PHD Comics
Multi-tasking? A PhD must have ... From: http://www.phdcomics.com/
Posts
GBK parser
Last day, le Jacou asks me about the GenBank format, because he is writing a parser for this to integrate in his super-shining-colorfull-visual man-see annotation interface, so he needs a parser to split the file by sequences, each one will be in a separate HTML file. Later he show me his code in C# and after I think how it can be translate in Perl, I suggest: #!/usr/bin/perl -w # parseGBK2HTML.pl # Juan Caballero @ 2008 $ARGV[0] or die "Usage: parseGBK2HTML \n"; use CGI qw(:standard); use BIO:SeqIO; my $file_in = shift @ARGV; my ($seq_in, $seq_out, $file_out, $seq, $features); $seq_in = Bio::SeqIO->new(-format=>'genbank', -file=>$file_in); while ($seq = $seq_n->next_seq() ) { $file_out = $seq->accession_number; $file_out .= '.html'; $features = $seq->get_SeqFeatures; open OUT, ">$file_out" or die "Cannot open $file_out"; print OUT header, start_html("$file_out"); print OUT p($features); pri...
Working with Mac
This weeks had been a transition, new home, new work, new projects. All things are a little different, this week finally I got a computer to work and it's a Mac, its name is Broadcast. Many times I had used the Mac, specially from OS X, now I need to use it every day. The Unix inside is working great, all is simply and pretty, and the best is the 24" screen, larger than my old TV, my software selections are: Web browser: Mozilla Firefox Multichat: Adium Text edit: jEdit RSS reader: Vienna Seqs Tools: eBioX CHM Reader: Chmox FTP Client: Fetch Screensaver: Tron/RedPill I miss Linux, but many server and clusters are Linux-based, so I use my Mac to connect with it. Maybe later I try Xcode to develop some application for Mac.