murat ajuni sabham guru parsad jap aad sach jugaad sach hai bhi sach nanak hose bhi sach soche soch na ho wai jo sochi lakh waar chhupe chhup na howai je laai har lakhtaar ukhiya pukh na utari je banna puriya paar sahasyanpa lakh woh hai ta ek na chale naal ke ve sach yaara hoi ae ke ve kude tutte paal hukum rajai chalna nanak likheya naal Hope you enjoyed :)

Thursday, April 20, 2006

Life is a highway... a thought

Life is a highway... a thought for a Game! The title reminds me of Tom Cochran's song "Life Is A Highway ..." and Bhagwat Gita Verse 2.22: Vasansi jeernani yatha vihaya navani grunhati naroparani, Tatha shareerani vihaya jeeranyanyani sanyati navani dehi. which essentially means "As a person puts on new garments, giving up old ones, the soul similarly accepts new material bodies, giving up the old and useless ones" [Taken from Srila Prabhupada's GITA translation]. I have a weird idea for a game, I have been thinking this quite often, making a game, Life is like a highway, with Soul being the Traveller in time, Body being the carrier, several distractions with their sign boards and exits (Like millions of McDonald's sign and the exits to them on US highways!). The journey starts with soul coming out of the super-soul due to its Karm vector changing its score from NULL to NOT NULL (Discussed below). The highway it has to go through is also based on Karm vector (Like say, the super-soul reads the Karm verctor and decides that the soul has to ride Highway 911!). The purpose is to reach back the super-soul (but you are not allowed to travel backwards, it is a one way road!). There are various short cuts (Like various Yog [Karm, Gyaan, Raaj, Bhakti]) and long cuts (the distraction exit, some of them just prolong the length and some of them take you on a circle!). While you are on the way, based on your behavior (with other travelers [material and non-material] and yourself) your Karm points go up (Good behavious) or down (Bad behaviour) on various dimensions (Karm score is a multidimensional vector, so the counter of specific Karm increments). You can reduce the time of journey by either Moving FAST (Better tools of journey eg, making the mind and body efficient) and/or Taking SHORTCUTS and/or Avoiding LONG-CUTS. The body and other material things might time-out but you will again get a new body based on your latest Karm vector. By the time you reach the Final Destination, your Karm vector should be a null vector too, to get in union with Super-soul, the time when your game ENDS. I have avoided the complication of having Enemies... I feel the LONG CUTS are enemies anyways! I wish I could do some game programming too... like the way GOD does... Lets see what is humanly possible first... I guess everything is possible though!