Errata

Mastering Python for Bioinformatics

Errata for Mastering Python for Bioinformatics

Submit your own errata for this product.

The errata list is a list of errors and their corrections that were found after the product was released. If the error was corrected in a later version or reprint the date of the correction will be displayed in the column titled "Date Corrected".

The following errata were submitted by our customers and approved as valid errors by the author or editor.

Color key: Serious technical mistake Minor technical mistake Language or formatting error Typo Question Note Update

Version Location Description Submitted By Date submitted Date corrected
Page 84
"Getting Started" 1st code

The code of book is below:

```
$ cd 04_fib/
$ cp solution1_list.py fib.py
```

but I can't find that file.

```
$cp solution1_list.py fib.py
cp: solution1_list.py: No such file or directory
```

​I think the correct file could be either of the following two:

```
cp solution1_list_closure.py fib.py
cp solution1_list_function.py fib.py
​```

Note from the Author or Editor:
Yes, that is a mistake. You can use the program "solution1_list_function.py" instead.

 Yuri  Mar 05, 2023 
PDF
Page 232
First code example

The "fetch_fasta.sh" program has two errors:

while read -r PROT_ID; do
echo "$PROT_ID"
URL="{...}.fasta" <1>
echo $URL
OUT_FILE="$OUT_DIR/${PROT_ID}.fasta"
wget -q -O "$OUT_FILE" "$URL" <2>
done < $1

<1> Need to add ".fasta" to the URL
<2> The "-o" flag should be "-O"

 Ken Youens-Clark
Ken Youens-Clark
 		 Jul 14, 2021  Dec 16, 2022
PDF
Page 281
Middle

orfs.append(''.join(aa[start:stop]))

Is better written as

orfs.append(aa[start:stop])

 Ken Youens-Clark
Ken Youens-Clark
 		 Jul 28, 2021  Dec 16, 2022
Printed, PDF
Page 319
Figure 16-3

The FSM should have an arrow from the first "a" to the terminus for the pattern "fa."

 Ken Youens-Clark
Ken Youens-Clark
 		 Aug 09, 2021  Dec 16, 2022