def fasta(self):
"""The fasta file containing the filtered genes of this cluster
The names now will correspond to long descriptive names"""
fasta = FASTA(self.p.fasta)
if not fasta:
fasta.create()
for gene in self.filtered_genes: fasta.add_str(str(gene), name=gene.name)
fasta.close()
return fasta
def fasta(self):
"""The fasta file containing the filtered genes of this cluster
The names now will correspond to long descriptive names"""
fasta = FASTA(self.p.fasta)
if not fasta:
fasta.create()
for gene in self.filtered_genes:
fasta.add_str(str(gene), name=gene.name)
fasta.close()
return fasta
def test(self):
"""Search one sequence, and see if it works."""
# New directory #
directory = new_temp_dir()
# A randomly chosen sequence (H**o sapiens mRNA for prepro cortistatin) #
seq = """ACAAGATGCCATTGTCCCCCGGCCTCCTGCTGCTGCTGCTCTCCGGGGCCACGGCCACCGCTGCCCTGCC
CCTGGAGGGTGGCCCCACCGGCCGAGACAGCGAGCATATGCAGGAAGCGGCAGGAATAAGGAAAAGCAGC
CTCCTGACTTTCCTCGCTTGGTGGTTTGAGTGGACCTCCCAGGCCAGTGCCGGGCCCCTCATAGGAGAGG
AAGCTCGGGAGGTGGCCAGGCGGCAGGAAGGCGCACCCCCCCAGCAATCCGCGCGCCGGGACAGAATGCC
CTGCAGGAACTTCTTCTGGAAGACCTTCTCCTCCTGCAAATAAAACCTCACCCATGAATGCTCACGCAAG
TTTAATTACAGACCTGAA"""
seq = seq.replace('\n','')
seq = seq.replace(' ','')
# Make input #
input_fasta = FASTA(directory + 'input.fasta')
input_fasta.create()
input_fasta.add_str(seq, "My test sequence")
input_fasta.close()
# Make output #
out_path = directory + 'output.blast'
# Make extras parameters #
params = {'-outfmt': 0,
'-evalue': 1e-5,
'-perc_identity': 99}
# Make the search #
search = SeqSearch(input_fasta,
self.blast_db,
'nucl',
'blast',
num_threads = 1,
out_path = out_path,
params = params)
# Run it #
search.run()
# Print result #
print "Success", directory
def test(self):
"""Search one sequence, and see if it works."""
# New directory #
directory = new_temp_dir()
# A randomly chosen sequence (H**o sapiens mRNA for prepro cortistatin) #
seq = """ACAAGATGCCATTGTCCCCCGGCCTCCTGCTGCTGCTGCTCTCCGGGGCCACGGCCACCGCTGCCCTGCC
CCTGGAGGGTGGCCCCACCGGCCGAGACAGCGAGCATATGCAGGAAGCGGCAGGAATAAGGAAAAGCAGC
CTCCTGACTTTCCTCGCTTGGTGGTTTGAGTGGACCTCCCAGGCCAGTGCCGGGCCCCTCATAGGAGAGG
AAGCTCGGGAGGTGGCCAGGCGGCAGGAAGGCGCACCCCCCCAGCAATCCGCGCGCCGGGACAGAATGCC
CTGCAGGAACTTCTTCTGGAAGACCTTCTCCTCCTGCAAATAAAACCTCACCCATGAATGCTCACGCAAG
TTTAATTACAGACCTGAA"""
seq = seq.replace('\n','')
seq = seq.replace(' ','')
# Make input #
input_fasta = FASTA(directory + 'input.fasta')
input_fasta.create()
input_fasta.add_str(seq, "My test sequence")
input_fasta.close()
# Make output #
out_path = directory + 'output.blast'
# Make extras parameters #
params = {'-outfmt': 0,
'-evalue': 1e-5,
'-perc_identity': 99}
# Make the search #
search = SeqSearch(input_fasta,
self.blast_db,
'nucl',
'blast',
num_threads = 1,
out_path = out_path,
params = params)
# Run it #
search.run()
# Print result #
print("Success", directory)
faas_genes = [strip(seq) for seq in faa]
fnas_genes = [strip(seq) for seq in fna]
print faa, len(set(fnas_genes) ^ set(faas_genes)), "discrepancies"
#print "- in fna but not in faa:", [x for x in set(fnas_genes) - set(faas_genes)]
#print "- in faa but not in fna:", [x for x in set(faas_genes) - set(fnas_genes)]
#print ""
fnas_genes = [strip(seq) for fna in fnas for seq in fna]
print len(fnas_genes), len(set(fnas_genes))
for genome in faas:
out_path = genomes_dir + genome.short_prefix + '.fasta'
out_fasta = FASTA(out_path)
out_fasta.create()
for seq in genome:
out_fasta.add_str(str(seq.seq), strip(seq))
out_fasta.close()
out_fasta.gzip_to()
out_fasta.remove()
def lines():
for genome in faas:
for gene in genome:
name = strip(gene)
yield name + '\t' + gene.description[len(name):].rstrip(
' |') + '\n'
annotations_path = current_dir + '../ld12/data/annotations.tsv'
with open(annotations_path, 'w') as handle:
seq = seq.split('[')[0]
return seq
for faa,fna in zip(faas, fnas):
faas_genes = [strip(seq) for seq in faa]
fnas_genes = [strip(seq) for seq in fna]
print faa, len(set(fnas_genes) ^ set(faas_genes)), "discrepancies"
#print "- in fna but not in faa:", [x for x in set(fnas_genes) - set(faas_genes)]
#print "- in faa but not in fna:", [x for x in set(faas_genes) - set(fnas_genes)]
#print ""
fnas_genes = [strip(seq) for fna in fnas for seq in fna]
print len(fnas_genes), len(set(fnas_genes))
for genome in faas:
out_path = genomes_dir + genome.short_prefix + '.fasta'
out_fasta = FASTA(out_path)
out_fasta.create()
for seq in genome: out_fasta.add_str(str(seq.seq), strip(seq))
out_fasta.close()
out_fasta.gzip_to()
out_fasta.remove()
def lines():
for genome in faas:
for gene in genome:
name = strip(gene)
yield name + '\t' + gene.description[len(name):].rstrip(' |') + '\n'
annotations_path = current_dir + '../ld12/data/annotations.tsv'
with open(annotations_path, 'w') as handle: handle.writelines(lines())
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()
