Errata

The example

>>> 3 > 13 % 5
False

is misleading for non-programmers since the precedence of the operations in this case is "%" first and ">" second. While the example is correct in its answer, it is also correct if one uses the wrong precedence. Changing the "13" to another value would be helpful, but may introduce complexity to your description.

>>> 3 > 12 % 5
True

You could also use a footnote saying "see page 16, Compound Expressions" for a treatment of precedence. Alternately, you can refer back to the example on p. 8 from p. 16 and show how changing the "13" to a different value changes the answer and exposes the precedence rule.

Note from the Author or Editor:
This example and the one before it are both confusing. Change "2 == 5 // 2" to just "2 == 2" and change "3 > 13 % 5" to just "3 > 3".

The sequence:
'''MWNSNLPKPN AIYVYGVANA NITFFKGSDI LSYETREVLL KYFDILDKDE RSLKNALKD LEN PFGFAPYI TRAYEHKRNF LTTTRLKASF RPTTF'''

when entered shows this part "D LEN" modifies to be "DL EN" when it should remain "D LEN".

Also, without a cross reference to other formats, some (perhaps most) of the errata is lost on people with other formats. Columns listing the location in each format would be most helpful.

Note from the Author or Editor:
There is some confusion in the output of the examples on this page. Replace the lines of these examples after the first four with the following, but without the blank lines. The blank lines are here to indicate where new lines begin, since these lines will probably be broken up differently when this erratum is displayed in a browser.

'''MKQLNFYKKN SLNNVQEVFS YFMETMISTN RTWEYFINWD KVFNGADKYR NELMKLNSLC GSLFPGEELK

SLLKKTPDVV KAFPLLLAVR DESISLLD'''

'MKQLNFYKKN SLNNVQEVFS YFMETMISTN RTWEYFINWD KVFNGADKYR NELMKLNSLC GSLFPGEELK\nSLLKKT

PDVV KAFPLLLAVR DESISLLD'

'''MWNSNLPKPN AIYVYGVANA NITFFKGSDI LSYETREVLL KYFDILDKDE RSLKNALKDL
ENPFGFAPYI

RKAYEHKRNF LTTTRLKASF RPTTF'''

'MWNSNLPKPN AIYVYGVANA NITFFKGSDI LSYETREVLL KYFDILDKDE RSLKNALKDL ENPFGFAPYI\nRKAYEH

KRNF LTTTRLKASF RPTTF'

Finally, before the line "There are three situations that cause ..." Add "If you type these examples to Python you may see slight differences in where one line ends and another begins."

the variable "m" is not defined. Is "m" supposed to be "matchobj"?

Note from the Author or Editor:
Replace "while m" with "while matchobj" and in the next line, "m.group" with "matchobj.group".

Also, on the last line of the next Example (7-5) replace "m =" with "matchobj =".

newbase = bases[randint(0,2)]

should be

newbase = bases[randint(0,3)]

in order to include base 'G' as a possible mutation

Note from the Author or Editor:
Change (0, 2) to (0, 3).

First line after the doc string of extract_gi_id should be indented four spaces fewer and "line" should be replaced with "description".

(This is page 134 not 127)

Note from the Author or Editor:
The line beginning "if line[0]" should be indented 4 fewer spaces and the word "line" should be replaced with the word "description".

The code line:

bases.replace(base, '')

is not altering the bases string in Python 3.0. Changing the code to:

bases = bases.replace(base, '') fixed this for me.

Note from the Author or Editor:
Yes. Strings are modifiable in some languages and not in others. This often leads to confusion, including among people like myself who have used many of each kind of language!

You can use Ctrl-P or the down arrow to move to a later
line in the input history.

instead of :

You can use Ctrl-N ...

Note from the Author or Editor:
yes

It's a table of two columns: Statement and Equivalent. The mistake is on the last row.

First column reads: name **= expression
Second column reads: name = name * expression

(second column should be: name = name ** expression .)

Note from the Author or Editor:
yes

In Example 3-24, it states

>>>some({'a string', ''}, len)
False

This is incorrect. The output is True because len('a string') = 8. Running the provided sample code ch03_24.py confirms this.

on Page 11, the output ist wrong:

Book:
>>> 'MNKMDLVADVAEKTDLSKAKATEVIDAVFA'[:8]
'MNKMDLVADVAEKTDLSKAKAT'

Python3:
>>> 'MNKMDLVADVAEKTDLSKAKATEVIDAVFA'[:8]
'MNKMDLVA'

Note from the Author or Editor:
Whoops. Should be -8, not 8.

The explanation of conditional expressions is incorrect: "Written using the keywords if and else, it returns the value **preceding** (not following) the if when the condition is true and the value following the else when it is false.

