if crf: f=open(contigfile,'w')
x=1
for i in contigs:
#print "A contig, ", i
if crf:
string_seq = i[1]
#print "String seq is", string_seq
nuc_index = i[0][0]
dict_seq = {}
# the sequence string at
for nuc in string_seq:
dict_seq[nuc_index] = nuc
nuc_index += 1
#print "original dict_seq is", dict_seq
# add info for consensus dictionary
mut_events = mtvcf_main_analysis(mt_table, sam_file, sample_name, tail=tail)
consensus_single = get_consensus_single(mut_events[mut_events.keys()[0]],hf=hf)
#print consensus_single
# alter dict_seq keys for the implementation
# of the consensus information
#
#print "CONSENSUS SINGLE: ", consensus_single
for p_info in consensus_single:
if p_info[0] in dict_seq.keys():
#print "P_INFO: ", p_info
# maybe I don't need to consider mismatch but I'll do anyway
if p_info[-1] == 'mism':
dict_seq[p_info[0]] = p_info[1][0] # check THIS
elif p_info[-1] == 'ins':
# in the consensus, the ins is reported as the nuc of pos of the ins + the inserted bases
dict_seq[p_info[0]+'.1'] = p_info[1][0][1:]
x = 1
for i in contigs:
#print "A contig, ", i
if crf:
string_seq = i[1]
#print "String seq is", string_seq
nuc_index = i[0][0]
dict_seq = {}
# the sequence string at
for nuc in string_seq:
dict_seq[nuc_index] = nuc
nuc_index += 1
#print "original dict_seq is", dict_seq
# add info for consensus dictionary
mut_events = mtvcf_main_analysis(mt_table,
sam_file,
sample_name,
tail=tail)
consensus_single = get_consensus_single(
mut_events[mut_events.keys()[0]], hf=hf)
#print consensus_single
# alter dict_seq keys for the implementation
# of the consensus information
#
#print "CONSENSUS SINGLE: ", consensus_single
for p_info in consensus_single:
if p_info[0] in dict_seq.keys():
#print "P_INFO: ", p_info
# maybe I don't need to consider mismatch but I'll do anyway
if p_info[-1] == 'mism':
dict_seq[p_info[0]] = p_info[1][0] # check THIS
elif p_info[-1] == 'ins':
# [((contig1_start, contig1_end), dict_seq = {pos : nuc, ...}), ((contig2_start, contig2_end), dict_seq = {pos : nuc, ...}), ...]
#
# so that each dict_seq can be handled with the Consensus dict information for ambiguities and indels.
# SAMFILE, MT-TABLE FOR MTVCF_GENERATOR.
# Sample name is defined as sample_name = os.getcwd().split('/')[-1].split('_')[1]
sam_handle = basext + '.sam'
mt_table_handle = tablefile
sam_file = open(basext + '.sam', 'r')
mt_table = open(tablefile, 'r').readlines()
if type(sample_name) == (list):
sample_name = sample_name[0]
mut_events = mtvcf_main_analysis(mt_table,
sam_file,
sample_name,
tail=tail,
Q=mqual,
minrd=cov)
print "Heteroplasmic range for IUPAC in consensus is = {0} - {1}\n".format(
hf_min, hf_max)
if os.path.exists('../VCF_dict_tmp'):
VCF_dict = ast.literal_eval(open('../VCF_dict_tmp',
'r').read()) # global VCF dict
else:
VCF_dict = {} # global VCF dict
contigs_wdict = []
if crf: f = open(contigfile, 'w')
x = 1
for i in contigs:
#initialize new_i
new_i = i
print '============================='
print ""
#
sam_file = open(basext+'.sam', 'r')
sam = sam_file.readlines()
sam_file.close()
mt_table_file = open(tablefile, 'r')
mt_table = mt_table_file.readlines()
mt_table_file.close()
# Calling of indels and mismatches. In the case of indels, mt_table (file that was generated in a
# previous step) is not used. However, for calling mismatches I think it is.
print " -Calling mtvcf_main_analysis..."
mut_events = mtVariantCaller.mtvcf_main_analysis(mt_table, sam, sample_name, cov, indel_obs, tail)
print " -mtvcf_main_analysis DONE"
if os.path.exists('..'+os.sep+'VCF_dict_tmp'):
VCF_dict = ast.literal_eval(open('..'+os.sep+'VCF_dict_tmp', 'r').read()) # global VCF dict
print "Mutation events will be appended to existing global VCF dict ../VCF_dict_tmp"
else:
VCF_dict = {} # global VCF dict
print "Creating new global VCF dict ../VCF_dict_tmp"
if mut_events:
print "Updating the VCF dict..."
VCF_dict.update(mut_events)
mut_events_cellar = open('..'+os.sep+'VCF_dict_tmp', 'w')
mut_events_cellar.write(str(VCF_dict))
mut_events_cellar.close()
