def trim_ambiguous_nucleotides (sequence):
return ambiguous_pattern.sub("",sequence)
def longest_ORF (sequence):
open_reading_frames = orf_pattern.findall(sequence);
if open_reading_frames:
#trim M and X
return max(open_reading_frames,key=len)[1:-1]
else:
return ""
if __name__=="__main__":
parser = argparse.ArgumentParser(__doc__)
parser.add_argument("input_file",type=str,help="Target fasta file")
args = parser.parse_args()
sequences = (seq for seq in split_fasta(args.input_file))
for seq in sequences:
data = trim_ambiguous_nucleotides(seq.data.lower())
header = seq.header
#keep track of longest ORF for each of 3 forward frames
peptides = []
for translation in forward_frame_translate(data):
peptides.append(longest_ORF(translation))
print header
print max(peptides,key=len)
"""
Given a fasta reference, only print requested sequences (search by identifiers)
"""
import argparse
import fastaparse
parser = argparse.ArgumentParser()
parser.add_argument("reference_file",type=str,help="Reference fasta database")
parser.add_argument("id_file",type=str,help="File containing references to sequences")
args = parser.parse_args()
sequences = fastaparse.split_fasta(args.reference_file)
results = list()
for seq_id in open(args.id_file):
for seq in sequences:
if seq_id.strip() in seq.header:
results.append(seq.fasta())
for seq in results:
print seq
