Mastering Perl for Bioinformatics
by James Tisdall

This errata page lists errors outstanding in the most recent printing.

If you have technical questions or error reports, you can send them to
booktech@oreilly.com.  Please specify the printing date of your copy.

This page was updated October 20, 2004.

Here's a key to the markup:
	[page-number]: serious technical mistake
	{page-number}: minor technical mistake
	<page-number>: important language/formatting problem
	(page-number): language change or minor formatting problem
	?page-number?: reader question or request for clarification



Confirmed errors:


{32}  Exercise 1.7;
in exercise 1.7, the alternative construct given to translate dna to protein
doesn't work properly.  Since $i is incremented during the first iteration of
the loop the first codon is skipped.

    This is how it is given:

    my $i=0;
    while (my $codon = substr($dna, $i += 3, 3) ) {
        $protein .= Geneticcode1::codon2aa($codon);
    }

    BUT it should be:

    my $i = -3;
    while (my $codon = substr($dna, $i += 3, 3) ) {
        $protein .= Geneticcode1::codon2aa($codon);
    }



(34)  Fourth paragraph;
Missing the example for initializing hash.

Text says:

"....as a key with its value, as in: "

And then proceeds to the next paragraph.  The promised example is left out.


(76)  Lower half;
A great many modules such as ioperl
->
A great many modules such as Bioperl



(145) Chapter 4 The footnote under Analysis of SeqFileIO.prn 
http://iobio.bio.indiana.edu/soft/molbio/readseq
Should be:
http://iubio.bio.indiana.edu/soft/molbio/readseq


{155}  Paragraph before parse_methods;
http://www.perdoc.com should be http://www.perldoc.com


(169) under the Heading "Resources"
http://iobio.bio.indiana.edu/soft/molbio/readseq
Should be:
http://iubio.bio.indiana.edu/soft/molbio/readseq


(222-223)  sample code 
mysql&gt;
should be:
mysql>



(285)  First part of code on top of the page;
Problem in the typesetting, probably, since it's not the only place it occurs in the
book (see previously error in "unconfirmed error reports", pages 329 and 331).

Here it shows, in the book:

# plot the data on the graph
my $gd = $graph-> plot(
    [ ^xsizes,
      ^ycounts
    ]
);

while it should have been:

# plot the data on the graph
my $gd = $graph-> plot(
    [\@xsizes,
     \@ycounts
    ]
);