Difference between revisions of "CH391L/BLOSUM"
From Marcotte Lab
< CH391L
(Created page with "== Source Code == * http://www.marcottelab.org/users/CH391L/FromTA/BLOSUM.pl.txt * You also need BLOSUM50.txt file to run this script: http://www.marcottelab.org/users/CH391L/Fro...") |
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== Comments == | == Comments == | ||
| + | Two 'not-easy' method used to read BLOSUM table in PERL. | ||
| + | |||
| + | my @aa1_list = split(/\s+/,$aa1_line); | ||
| + | * This splits the line with whitespace (space, tab, etc.). The pattern in '//' sign is called regular expression (I mentioned this in my lecture), and it recognize a pattern in the string. For example, '\s+' means 'one or more(+) whitespace(\s)'. You can find more information about PERL regular expression at http://perldoc.perl.org/perlretut.html . | ||
| + | |||
| + | $score_map{$tmp[0]}->{$aa1_list[$i]} = $tmp[$i]; | ||
| + | * This is called 'hash of hashes'. The reason why I use this data structure is (1) I cannot initialize two dimensional array in PERL (means it is little bit complex to handle this in array form), and (2) all I need is to access the value with two amino acids. $tmp[0] (row) and $aa_list[$i] (column) are two amino acids, and $tmp[$i] is BLOSUM50 score for their substitution. As you see later in the code, you can call this score by $score_map{'A'}->{'S'}. See [http://www.cs.mcgill.ca/~abatko/computers/programming/perl/howto/hash/#create_a_hash_of_hashes__via_references here] for more about 'hash of hashes'. | ||
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[[Category:CH391L]] | [[Category:CH391L]] | ||
Latest revision as of 21:44, 9 February 2011
Source Code
- http://www.marcottelab.org/users/CH391L/FromTA/BLOSUM.pl.txt
- You also need BLOSUM50.txt file to run this script: http://www.marcottelab.org/users/CH391L/FromTA/BLOSUM50.txt
How it works
Comments
Two 'not-easy' method used to read BLOSUM table in PERL.
my @aa1_list = split(/\s+/,$aa1_line);
- This splits the line with whitespace (space, tab, etc.). The pattern in '//' sign is called regular expression (I mentioned this in my lecture), and it recognize a pattern in the string. For example, '\s+' means 'one or more(+) whitespace(\s)'. You can find more information about PERL regular expression at http://perldoc.perl.org/perlretut.html .
$score_map{$tmp[0]}->{$aa1_list[$i]} = $tmp[$i];
- This is called 'hash of hashes'. The reason why I use this data structure is (1) I cannot initialize two dimensional array in PERL (means it is little bit complex to handle this in array form), and (2) all I need is to access the value with two amino acids. $tmp[0] (row) and $aa_list[$i] (column) are two amino acids, and $tmp[$i] is BLOSUM50 score for their substitution. As you see later in the code, you can call this score by $score_map{'A'}->{'S'}. See here for more about 'hash of hashes'.
