def do_buffer(buffer, msr, spc, psc, args):
outputs = []
for entries in buffer:
l = []
r = []
for sam in entries:
#Print line if its not a pair
if not_a_mate_sam(sam):
if not args.mates_only:
outputs.append(sam.get_line())
continue
if sam.check_flag(64): l.append(sam)
if sam.check_flag(128): r.append(sam)
if not (len(l) == 1 and len(r) == 1):
# more than just a unique pair here
if not args.mates_only:
for sam in l:
outputs.append(sam.get_line())
for sam in r:
outputs.append(sam.get_line())
continue
#Verify pairing by reference and direction
if l[0].value('rname') != r[0].value('rname') or l[0].check_flag(
16) == r[0].check_flag(16):
sys.stderr.write(
"ERROR, these are not actually properly paired as we were led to believe\n"
)
sys.exit()
p1 = PSL(spc.convert_line(l[0].get_line()))
if not re.search('[HP]', l[0].value('cigar')):
p1.set_query(l[0].value('seq'))
p1.set_quality_seq(l[0].value('qual'))
if l[0].check_flag(16):
# set the query to what it actually is
p1.set_query(rc(l[0].value('seq')))
p1.set_quality_seq(l[0].value('qual')[::-1])
p2 = PSL(spc.convert_line(r[0].get_line()))
if not re.search('[HP]', r[0].value('cigar')):
p2.set_query(r[0].value('seq'))
p2.set_quality_seq(r[0].value('qual'))
if r[0].check_flag(16):
# set the query to what it actually is
p2.set_query(rc(r[0].value('seq')))
p2.set_quality_seq(r[0].value('qual')[::-1])
p12 = join_mated(p1, p2)
if not p12:
if not args.mates_only:
outputs.append(l[0].get_line())
outputs.append(r[0].get_line())
continue
#if p1.value('strand') == '-' and p2.value('strand') == '+' \
#and p2.value('tEnd') < p1.value('tStart'):
sline = psc.convert_line(p12.get_line(),
query_sequence=p12.get_query(),
quality_sequence=p12.get_quality_seq())
#print p12.get_line()
outputs.append(sline)
return outputs
def overlapped(seq1, seq2, thresh):
v1 = starts_with(seq1, seq2, thresh)
if v1: return v1
v2 = starts_with(seq2, seq1, thresh)
if v2: return v2
v3 = starts_with(seq1, rc(seq2), thresh)
if v3: v3
v4 = starts_with(seq2, rc(seq1), thresh)
if v4: v4
return False
def overlapped(seq1,seq2,thresh): v1 = starts_with(seq1,seq2,thresh) if v1: return v1 v2 = starts_with(seq2,seq1,thresh) if v2: return v2 v3 = starts_with(seq1,rc(seq2),thresh) if v3: v3 v4 = starts_with(seq2,rc(seq1),thresh) if v4: v4 return False
def add_sequence(self,seq):
seq = seq.upper()
for i in range(len(seq)+1-self.ksize):
mer = seq[i:i+self.ksize]
if mer not in self.mers:
self.mers[mer] = 0
self.mers[mer] += 1
if rc(mer) not in self.mers:
self.mers[rc(mer)] = 0
self.mers[rc(mer)] += 1
return
def add_sequence(self, seq):
seq = seq.upper()
for i in range(len(seq) + 1 - self.ksize):
mer = seq[i:i + self.ksize]
if mer not in self.mers:
self.mers[mer] = 0
self.mers[mer] += 1
if rc(mer) not in self.mers:
self.mers[rc(mer)] = 0
self.mers[rc(mer)] += 1
return
def do_buffer(buffer,msr,spc,psc,args):
outputs = []
for entries in buffer:
l = []
r = []
for sam in entries:
#Print line if its not a pair
if not_a_mate_sam(sam):
if not args.mates_only:
outputs.append(sam.get_line())
continue
if sam.check_flag(64): l.append(sam)
if sam.check_flag(128): r.append(sam)
if not (len(l)==1 and len(r)==1):
# more than just a unique pair here
if not args.mates_only:
for sam in l: outputs.append(sam.get_line())
for sam in r: outputs.append(sam.get_line())
continue
#Verify pairing by reference and direction
if l[0].value('rname') != r[0].value('rname') or l[0].check_flag(16) == r[0].check_flag(16):
sys.stderr.write("ERROR, these are not actually properly paired as we were led to believe\n")
sys.exit()
p1 = PSL(spc.convert_line(l[0].get_line()))
if not re.search('[HP]',l[0].value('cigar')):
p1.set_query(l[0].value('seq'))
p1.set_quality_seq(l[0].value('qual'))
if l[0].check_flag(16):
# set the query to what it actually is
p1.set_query(rc(l[0].value('seq')))
p1.set_quality_seq(l[0].value('qual')[::-1])
p2 = PSL(spc.convert_line(r[0].get_line()))
if not re.search('[HP]',r[0].value('cigar')):
p2.set_query(r[0].value('seq'))
