Conventions used

There are a number of text conventions used throughout this book.

Code in text: Indicates code words in text, database table names, folder names, filenames, file extensions, pathnames, dummy URLs, user input, and Twitter handles. Here is an example: “call_genotype has a shape of 56,241x1,1198,2, that is it is dimensioned variants, samples, ploidy.”

A block of code is set as follows:

from Bio import SeqIO
genome_name = 'PlasmoDB-9.3_Pfalciparum3D7_Genome.fasta'
recs = SeqIO.parse(genome_name, 'fasta')
for rec in recs:
    print(rec.description)

When we wish to draw your attention to a particular part of a code block, the relevant lines or items are set in bold:

AgamP4_2L | organism=Anopheles_gambiae_PEST | version=AgamP4 | length=49364325 | SO=chromosome
AgamP4_2R | organism=Anopheles_gambiae_PEST | version=AgamP4 | length=61545105 | SO=chromosome

Bold: Indicates a new term, an important word, or words that you see onscreen. For example, words in menus or dialog boxes appear in the text like this. Here is an example: “For the Chunk column, see Chapter 11 – but you can safely ignore it for now.”

Tips or important notes

Appear like this.