def read_contigs_file(open_contigs_file, start_position=False,taxonomy_info=True):
""" Read contigs file generated by generate_contigs script"""
contigs = []
seqs = list(SeqIO.parse(open_contigs_file, "fasta"))
for seq in seqs:
if taxonomy_info:
contig_id_hash = parse_contig_description(seq.description, start_position=start_position)
contig = DNA(id=contig_id_hash["genome"], seq=str(seq.seq))
if start_position:
contig.start_position = contig_id_hash["start_position"]
contig.family = contig_id_hash["family"]
contig.genus = contig_id_hash["genus"]
contig.species = contig_id_hash["species"]
contig.contig_id = contig_id_hash["contig_id"]
else:
contig = DNA(id=seq.id,seq=str(seq.seq))
contig.contig_id = seq.id
contigs.append(contig)
return contigs
def sample_contig(genome, x_st, contig_id, start_position=False):
""" Generates a contig from genome genome
:genome - DNA object
:x_st - SampleSetting object
:contig_id - The unique id given to this contig"""
min_length = x_st.contig_min_length
max_length = x_st.contig_max_length
l = randint(min_length, max_length)
gen_l = len(genome.full_seq)
if x_st.debug_mode:
start = 0
else:
start = randint(0, (gen_l - l))
end = start + l
contig = DNA(id=genome.id + " contig", seq=genome.full_seq[start:end])
contig.contig_id = contig_id
if start_position:
contig.start_position = start
return contig