p2.set_quality_seq(r[0].value('qual'))
if r[0].check_flag(16):
# set the query to what it actually is
p2.set_query(rc(r[0].value('seq')))
p2.set_quality_seq(r[0].value('qual')[::-1])
p12 = join_mated(p1,p2)
if not p12:
if not args.mates_only:
outputs.append(l[0].get_line())
outputs.append(r[0].get_line())
continue
#if p1.value('strand') == '-' and p2.value('strand') == '+' \
#and p2.value('tEnd') < p1.value('tStart'):
sline = psc.convert_line(p12.get_line(),query_sequence=p12.get_query(),quality_sequence=p12.get_quality_seq())
#print p12.get_line()
outputs.append(sline)
return outputs
def construct_sequences(self,ref_hash):
self.sequence = ''
for b in self.bounds:
arr = b.get_bed_array()
if re.search(',',arr[0]) or re.search('/',arr[0]) or re.search('\|',arr[0]):
sys.stderr.write("ERROR: original reference chromosome cannot have a comma, forward slash or vertical bar in its name\n")
sys.exit()
if arr[0] not in ref_hash:
sys.stderr.write("ERROR: sequence "+str(arr[0])+" not found in reference\n")
sys.exit()
seq = ''
if arr[3] == '+':
seq = ref_hash[arr[0]][arr[1]:arr[2]]
elif arr[3] == '-':
seq = rc(ref_hash[arr[0]][arr[1]:arr[2]])
else:
sys.stderr.write("ERROR: no direction set in bed\n")
self.sequence += seq.upper()
return
def align(self):
self.s1 = self.input_s1
self.s2 = self.input_s2
self.M = None
outs1 = self.execute_sw_alignment()
outs1.append('+')
outs1.append('+')
if self.bidirectional:
self.s1 = self.input_s1
self.s2 = rc(self.input_s2)
self.M = None
outs2 = self.execute_sw_alignment()
outs2.append('+')
outs2.append('-')
if outs2[0] > outs1[0]:
outs1 = outs2
result = Alignment()
result.set_alignment(self.gapopen,self.gapextend,self.match,\
self.mismatch,self.bidirectional,outs1[0],outs1[1],\
outs1[2],outs1[3],outs1[4],outs1[5],outs1[6],\
self.input_s1,self.input_s2)
return result
def align(self):
self.s1 = self.input_s1
self.s2 = self.input_s2
self.M = None
outs1 = self.execute_sw_alignment()
outs1.append('+')
outs1.append('+')
if self.bidirectional:
self.s1 = self.input_s1
self.s2 = rc(self.input_s2)
self.M = None
outs2 = self.execute_sw_alignment()
outs2.append('+')
outs2.append('-')
if outs2[0] > outs1[0]:
outs1 = outs2
result = Alignment()
result.set_alignment(self.gapopen,self.gapextend,self.match,\
self.mismatch,self.bidirectional,outs1[0],outs1[1],\
outs1[2],outs1[3],outs1[4],outs1[5],outs1[6],\
self.input_s1,self.input_s2)
return result
def construct_sequences(self, ref_hash):
self.sequence = ''
for b in self.bounds:
arr = b.get_bed_array()
if re.search(',', arr[0]) or re.search('/', arr[0]) or re.search(
'\|', arr[0]):
sys.stderr.write(
"ERROR: original reference chromosome cannot have a comma, forward slash or vertical bar in its name\n"
)
sys.exit()
if arr[0] not in ref_hash:
sys.stderr.write("ERROR: sequence " + str(arr[0]) +
" not found in reference\n")
sys.exit()
seq = ''
if arr[3] == '+':
seq = ref_hash[arr[0]][arr[1]:arr[2]]
elif arr[3] == '-':
seq = rc(ref_hash[arr[0]][arr[1]:arr[2]])
else:
sys.stderr.write("ERROR: no direction set in bed\n")
self.sequence += seq.upper()
return
def main():
parser = argparse.ArgumentParser(description="Correct the matches/mismatches and Ncount of a PSL file")
parser.add_argument('input',help="PSLFILE or - for STIDN")
parser.add_argument('reference',help="FASTAFILE reference genome")
parser.add_argument('query',help="FASTAFILE query sequences")
parser.add_argument('--minimum_intron_size',type=int,default=68,help="INT")
#parser.add_argument('--ordered_query',action='store_true',help="The query psl and fasta are both ordered by query name for optimal performance")
args = parser.parse_args()
# Read in the reference genome
sys.stderr.write("Reading in reference genome\n")
g = read_fasta_into_hash(args.reference)
sys.stderr.write("Finished reading "+str(len(g.keys()))+" reference sequences\n")
inf = sys.stdin
if args.input != '-':
inf = open(args.input)
fhr = FastaHandleReader(open(args.query))
last_fasta = fhr.read_entry()
if not last_fasta:
