Errata and updates for Chapter 10

[haruosuz]

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Page 346

library(BiocInstaller)
biocLite('qrqc')

should be

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("qrqc")

https://www.bioconductor.org/packages/release/bioc/html/qrqc.html

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Page 350-351

counts.update(seq.upper())

The Counter.update() method

should be

The counts.update() method

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Page 351

Contributed by Itaya, KH.

For Python 3.7.3, cat contam.fastq | ./nuccount.py printed the following messages:

  File "./nuccount.py", line 18
    print base + "\t" + str(counts[base])
             ^
SyntaxError: invalid syntax

#) nuccount.py

nuccount.py:18:    print base + "\t" + str(counts[base])

should be

nuccount.py:18:    print ( base + "\t" + str(counts[base]) )

#) readfq.py

readfq.py:39:    print n, '\t', slen, '\t', qlen

should be

readfq.py:39:    print ( n, '\t', slen, '\t', qlen )

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