"In Python 2, it would have printed as 0.0089999999999999993, and 0.003 would have printed as 0.0089999999999999993."

should be

"In Python 2, it would have printed as 0.0089999999999999993, and 0.03 would have printed as 0.029999999999999999."

I think the returned value would be False each time "some" is called with the same arguments. I suspect that the arguments are wrong in the first call to "some".

>>> some([0, '', False])
True
>>> some([0, '', False])
False

Note from the Author or Editor:
change first call to some([0, 'A', False])

string1.find(string2[, start[, end]])
Returns the position of the last occurrence of string2 in string1


should be


string1.find(string2[, start[, end]])
Returns the position of the first occurrence of string2 in string1

>>> 'MNKMDLVADVAEKTDLSKAKATEVIDAVFA'[:8]
'MNKMDLVADVAEKTDLSKAKAT'

should be

>>> 'MNKMDLVADVAEKTDLSKAKATEVIDAVFA'[:-8]
'MNKMDLVADVAEKTDLSKAKAT'

1) gc_content doesn't work with lowercase input because of a minor mistake:

def gc_content(base_seq):
assert validate_base_sequence(base_seq), 'Argument has invalid characters'
seq = base_seq.upper()
return (base_seq.count('G') + base_seq.count('C')) / len(base_seq)

should be changed to:

def gc_content(base_seq):
assert validate_base_sequence(base_seq), 'Argument has invalid characters'
seq = base_seq.upper()
return (seq.count('G') + seq.count('C')) / len(base_seq)

2) gc_content doesn't work with RNA input (raises assertion error). I'm not sure if this was by design. If not, it could be fixed by adding the RNAflag parameter to its definition:

def gc_content(base_seq, RNAflag=False):
assert validate_base_sequence(base_seq, RNAflag), 'Argument has invalid characters'
seq = base_seq.upper()
return (base_seq.count('G') + base_seq.count('C')) / len(base_seq)

>>> 'MNKMDLVADVAEKTDLSKAKATEVIDAVFA'[7//2]
'K'

should be changed to:

>>> 'MNKMDLVADVAEKTDLSKAKATEVIDAVFA'[7//2]
'M'

Note from the Author or Editor:
Thank you!

The code for the while loop should be:

while itm:
itm, nxtpos = next_item(buffer, curpos) # reread to ensure complete
yield itm
itm, curpos, nxtpos = nxtitm, nxtpos, nxtend
nxtitm, buffer, nxtend = get_item(file, buffer, nxtpos, chunksize)

In the last line of __init__ (the call to super) filename should be ps_filename

x_label_height should be xlabel_height

In the definition of run, portnum, portnumbe, and portnumber should each be just port

The second line of open_port should be
for portnum in range(startport, startport+100):

The next to last line of the definition of run should use CGIHTTPRequestHandler not HTTPRequestHandler

6th line from bottom:
SimpleHTTPRequestHandler
should be
http.server.SimpleHTTPRequestHandler

The names protnum in the parameter list and portnumber in the next to last line of the definition of run should both be port

The 2nd line of open_port should be:
for portnum in range(startport, startport+100):

The parameter server_class should be handler_class

Add parameter handler_class to open_port and handler_class to its call in run

After assignments to HOST and PORT add:

encoding = 'ASCII'

First line on page, the l at the end of the line should be )

Add 'name' at the end of the function name make_html_for_file

The syllable write_ would have been a better first syllable for all the names beginning with make_ in Example 9-20.

In the line
atagformat = "<li><a href="{0}">{1}</a></li>\n"
replace
href="{0}"
with
{0}

Remove p in the for places it appears in
from self.parser.p

remove the s from tagnames

remove the right parenthesis from the first line

add a single quote before the comma on the second line

replace the right parenthesis on the third line with a single quote

Add a colon at the end of the second to last line of the example (that begins with def remove_html)

>>>return ((base_seq.count('G') + base_seq.count('C')) /
>>> len(base_seq))

should be

>>>return ((seq.count('G') + seq.count('C')) /
>>> len(base_seq))

Note from the Author or Editor:
Yes, and might as well make it len(seq) too.

"For a string of length N, an index (i.e., the value between square brackets) must be in the range -N <= index < N-1."

should read

"[...] must be in the range -N <= index < N."
or
"[...] must be in the range -N <= index <= N-1."