sys.stderr.write("ERROR: No query sequences\n")
sys.exit()
for line in inf:
p = PSLBasics.PSL(line)
if not p.validate():
sys.stderr.write("WARNING skipping invalid PSL entry. This script fixes improper mismatch and match counts .. and gap counts... it doesn't perform miracles. Problem line:\n"+line.rstrip()+"\n")
n = p.value('qName')
if not last_fasta:
sys.stderr.write("ERROR: Ran out of query sequences too soon. Are they sorted properly\n")
sys.exit()
while last_fasta['name'] != n:
last_fasta = fhr.read_entry()
p.set_query(last_fasta['seq'])
p.set_reference_dictionary(g)
p.correct_stats()
print p.get_line()
continue
f = last_fasta
nCount = 0
matches = 0
misMatches = 0
prev_qE = 0
prev_tE = 0
qNumInsert = 0
qBaseInsert = 0
tNumInsert = 0
tBaseInsert = 0
for i in range(p.value('blockCount')):
blen = p.value('blockSizes')[i]
qS = p.value('qStarts')[i] #query start
qE = qS + blen #query end
tS = p.value('tStarts')[i] #target start
tE = tS + blen #target end
#Work on gaps
if prev_qE > 0 or prev_tE > 0: #if its not our first time through
tgap = tS-prev_tE
if tgap < args.minimum_intron_size and tgap > 0:
tNumInsert += 1
tBaseInsert += tgap
qgap = qS-prev_qE
if qgap > 0:
qNumInsert += 1
qBaseInsert += qgap
query = f['seq']
if p.value('strand') == '-':
query = rc(f['seq'])
qseq = query[qS:qE].upper()
rseq = g[p.value('tName')][tS:tE].upper()
#print qseq+"\n"+rseq+"\n"
for j in range(0,blen):
if qseq[j] == 'N':
nCount += 1
elif qseq[j] == rseq[j]:
matches += 1
else:
misMatches += 1
prev_qE = qE
prev_tE = tE
p.entry['matches'] = matches
p.entry['misMatches'] = misMatches
p.entry['nCount'] = nCount
p.entry['qNumInsert'] = qNumInsert
p.entry['qBaseInsert'] = qBaseInsert
p.entry['tNumInsert'] = tNumInsert
p.entry['tBaseInsert'] = tBaseInsert
p.entry['qSize'] = len(query)
p.entry['tSize'] = len(g[p.value('tName')])
print p.get_line()
#p.pretty_print(100)
fhr.close()
def combine(left,right,args,reference_splices,seq,read,orientation):
#Kind of the business end where we combine two psl entries
# Perform a check for an overlap (or near gap) sufficient for consideration
if left['qEnd'] < right['qStart']-args.max_gap_size: # no overlap may want to have a seperate parameter for a max gap size
return None
target_options = get_options(left, \
min(left['qEnd'],right['qStart']+1), \
left['qEnd'], \
right, \
right['qStart']+1, \
max(left['qEnd'],right['qStart']+1))
# Try to find the junction site
junction_choice = None
reference_options = []
for j in [json.loads(x) for x in reference_splices]:
if j[0] in target_options:
if j[1] in target_options[j[0]]:
for op in target_options[j[0]][j[1]]:
dist = abs(op[2]-1)+op[3]+op[4]
# this is where we keep ourselves from looking too far away
if dist < args.max_search_expand:
reference_options.append([j[0],j[1]] + op)
# check for a cannonical spice site
strand = left['strand']
candidate_options = []
for l_t in target_options:
for r_t in target_options[l_t]:
candidate = seq[l_t:l_t+2].upper()+'-'+seq[r_t-3:r_t-1].upper()
iscan = False
if strand == '+' and is_canon(candidate):
iscan = True
if strand == '-' and is_revcanon(candidate):
iscan = True
if iscan:
for entry in target_options[l_t][r_t]:
dist = abs(entry[2]-1)+entry[3]+entry[4]
# this is where we keep ourselves from looking too far away
if dist < args.max_search_expand:
candidate_options.append([l_t,r_t]+entry+[strand,candidate])
#for c in candidate_options: print c
if len(candidate_options) == 0: return None
# For choosing the best candidate we don't need to align all of the seq
prefered_alignment_length = 50
# Which left alignment segment has candidates in it?
leftlen = len(left['qStarts'])
minleft_query = min([x[2] for x in candidate_options])
left_nearest = 0
for i in range(0,leftlen):
if minleft_query >= left['qStarts'][i] + 1:
left_nearest = i
else:
break
left_choice = left_nearest
if left_nearest > 0:
for i in range(left_nearest,0-1,-1):
tot = left['qStarts'][left_nearest]-left['qStarts'][i]
if tot > prefered_alignment_length:
