BINF 634 Bioinformatics Programming - George Mason …：binf 634生物信息学编程-梅森….ppt

BINF 634 Fall 2013 Lect 5 * Homework Remember we meet Tuesday of week 10/15/13 at the usual place and time due to the Columbus day Holiday. Program 2 due Tuesday 10/7/13 at 7:00 pm. Quiz 3 will occur next week. Remember that on Tuesday October 15, 2012 we will have our in class midterm exam. It will be open book and notes. On the Horizon BINF 634 Fall 2013 Lect 5 * Regular Expression Lab Counts as a quiz grade 100 possible points Our Regular Expression Lab * * * * * * * * * * * * * * * * * * * * * * * * * BINF 634 Fall 2013 Lect 5 BINF 634 Fall 2013 Lect 5 BINF 634 Fall 2013 Lect 5 * BINF634 Lecture 5 Program 1 Solution Quiz 2 Solution Program 2 Discussions Regular Expressions Regular Expressions Lab Time to Work on Program 2 Outline Program 1 Discussions You must test all of your code on binf I am testing your code on binf I can’t possibly know what configuration of what machine that your code runs under The perl on binf must be the first line in your program #!/usr/bin/perl BINF 634 Fall 2013 Lect 5 * BINF 634 Fall 2013 Lect 5 * Program 1 Solution #!/usr/bin/perl use strict; use warnings; # File: cpg.pl # Author: Jeff Solka # Date: 01 Aug 2011 # # Purpose: Read sequences from a FASTA format file # Programming Assignment #1 # the argument list should contain the file name die usage: fasta.pl filename\n if scalar @ARGV 1; # get the filename from the argument list my ($filename) = @ARGV; # Open the file given as the first argument on the command line open(INFILE, $filename) or die Cant open $filename\n; # variable declarations: my @header = (); # array of headers my @sequence = (); # array of sequences my $count = 0; # number of sequences # read FASTA file my $n = -1; # index of current sequence while (my $line = INFILE) { chomp $line; # remove training \n from line if ($line =~ /^/) { # line starts with a $n++; # this starts a new header $header[$n] = $line; # save header line $sequence[$n] = ; # start a