dictionary[key] = valuelist[0:10]
from pprint import pprint
fielddict_file = open("global.dict", "w")
pprint(dictionary, fielddict_file)
fielddict_file.close()
reference = []
for i, j in dictionary.iteritems():
n = 0
combined_seq = MultipleSeqAlignment([
SeqRecord(Seq('', generic_dna), id="hg19"),
SeqRecord(Seq('', generic_dna), id="panTro4"),
SeqRecord(Seq('', generic_dna), id="gorGor3"),
SeqRecord(Seq('', generic_dna), id="rheMac3"),
SeqRecord(Seq('', generic_dna), id="ponAbe2")
])
combined_seq.sort()
for ref in j:
n = n + 1
seq_records = AlignIO.read(ref, 'fasta')
seq_records.description = ""
seq_records.sort()
combined_seq = combined_seq + seq_records
combined_seq.description = ""
with open('%s.ref' % i, 'w') as write_file:
AlignIO.write(combined_seq, write_file, 'fasta')
referencelist = open('reference.list', 'a')
referencelist.write('%s\t%i\n' % (i, n))