left_choice = i
break
left_choice = i
# Which right alignment segment has candidates in it?
rightlen = len(right['qStarts'])
maxright_query = max([x[3] for x in candidate_options])
right_nearest = 0
for i in range(0,rightlen):
if maxright_query <= right['qStarts'][i]+right['blockSizes'][i]:
break
else:
right_nearest = i
right_choice = right_nearest
if right_nearest > 0:
for i in range(right_nearest,rightlen):
tot = (right['qStarts'][i]+right['blockSizes'][i])-(right['qStarts'][right_nearest]+right['blockSizes'][right_nearest])
if tot > prefered_alignment_length:
right_choice = i
break
right_choice = i
# now left_choice and right_choice contain bounds to align
# we can come up with options based on a needleman wunsch across the entire thing
wread = read
if strand == '-': wread = rc(read)
newoptions = []
for option in reference_options + candidate_options:
#leftlen = len(left['qStarts'])
#rightlen = len(right['qStarts'])
[a1,a2,score] = needleman_wunsch( \
wread[left['qStarts'][left_choice]:right['qStarts'][right_choice]+right['blockSizes'][right_choice]].upper(), \
seq[left['tStarts'][left_choice]:option[0]].upper() + \
seq[option[1]-1:right['tStarts'][right_choice]+right['blockSizes'][right_choice]].upper())
newoptions.append([score,a1,a2]+[option])
#best_option = get_best_option(reference_options, candidate_options, args, strand)
#if not best_option:
# return None
[best_option,best_score,best_align] = get_best_option2(newoptions)
if not best_option:
return None
#print best_option
#print best_align[0]
#print best_align[1]
combo = do_combine_operation(best_option,left,right,read,seq,args)
return combo
def sam_to_nav(self,line):
self.line_count += 1
if self.line_count % self.thread_count != self.thread_index-1:
return None
if not self.LR_seq:
sys.stderr.write("ERROR initialize target first\n")
if not self.SR_file:
sys.stderr.write("ERROR initialize query first\n")
if (line[0] == '@'):
return None
line_fields = line.strip().split('\t')
cigar = line_fields[5]
if ((cigar == '*') or (cigar == '.')):
return None
SR_name = line_fields[0]
if (SR_name != self.current_query):
[self.SR_seq, self.SR_idx_seq] = get_SR_sequence(self.SR_file, self.SR_idx_file, SR_name)
self.SR_seq_rvs_cmplmnt = rc(self.SR_seq)
self.current_query = SR_name
if (int(line_fields[1]) & 0x10): # Check if seq is reversed complement
line_fields[3] = '-' + line_fields[3]
else:
line_fields[3] = '+' + line_fields[3]
align_list = [','.join([line_fields[2], line_fields[3], line_fields[5], str(0)])]
if (not self.one_line_per_alignment): # BWA reports all alignment per read in one line
multi_align_str = ','.join([line_fields[2], line_fields[3], line_fields[5], str(0)]) + ';'
for fields_idx in range(11, len(line_fields)):
if (line_fields[fields_idx][0:5] == 'XA:Z:'):
multi_align_str += line_fields[fields_idx][5:]
break
align_list = multi_align_str[:-1].split(';')
read_seq_len = len(self.SR_seq)
ostrings = []
for align_str in align_list:
err_state = False
fields = align_str.split(',')
ref_seq = self.LR_seq[fields[0]]
ref_seq_len = len(ref_seq)
if (fields[1][0] == '-'): # Check if seq is reversed complement
read_seq = self.SR_seq_rvs_cmplmnt
pseudo_SR_name = "-" + SR_name
else:
read_seq = self.SR_seq
pseudo_SR_name = SR_name
fields[1] = fields[1][1:]
read_idx = 0
sub_ref_idx = 1 # 1-offset address
ref_idx = int(fields[1]) - 1 # convert to 0-offset address
diff_list = []
cigar_list = re.split('(M|I|D)', fields[2])
num_err = 0
for idx in range(1, len(cigar_list), 2):
if (cigar_list[idx - 1].isdigit()):
if (cigar_list[idx] == 'M'):
subseq_len = int(cigar_list[idx - 1])
if ((read_idx + subseq_len > read_seq_len) or
(ref_idx + subseq_len > ref_seq_len)):
err_state = True
break
read_subseq = list(read_seq[read_idx:(read_idx + subseq_len)])
ref_subseq = list(ref_seq[ref_idx:(ref_idx + subseq_len)])
mut_indices = [x for x in range(len(read_subseq)) if read_subseq[x] != ref_subseq[x]]
for mut_idx in mut_indices:
if (read_subseq[mut_idx] != "N"):
diff_list += [str(sub_ref_idx + mut_idx) + ref_subseq[mut_idx] + '>' + read_subseq[mut_idx]]
read_idx += subseq_len
ref_idx += subseq_len
sub_ref_idx += subseq_len
num_err += len(mut_indices)
elif (cigar_list[idx] == 'I'):
subseq_len = int(cigar_list[idx - 1])
if (read_idx + subseq_len > read_seq_len):
err_state = True
break
insert_str = re.sub(r'N|n', '', read_seq[read_idx:(read_idx + int(cigar_list[idx - 1]))])
if (insert_str != ""):
diff_list += [str(sub_ref_idx) + '+' + read_seq[read_idx:(read_idx + subseq_len)]]
read_idx += subseq_len
num_err += subseq_len
elif (cigar_list[idx] == 'D'):
subseq_len = int(cigar_list[idx - 1])
if (ref_idx + subseq_len > ref_seq_len):
err_state = True
break
for del_idx in range(subseq_len):
diff_list += [str(sub_ref_idx + del_idx) + '-' + ref_seq[ref_idx + del_idx]]
ref_idx += subseq_len
sub_ref_idx += subseq_len
num_err += subseq_len
else:
#print 'Err in cigar: tag : ' + line
err_state = True
break
if ((cigar_list[-1] == '') and (not err_state)):
if (len(diff_list) == 0):
diff_list.append("*")
err_rate = (100 * num_err) / read_seq_len
if (err_rate <= self.error_rate_threshold):
ostrings.append('\t'.join([pseudo_SR_name, fields[0], fields[1], ' '.join(diff_list),self.SR_seq, self.SR_idx_seq]))
if len(ostrings) == 0: return None
return ostrings
def main():
parser = argparse.ArgumentParser(
description="Convert a sam file into a psl file")
parser.add_argument('--genome',
help="FASTA input file of reference genome")
parser.add_argument('--get_secondary_alignments',
action='store_true',
help="Report SA:Z secondary alignments as well")
parser.add_argument('--get_alternative_alignments',
action='store_true',
help="Report XA:Z alternative alignments as well")
parser.add_argument(
'--get_all_alignments',
action='store_true',
help="Report SA:Z and XA:Z alternative alignments as well")
parser.add_argument('--give_unique_names',
action='store_true',
help="Output query names will be unique.")
group = parser.add_mutually_exclusive_group()
group.add_argument(
'--output_fasta',
help=
"FILENAME to save an outgoing fasta. Only works for primary alignments."
