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# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
#
"""Example using Bio.SeqIO to parse a FASTA file."""
from Bio import SeqIO
def extract_organisms(file_to_parse, fmt):
"""Extract species names from sequence description line."""
all_species = set()
for cur_record in SeqIO.parse(open(file_to_parse), fmt):
# extract the info from the description
new_species = cur_record.description.split()[1]
all_species.add(new_species)
# sorting the species wil convert the set to a list
all_species = sorted(all_species)
return all_species
if __name__ == "__main__":
print("Using Bio.SeqIO on a FASTA file")
all_species = extract_organisms("ls_orchid.fasta", "fasta")
print("number of species: %i" % len(all_species))
print("species names: %s" % all_species)
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