Biopython Tutorial and Cookbook Japanese translation (4.6)

4.6 The format method To 4.5 The format() method of the SeqRecord class gives a string containing your record formatted using one of the output file formats supported by Bio.SeqIO, such as FASTA: ** SeqRecord format () can convert record (array) to a string supported by Bio.SeqIO, for example FASTA **

from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord
from Bio.Alphabet import generic_protein

record = SeqRecord(
    Seq(
        "MMYQQGCFAGGTVLRLAKDLAENNRGARVLVVCSEITAVTFRGPSETHLDSMVGQALFGD"
        "GAGAVIVGSDPDLSVERPLYELVWTGATLLPDSEGAIDGHLREVGLTFHLLKDVPGLISK"
        "NIEKSLKEAFTPLGISDWNSTFWIAHPGGPAILDQVEAKLGLKEEKMRATREVLSEYGNM"
        "SSAC",
        generic_protein,
    ),
    id="gi|14150838|gb|AAK54648.1|AF376133_1",
    description="chalcone synthase [Cucumis sativus]",
)

print(record.format("fasta"))

which should give:

>gi|14150838|gb|AAK54648.1|AF376133_1 chalcone synthase [Cucumis sativus]
MMYQQGCFAGGTVLRLAKDLAENNRGARVLVVCSEITAVTFRGPSETHLDSMVGQALFGD
GAGAVIVGSDPDLSVERPLYELVWTGATLLPDSEGAIDGHLREVGLTFHLLKDVPGLISK
NIEKSLKEAFTPLGISDWNSTFWIAHPGGPAILDQVEAKLGLKEEKMRATREVLSEYGNM
SSAC

This format method takes a single mandatory argument, a lower case string which is supported by Bio.SeqIO as an output format (see Chapter 5). However, some of the file formats Bio.SeqIO can write to require more than one record (typically the case for multiple sequence alignment formats), and thus won’t work via this format() method. See also Section 5.5.4. The *** format method requires an argument, the format of the output supported by Bio.SeqIO (lowercase string). But if you have multiple arrays, you can't use the format () method. See 5.5.4. *** ***