def getPopGenomeStats(inputFile):
totleng = 0
totcount = 0
for head, seq in FastaReader(inputFile):
totcount += 1
totleng += len(seq)
averagegenomesize = float(totleng) / float(totcount)
popgenomesamples = totcount
return averagegenomesize, popgenomesamples
def load_chasis(inputFile):
fr = FastaReader(inputFile)
counter = 0
h = None
s = None
for header, seq in fr:
h = header
s = seq
counter += 1
if counter > 1:
raise ValueError(
"Chasis file must only contain a single reference genome")
return h, s
def read_te_fasta(self, fasta_file):
from fastaIO import FastaReader
seq_dict1 = {}
seq_dict2 = {}
ct = 1
handle = FastaReader(fasta_file)
for seq_id, seq in handle:
seq_dict1[ct] = seq_id
seq_dict2[ct] = seq
ct = ct + 1
handle.close()
return seq_dict1, seq_dict2
def read_chesis_fasta(self, fasta_file):
from fastaIO import FastaReader
seq_dict = {}
ct = 1
handle = FastaReader(fasta_file)
seq_id = ""
seq_length = 0
chr_seq = ""
for seq_id, seq in handle:
seq_length = len(seq)
chr_seq = seq
handle.close()
return seq_id, seq_length, chr_seq