)
group.add_argument(
'--output_fastq',
help=
"FILENAME to save an outgoing fastq. Only works for primary alignments."
)
parser.add_argument('infile', help="FILENAME input file or '-' for STDIN")
parser.add_argument('-o',
'--output',
help="FILENAME for the output, STDOUT if not set.")
args = parser.parse_args()
if (args.output_fasta
or args.output_fastq) and (args.get_secondary_alignments
or args.get_alternative_alignments
or args.get_all_alignments):
sys.stderr.write(
"ERROR, can only output the fastq/fasta if we are doing primary alignments only.\n"
)
sys.exit()
inf = sys.stdin
if args.infile != '-':
inf = open(args.infile)
of = sys.stdout
if args.output:
of = open(args.output, 'w')
spcf = SamBasics.SAMtoPSLconversionFactory()
if args.genome: spcf.set_genome(args.genome)
off = None
if args.output_fasta:
off = open(args.output_fasta, 'w')
if args.output_fastq:
off = open(args.output_fastq, 'w')
z = 0
for line in inf:
line = line.rstrip()
if SamBasics.is_header(line):
spcf.read_header_line(line)
continue
# We have a line to convert
psl = spcf.convert_line(line)
if psl:
pobj = PSL(psl)
z += 1
if args.give_unique_names:
pobj.entry['qName'] = 'Q' + str(z)
of.write(pobj.get_line() + "\n")
if args.output_fastq or args.output_fasta:
sam = SamBasics.SAM(line)
sequence = sam.value('seq').upper()
quality = sam.value('qual')
if sam.check_flag(16):
sequence = rc(sam.value('seq').upper())
quality = sam.value('qual')[::-1]
if args.output_fasta:
off.write(">" + pobj.value('qName') + "\n" + sequence +
"\n")
elif args.output_fastq:
if len(sequence) == len(quality):
off.write("@" + pobj.value('qName') + "\n" + sequence +
"\n" + "+\n" + quality + "\n")
else:
sys.stderr.write("ERROR: sequence " + sequence +
" length (" + str(len(sequence)) +
") doesnt match quality " + quality +
" length (" + str(len(quality)) +
")\n")
sys.exit()
# Lets look for secondary alignments to convert
if args.get_secondary_alignments or args.get_all_alignments:
secondary_alignments = SamBasics.get_secondary_alignments(
line.rstrip())
for samline in secondary_alignments:
psl = spcf.convert_line(samline)
if psl:
#print "\nsecondary"
#print samline
z += 1
pobj = PSL(psl)
if args.give_unique_names:
pobj.entry['qName'] = 'Q' + str(z)
of.write(pobj.get_line() + "\n")
if args.get_alternative_alignments or args.get_all_alignments:
alternative_alignments = SamBasics.get_alternative_alignments(
line.rstrip())
for samline in alternative_alignments:
psl = spcf.convert_line(samline)
if psl:
#print "\nsecondary"
#print samline
z += 1
pobj = PSL(psl)
if args.give_unique_names:
pobj.entry['qName'] = 'Q' + str(z)
of.write(pobj.get_line() + "\n")
inf.close()
of.close()
def combine(left, right, args, reference_splices, seq, read, orientation):
#Kind of the business end where we combine two psl entries
# Perform a check for an overlap (or near gap) sufficient for consideration
if left['qEnd'] < right[
'qStart'] - args.max_gap_size: # no overlap may want to have a seperate parameter for a max gap size
return None
target_options = get_options(left, \
min(left['qEnd'],right['qStart']+1), \
left['qEnd'], \
right, \
right['qStart']+1, \
max(left['qEnd'],right['qStart']+1))
# Try to find the junction site
junction_choice = None
reference_options = []
for j in [json.loads(x) for x in reference_splices]:
if j[0] in target_options:
if j[1] in target_options[j[0]]:
for op in target_options[j[0]][j[1]]:
dist = abs(op[2] - 1) + op[3] + op[4]
# this is where we keep ourselves from looking too far away
if dist < args.max_search_expand:
reference_options.append([j[0], j[1]] + op)
# check for a cannonical spice site
strand = left['strand']
candidate_options = []
for l_t in target_options:
for r_t in target_options[l_t]:
candidate = seq[l_t:l_t + 2].upper() + '-' + seq[r_t - 3:r_t -
1].upper()
iscan = False
if strand == '+' and is_canon(candidate):
iscan = True
if strand == '-' and is_revcanon(candidate):
iscan = True
if iscan:
for entry in target_options[l_t][r_t]:
dist = abs(entry[2] - 1) + entry[3] + entry[4]
# this is where we keep ourselves from looking too far away
if dist < args.max_search_expand:
candidate_options.append([l_t, r_t] + entry +
[strand, candidate])
