Errata for Bioinformatics Programming Using Python

"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."

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."

"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."

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.

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".

>>> 'MNKMDLVADVAEKTDLSKAKATEVIDAVFA'[7//2] 'K' should be changed to: >>> 'MNKMDLVADVAEKTDLSKAKATEVIDAVFA'[7//2] 'M'

Note from the Author or Editor:
Thank you!

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

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.

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

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

>>>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.

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

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!

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).

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.

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)

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

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

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)]

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

replace [0] with [1]

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

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".

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])

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.

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

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

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

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

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

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

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

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

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.

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

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

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('|')

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)]

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

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

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

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

Replace "print_translations" with "print_translations_with_open_reading_frame"

Replace "print_translations" with "print_translations_with_open_reading_frame_in_both_directions"

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

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

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

Add a right parentheses at the end of the doc string

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.

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

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

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

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.

Remove right parentheses after "path"

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

"return path" --> "return path"

val --> value

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 =".

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)

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)

remove the s from tagnames

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

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

indent 4 spaces

in the assignment of urlpart1, the semicolon after the question mark should be a colon quote_plus(words) --> quote_plus(' '.join(words))

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}

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

After assignments to HOST and PORT add: encoding = 'ASCII'

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

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

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

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

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:])

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

in return statement change sequence to seqdata

max(Name, --> max(Name)

add ' after Verdana

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

x_label_height should be xlabel_height

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

"+1 5" should be "+ 15"

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