def output_dinuc_shuffled_fasta(fasta_fname, shuffled_fasta_fname,
num_shuffles=1):
"""
Given a FASTA file, output a dinucleotide shuffled version of it.
"""
fasta_out = fastx_utils.write_open_fastx(shuffled_fasta_fname)
for fastx_entry in fastx_utils.get_fastx_entries(fasta_fname):
fastx_name, fastx_seq = fastx_entry
shuffled_recs = []
for shuffle_num in range(num_shuffles):
shuffled_seq = \
get_dinuc_shuffles(fastx_seq)[0]
shuffled_rec = (fastx_name, shuffled_seq)
shuffled_recs.append(shuffled_rec)
fasta_utils.write_fasta(fasta_out, shuffled_recs)
fasta_out.close()
def output_dinuc_shuffled_fasta(fasta_fname,
shuffled_fasta_fname,
num_shuffles=1):
"""
Given a FASTA file, output a dinucleotide shuffled version of it.
"""
fasta_out = fastx_utils.write_open_fastx(shuffled_fasta_fname)
for fastx_entry in fastx_utils.get_fastx_entries(fasta_fname):
fastx_name, fastx_seq = fastx_entry
shuffled_recs = []
for shuffle_num in range(num_shuffles):
shuffled_seq = \
get_dinuc_shuffles(fastx_seq)[0]
shuffled_rec = (fastx_name, shuffled_seq)
shuffled_recs.append(shuffled_rec)
fasta_utils.write_fasta(fasta_out, shuffled_recs)
fasta_out.close()
def download_misc_seqs(genome, output_dir):
"""
Download assorted sequences related to genome.
"""
# Mapping from sequence label (e.g. rRNA)
# to accession numbers
organism = None
if genome.startswith("hg"):
organism = "human"
elif genome.startswith("mm"):
organism = "mouse"
else:
print "Error: Unsupported genome."
sys.exit(1)
# Fetch the accession numbers for the organism's
# misc sequences and download them
misc_seqs = NCBI_MISC_SEQS[organism]
ncbi_outdir = os.path.join(output_dir, "ncbi")
misc_outdir = os.path.join(output_dir, "misc")
utils.make_dir(ncbi_outdir)
utils.make_dir(misc_outdir)
for seq_label, access_id in misc_seqs.iteritems():
if access_id is None:
continue
output_filename = os.path.join(misc_outdir, "%s.fa" %(seq_label))
if os.path.isfile(output_filename):
print "%s exists. Skipping download.." %(seq_label)
continue
print "Downloading: %s (NCBI: %s)" %(seq_label,
access_id)
url_filename = download_ncbi_fasta(access_id, ncbi_outdir)
fasta_in = fasta_utils.read_fasta(url_filename)
fasta_out = open(output_filename, "w")
print " - Writing to: %s" %(output_filename)
# Fetch first FASTA record
rec = fasta_in.next()
curr_label, fasta_seq = rec
# Output it with the required label
new_rec = (">%s" %(seq_label), fasta_seq)
fasta_utils.write_fasta(fasta_out, [new_rec])