#for c in candidate_options: print c
if len(candidate_options) == 0: return None
# For choosing the best candidate we don't need to align all of the seq
prefered_alignment_length = 50
# Which left alignment segment has candidates in it?
leftlen = len(left['qStarts'])
minleft_query = min([x[2] for x in candidate_options])
left_nearest = 0
for i in range(0, leftlen):
if minleft_query >= left['qStarts'][i] + 1:
left_nearest = i
else:
break
left_choice = left_nearest
if left_nearest > 0:
for i in range(left_nearest, 0 - 1, -1):
tot = left['qStarts'][left_nearest] - left['qStarts'][i]
if tot > prefered_alignment_length:
left_choice = i
break
left_choice = i
# Which right alignment segment has candidates in it?
rightlen = len(right['qStarts'])
maxright_query = max([x[3] for x in candidate_options])
right_nearest = 0
for i in range(0, rightlen):
if maxright_query <= right['qStarts'][i] + right['blockSizes'][i]:
break
else:
right_nearest = i
right_choice = right_nearest
if right_nearest > 0:
for i in range(right_nearest, rightlen):
tot = (right['qStarts'][i] + right['blockSizes'][i]) - (
right['qStarts'][right_nearest] +
right['blockSizes'][right_nearest])
if tot > prefered_alignment_length:
right_choice = i
break
right_choice = i
# now left_choice and right_choice contain bounds to align
# we can come up with options based on a needleman wunsch across the entire thing
wread = read
if strand == '-': wread = rc(read)
newoptions = []
for option in reference_options + candidate_options:
#leftlen = len(left['qStarts'])
#rightlen = len(right['qStarts'])
[a1,a2,score] = needleman_wunsch( \
wread[left['qStarts'][left_choice]:right['qStarts'][right_choice]+right['blockSizes'][right_choice]].upper(), \
seq[left['tStarts'][left_choice]:option[0]].upper() + \
seq[option[1]-1:right['tStarts'][right_choice]+right['blockSizes'][right_choice]].upper())
newoptions.append([score, a1, a2] + [option])
#best_option = get_best_option(reference_options, candidate_options, args, strand)
#if not best_option:
# return None
[best_option, best_score, best_align] = get_best_option2(newoptions)
if not best_option:
return None
#print best_option
#print best_align[0]
#print best_align[1]
combo = do_combine_operation(best_option, left, right, read, seq, args)
return combo
def do_combine_operation(best_option, left, right, read, seq, args):
#print "choice is "+str(best_option)
left_target = best_option[0]
right_target = best_option[1]
left_query = best_option[2]
right_query = best_option[3]
# store for output
q_start_array = []
t_start_array = []
block_size_array = []
left_query_start = left['qStarts'][0]
left_target_start = left['tStarts'][0]
for i in range(0, len(left['tStarts'])):
tstart = left['tStarts'][i]
tend = left['tStarts'][i] + left['blockSizes'][i]
qstart = left['qStarts'][i]
qend = left['qStarts'][i] + left['blockSizes'][i]
if left_query <= qstart + 1: break
left_query_start = qstart
left_target_start = tstart
if left_query <= qend: break
q_start_array.append(qstart)
t_start_array.append(tstart)
block_size_array.append(left['blockSizes'][i])
#print "left things"
#print [left_query_start+1,left_query]
#print [left_target_start+1,left_target]
right_query_end = right['qStarts'][0] + right['blockSizes'][0]
right_target_end = right['tStarts'][0] + right['blockSizes'][0]
right_outer_index = 0
for j in range(0, len(right['tStarts'])):
tstart = right['tStarts'][j]
tend = right['tStarts'][j] + right['blockSizes'][j]
qstart = right['qStarts'][j]
qend = right['qStarts'][j] + right['blockSizes'][j]
right_outer_index = j + 1
if right_query <= qstart + 1: break
right_query_end = qend
right_target_end = tend
if right_query < qend: break
#print "right things"
#print [right_query+1,right_query_end]
#print [right_target+1,right_target_end]
working_read = read.upper()
if left['strand'] == '-': working_read = rc(read.upper())
pread = working_read[left_query_start:right_query_end]
tseq = seq[left_target_start:left_target].upper(
) + seq[right_target - 1:right_target_end].upper()
res = needleman_wunsch(pread, tseq)
#print "short needleman wunsch"
#print res[0]
#print res[1]
# Fun part of making the new portion of the alignment
qindex = left_query_start
tindex = left_target_start
in_alignment = 0
alignment = None
bynumbers = None
for i in range(0, len(res[0])):
if res[0][i] == '-': #insertion in target (gap in query)
tindex += 1
in_alignment = 0
