def translateSixFrame(seq):
"""Translate seq in 6 frames"""
from cogent import DNA
from cogent.core.genetic_code import DEFAULT as standard_code
translations = standard_code.sixframes(seq)
stops_frame1 = standard_code.getStopIndices(seq, start=0)
print translations
return
def translateSixFrame(seq):
"""Translate seq in 6 frames"""
from cogent import DNA
from cogent.core.genetic_code import DEFAULT as standard_code
translations = standard_code.sixframes(seq)
stops_frame1 = standard_code.getStopIndices(seq, start=0)
print translations
return
if not protein in dna_sequence_dic:
nucleotide_not_found.append(protein)
continue
sequence_with_stop_codons = DNA.makeSequence(dna_sequence_dic[protein])
#Check if the sequence is the right one, and check for in frame stops
#It seems that in JGI annotation, when scaffolds are joined, the resulted proteins do not match
#the DNA sequence
#Right now, I'll just remove those sequences, and deal with that later
if len(sequence_with_stop_codons) % 3 == 0:
seq_no_stop_codon = sequence_with_stop_codons.withoutTerminalStopCodon()
#Chec for inframe stop codons
stops_frame = standard_code.getStopIndices(seq_no_stop_codon, start=0)
if len(stops_frame) > 0:
inframe_stops.append([cluster, genome_id, protein_id])
else:
curated_protein_list[protein] = seq_no_stop_codon
else:
frameshift_cases.append([cluster, genome_id, protein_id])
if len(curated_protein_list) < 2: # Only take those clusters with 3 sequences or more
clusters_too_short.append(cluster)
continue
#Alignments and output data
continue
sequence_with_stop_codons = DNA.makeSequence(
dna_sequence_dic[protein])
#Check if the sequence is the right one, and check for in frame stops
#It seems that in JGI annotation, when scaffolds are joined, the resulted proteins do not match
#the DNA sequence
#Right now, I'll just remove those sequences, and deal with that later
if len(sequence_with_stop_codons) % 3 == 0:
seq_no_stop_codon = sequence_with_stop_codons.withoutTerminalStopCodon(
)
#Chec for inframe stop codons
stops_frame = standard_code.getStopIndices(seq_no_stop_codon,
start=0)
if len(stops_frame) > 0:
inframe_stops.append([cluster, genome_id, protein_id])
else:
curated_protein_list[protein] = seq_no_stop_codon
else:
frameshift_cases.append([cluster, genome_id, protein_id])
if len(curated_protein_list
) < 2: # Only take those clusters with 3 sequences or more
clusters_too_short.append(cluster)
continue