"+1 5" should be "+ 15"

Delete the following extraneous lines are extraneous:
tic_width = 3
xaxis_width = yaxis_width = 0
xlabel_height = ylabel_width = 0

in return statement change sequence to seqdata

add ' after Verdana

max(Name, --> max(Name)

in the line after "try:" replace "get_connection" with sqlite3.connect

delete the next to last line of the definition of load_enzyme_data and the + at the end of the line before the deleted one

replace the last 5 lines of parse_organism (the if/elif/return code) with:

return (parts[0],
parts[1],
None if len(parts) == 2 else ' '.join(parts[2:])

table.get(sequence, set()).add(enzyme)
-->
if sequence in table:
table[sequence].add(enzyme)
else:
table[sequence] = {enzyme} # first enzyme for sequence

in the assignment of urlpart1, the semicolon after the question mark should be a colon

quote_plus(words) --> quote_plus(' '.join(words))

indent 4 spaces

val --> value

"return path" --> "return path"

"(command)" --> "(command, shell=True)"

add:
self.read_next_line()
at the end of the definition skip_intro, repeating the first line of the definition.

In the definition of __repr__, delete a space before the first quote of the doc string and before "repr" on the second line of the return statement.

Remove right parentheses after "path"

in definition of complement get rid of first self in self(self.get_sequence)

in class RNASequence, change ComplementTrans to ComplementTable

Note from the Author or Editor:
Yes. Clarification on the first: remove first left parentheses and final right parentheses on same line too.

change class AmbiguousDNASequence(DNASequence): to
class AmbiguousDNASequence(BaseSequence):

under creating char(n) should be chr(n), ord(char) should be ord(chr)

Note from the Author or Editor:
char(n) should be chr(n), but ord(char) does not need to be changed

At the end of the definition of run replace SimpleHTTPRequestHandler with CGIHTTPRequestHandler.

Delete the first line after the doc string in the definition of start_element.

In the definition of gc_content replace "get_sequence" with "get_sequence()".

Add a right parentheses at the end of the doc string

Before "click the search button" add "select Gene from the dropdown to the left of the search box, "

Replace "sites/entrez" with "gene" in the URL for Entrez Gene.

In the definition of test, delete the second space after "result =", and change "== 2" to "== 3559" in the first assertion statement.

Add a colon to the end of the first line of the definition of load_enzyme_data_into_table

Add a colon to the end of the first line of the definition of load_enzyme_data_into_table

Replace "RNA" with "DNA" in the example title

Replace "print_translations" with "print_translations_with_open_reading_frame_in_both_directions"

Replace "print_translations" with "print_translations_with_open_reading_frame"

In definition of translate_with_open_reading_frames "frame-1" should be "framenum-1"

Replace "RNA" with "DNA" in the code and the example title

Replace "RNA" with "DNA" in the code and the example title

Replace "RNA" with "DNA" in the code and the example title

"print" in the definition of print_translation_in_frame should line up with the first quote of the doc string

Rename next_item to item_generator and add the following definition:

def get_items(src, testfn=None):
"""Return all the items in src; if testfn then include only those
items for which testfn is true"""
return [item for item in item(src)
if not testfn or testfn(item)]

Remove the argument "testfn" from the call to item_generator at the beginning of find_item.

The next to last line of item_generator should eliminate the initial '>' and final '\n', reading:
description = line[1:-1].split('|')

In the definition of get_gene_info_from_file the open statement should have a second argument:
encoding = 'utf-8'
which is often necessary for HTML files saved from a web page.

The last two lines should be indented an additional 6 spaces each.

First line after the doc string of extract_gi_id should be indented four spaces fewer and "line" should be replaced with "description".

Add a colon at the end of the first line of the definition of list_sequences_in_file.

In the definition of is_number replace "elt" with "value"

On the right side of the table insert a right parentheses between the right parentheses and right bracket.

There should be no line break after "def" at the beginning of the table.

Add a right parentheses at the end of the code on the right side of the table.

First line after the docstring of extract_gi_id should be indented four spaces fewer and "line" should be replaced with "description".

Remove "[1:]" from the first line of the body of read_FASTA_sequences.

Replace the body of the definition of read_FASTA_sequences with:
return [[seq[0], seq[2].replace('\n', '')] # delete newlines
for seq in read_FASTA_entries(filename)]

The definition of first_common can be used with any two collections, so (1) replace "list1" and "list2" with "collection1" and "collection2"; and (2) in the sentence preceding the example replace "list" with "collection".

Replace with:

return {line.split('|')[2] for line in file
if line[0] == '>' and len(line.split('|')) > 2}

replace [0] with [1]

Delete one of the two spaces between "return" and "all".

The lines with the doc string and return statement should each begin with an additional space. In the definition of test, True and False should be exchanged.

>>> validate_base_sequence('AUCG')
>>> # second argument omitted; defaults to True
True

should be

>>> validate_base_sequence('AUCG')
>>> # second argument omitted; defaults to False
False