elif res[1][i] == '-': #insertion in query (gap in target)
qindex += 1
in_alignment = 0
else: # we are in an alignment
if in_alignment == 0:
# output buffered result
if alignment:
if len(alignment[0]) > 0:
q_start_array.append(bynumbers[0])
t_start_array.append(bynumbers[1])
block_size_array.append(len(alignment[0]))
alignment = ['', '']
bynumbers = [qindex, tindex, qindex, tindex]
in_alignment = 1
alignment[0] += res[0][i]
alignment[1] += res[1][i]
bynumbers[2] += 1
bynumbers[3] += 1
qindex += 1
tindex += 1
if qindex == right_query: # switch forward
#print "switch"
#print str(tindex) + "\t" + str(right_target)
#print str(qindex) + "\t" + str(right_query)
if not tindex == right_target:
in_alignment = 0
tindex = right_target
if alignment:
if len(alignment[0]) > 0:
q_start_array.append(bynumbers[0])
t_start_array.append(bynumbers[1])
block_size_array.append(len(alignment[0]))
#print bynumbers
for i in range(right_outer_index, len(right['blockSizes'])):
q_start_array.append(right['qStarts'][i])
t_start_array.append(right['tStarts'][i])
block_size_array.append(right['blockSizes'][i])
#now we can finally construct a psl line
#we won't keep track of repeats for now
matches = 0
misMatches = 0
repMatches = 0
nCount = 0
qNumInsert = 0
qBaseInsert = 0
tNumInsert = 0
tBaseInsert = 0
strand = left['strand']
qName = left['qName']
qSize = len(read)
qStart = q_start_array[0]
qEnd = q_start_array[len(q_start_array) -
1] + block_size_array[len(block_size_array) - 1]
tName = left['tName']
tSize = len(seq)
tStart = t_start_array[0]
tEnd = t_start_array[len(t_start_array) -
1] + block_size_array[len(block_size_array) - 1]
blockCount = len(block_size_array)
blockSizes = ','.join([str(x) for x in block_size_array]) + ','
qStarts = ','.join([str(x) for x in q_start_array]) + ','
tStarts = ','.join([str(x) for x in t_start_array]) + ','
prev_q_end = None
prev_t_end = None
for i in range(0, len(block_size_array)):
qseg = working_read[q_start_array[i]:q_start_array[i] +
block_size_array[i]]
tseg = seq[t_start_array[i]:t_start_array[i] +
block_size_array[i]].upper()
for j in range(0, len(qseg)):
if qseg[j] == 'N': nCount += 1
if qseg[j] == tseg[j]: matches += 1
else:
misMatches += 1
if prev_t_end:
t_dist = t_start_array[i] - prev_t_end
if t_dist > 0 and t_dist < args.min_intron_size: #we have an insert into the target and its not an intron
tNumInsert += 1
tBaseInsert += t_dist
if prev_q_end:
q_dist = q_start_array[i] - prev_q_end
if q_dist > 0:
qNumInsert += 1
qBaseInsert += q_dist
prev_q_end = q_start_array[i] + block_size_array[i]
prev_t_end = t_start_array[i] + block_size_array[i]
# now we have everything to make the line
combo_line = str(matches) + "\t" + str(misMatches) + "\t" + str(repMatches) + "\t" \
+ str(nCount) + "\t" + str(qNumInsert) + "\t" + str(qBaseInsert) + "\t" \
+ str(tNumInsert) + "\t" + str(tBaseInsert) + "\t" \
+ strand + "\t" + qName + "\t" + str(qSize) + "\t" \
+ str(qStart) + "\t" + str(qEnd) + "\t" \
+ tName + "\t" + str(tSize) + "\t" \
+ str(tStart) + "\t" + str(tEnd) + "\t" + str(blockCount) + "\t" \
+ blockSizes + "\t" + qStarts + "\t" + tStarts
#print combo_line
#print q_start_array
#print t_start_array
#print block_size_array
# print str(right['qStarts'][i])+"\t"+str(right['qStarts'][i]+right['blockSizes'][i])
# print i
return PSLBasics.line_to_entry(combo_line)
def main():
parser = argparse.ArgumentParser(description="Convert a sam file into a psl file")
parser.add_argument('--genome',help="FASTA input file of reference genome")
parser.add_argument('--get_secondary_alignments',action='store_true',help="Report SA:Z secondary alignments as well")
parser.add_argument('--get_alternative_alignments',action='store_true',help="Report XA:Z alternative alignments as well")
parser.add_argument('--get_all_alignments',action='store_true',help="Report SA:Z and XA:Z alternative alignments as well")
parser.add_argument('--give_unique_names',action='store_true',help="Output query names will be unique.")
group = parser.add_mutually_exclusive_group()
group.add_argument('--output_fasta',help="FILENAME to save an outgoing fasta. Only works for primary alignments.")
group.add_argument('--output_fastq',help="FILENAME to save an outgoing fastq. Only works for primary alignments.")
parser.add_argument('infile',help="FILENAME input file or '-' for STDIN")
parser.add_argument('-o','--output',help="FILENAME for the output, STDOUT if not set.")
