class Foraminifera(Database):
"""This is a custom database containing exlcusively Foraminifera sequences.
https://genev.unige.ch/research/laboratory/Jan-Pawlowski
You should place the file "foram_db_cor.fasta" in: ~/databases/foraminifera/
Then you can run this:
from seqsearch.databases.foraminifera import foraminifera
foraminifera.process()
print foraminifera.tax_depth_freq
"""
short_name = "foraminifera"
long_name = 'The custom made Foraminifera database as received by email on 7th April 2017'
all_paths = """
/foram_db_cor.fasta
/foram_mothur.fasta
/foram_mothur.tax
"""
@property
def rank_names(self):
"""The names of the ranks. Total 9 ranks."""
return ['Domain', # 0
'Kingdom', # 1
'Phylum', # 2
'Class', # 3
'Order', # 4
'Family', # 5
'Tribe', # 6
'Genus', # 7
'Species'] # 8
def __init__(self, base_dir=None):
# Base directory #
if base_dir is None: base_dir = home
self.base_dir = base_dir + 'databases/' + self.short_name + '/'
self.p = AutoPaths(self.base_dir, self.all_paths)
# The results #
self.alignment = FASTA(self.p.mothur_fasta)
self.taxonomy = FilePath(self.p.mothur_tax)
# The part that mothur will use for naming files #
self.nickname = "foram_mothur"
def process(self):
# The file that was received by email without documentation T_T #
raw = FASTA(self.p.cor)
# Open files #
self.alignment.create()
self.taxonomy.create()
# Loop #
for seq in raw:
# Parse #
name = seq.id[11:].split('|')
num = name.pop(0)
# Check #
for x in name: assert ';' not in x
for x in name: assert '\t' not in x
# Make ranks #
ranks = ['Eukaryota' , # 0 Domain
'Rhizaria' , # 1 Kingdom
'Foraminifera' , # 2 Phylum
name[0] , # 3 Class
name[1] , # 4 Order
name[2] , # 5 Family
name[3] , # 6 Tribe
name[4] , # 7 Genus
name[5]] # 8 Species
# The taxonomy string #
tax_line = ';'.join(ranks)
# Add sequence to the new fasta file #
self.alignment.add_str(str(seq.seq), name="foram" + num)
# Add the taxonomy to the tax file #
self.taxonomy.add_str("foram" + num + '\t' + tax_line + '\n')
# Close files #
self.alignment.close()
self.taxonomy.close()
