def peak2fasta(peak_ids, ref_genome):
'''
Convert peak_id into fasta object.
Args:
peak_id (str or list of str): Peak_id. e.g. "chr5_0930303_9499409"
or it can be a list of peak_id. e.g. ["chr5_0930303_9499409", "chr11_123445555_123445577"]
ref_genome (str): Reference genome name. e.g. "mm9", "mm10", "hg19" etc
Returns:
gimmemotifs fasta object: DNA sequence in fasta format
'''
genome_data = Genome(ref_genome)
def peak2seq(peak_id):
chromosome_name, start, end = decompose_chrstr(peak_id)
locus = (int(start), int(end))
tmp = genome_data[chromosome_name][locus[0]:locus[1]]
name = f"{tmp.name}_{tmp.start}_{tmp.end}"
seq = tmp.seq
return (name, seq)
if type(peak_ids) is str:
peak_ids = [peak_ids]
fasta = Fasta()
for peak_id in peak_ids:
name, seq = peak2seq(peak_id)
fasta.add(name, seq)
return fasta
def remove_zero_seq(fasta_object):
"""
Remove DNA sequence with zero length
"""
fasta = Fasta()
for i, seq in enumerate(fasta_object.seqs):
if seq:
name = fasta_object.ids[i]
fasta.add(name, seq)
return fasta