args = parser.parse_args()
if (args.output_fasta or args.output_fastq) and (args.get_secondary_alignments or args.get_alternative_alignments or args.get_all_alignments):
sys.stderr.write("ERROR, can only output the fastq/fasta if we are doing primary alignments only.\n")
sys.exit()
inf = sys.stdin
if args.infile != '-':
inf = open(args.infile)
of = sys.stdout
if args.output:
of = open(args.output,'w')
spcf = SamBasics.SAMtoPSLconversionFactory()
if args.genome: spcf.set_genome(args.genome)
off = None
if args.output_fasta:
off = open(args.output_fasta,'w')
if args.output_fastq:
off = open(args.output_fastq,'w')
z = 0
for line in inf:
line = line.rstrip()
if SamBasics.is_header(line):
spcf.read_header_line(line)
continue
# We have a line to convert
psl = spcf.convert_line(line)
if psl:
pobj = PSL(psl)
z += 1
if args.give_unique_names:
pobj.entry['qName'] = 'Q'+str(z)
of.write(pobj.get_line()+"\n")
if args.output_fastq or args.output_fasta:
sam = SamBasics.SAM(line)
sequence = sam.value('seq').upper()
quality = sam.value('qual')
if sam.check_flag(16):
sequence = rc(sam.value('seq').upper())
quality = sam.value('qual')[::-1]
if args.output_fasta:
off.write(">"+pobj.value('qName')+"\n"+sequence+"\n")
elif args.output_fastq:
if len(sequence) == len(quality):
off.write("@"+pobj.value('qName')+"\n"+sequence+"\n"+"+\n"+quality+"\n")
else:
sys.stderr.write("ERROR: sequence "+sequence+" length ("+str(len(sequence))+") doesnt match quality "+quality+" length ("+str(len(quality))+")\n")
sys.exit()
# Lets look for secondary alignments to convert
if args.get_secondary_alignments or args.get_all_alignments:
secondary_alignments = SamBasics.get_secondary_alignments(line.rstrip())
for samline in secondary_alignments:
psl = spcf.convert_line(samline)
if psl:
#print "\nsecondary"
#print samline
z += 1
pobj = PSL(psl)
if args.give_unique_names:
pobj.entry['qName'] = 'Q'+str(z)
of.write(pobj.get_line()+"\n")
if args.get_alternative_alignments or args.get_all_alignments:
alternative_alignments = SamBasics.get_alternative_alignments(line.rstrip())
for samline in alternative_alignments:
psl = spcf.convert_line(samline)
if psl:
#print "\nsecondary"
#print samline
z += 1
pobj = PSL(psl)
if args.give_unique_names:
pobj.entry['qName'] = 'Q'+str(z)
of.write(pobj.get_line()+"\n")
inf.close()
of.close()
def sam_to_nav(self, line):
self.line_count += 1
if self.line_count % self.thread_count != self.thread_index - 1:
return None
if not self.LR_seq:
sys.stderr.write("ERROR initialize target first\n")
if not self.SR_file:
sys.stderr.write("ERROR initialize query first\n")
if (line[0] == '@'):
return None
line_fields = line.strip().split('\t')
cigar = line_fields[5]
if ((cigar == '*') or (cigar == '.')):
return None
SR_name = line_fields[0]
if (SR_name != self.current_query):
[self.SR_seq,
self.SR_idx_seq] = get_SR_sequence(self.SR_file, self.SR_idx_file,
SR_name)
self.SR_seq_rvs_cmplmnt = rc(self.SR_seq)
self.current_query = SR_name
if (int(line_fields[1]) & 0x10): # Check if seq is reversed complement
line_fields[3] = '-' + line_fields[3]
else:
line_fields[3] = '+' + line_fields[3]
align_list = [
','.join([line_fields[2], line_fields[3], line_fields[5],
str(0)])
]
if (not self.one_line_per_alignment
): # BWA reports all alignment per read in one line
multi_align_str = ','.join(
[line_fields[2], line_fields[3], line_fields[5],
str(0)]) + ';'
for fields_idx in range(11, len(line_fields)):
if (line_fields[fields_idx][0:5] == 'XA:Z:'):
multi_align_str += line_fields[fields_idx][5:]
break
align_list = multi_align_str[:-1].split(';')
read_seq_len = len(self.SR_seq)
ostrings = []
for align_str in align_list:
err_state = False
fields = align_str.split(',')
ref_seq = self.LR_seq[fields[0]]
ref_seq_len = len(ref_seq)
if (fields[1][0] == '-'): # Check if seq is reversed complement
read_seq = self.SR_seq_rvs_cmplmnt
pseudo_SR_name = "-" + SR_name
else:
read_seq = self.SR_seq
pseudo_SR_name = SR_name
fields[1] = fields[1][1:]
read_idx = 0
sub_ref_idx = 1 # 1-offset address
ref_idx = int(fields[1]) - 1 # convert to 0-offset address
diff_list = []
cigar_list = re.split('(M|I|D)', fields[2])
num_err = 0
for idx in range(1, len(cigar_list), 2):
if (cigar_list[idx - 1].isdigit()):
if (cigar_list[idx] == 'M'):
subseq_len = int(cigar_list[idx - 1])
if ((read_idx + subseq_len > read_seq_len)
or (ref_idx + subseq_len > ref_seq_len)):
err_state = True
break
read_subseq = list(read_seq[read_idx:(read_idx +
subseq_len)])
ref_subseq = list(ref_seq[ref_idx:(ref_idx +
subseq_len)])
mut_indices = [
x for x in range(len(read_subseq))
if read_subseq[x] != ref_subseq[x]
]
for mut_idx in mut_indices:
if (read_subseq[mut_idx] != "N"):
diff_list += [
str(sub_ref_idx + mut_idx) +
ref_subseq[mut_idx] + '>' +
read_subseq[mut_idx]
]
read_idx += subseq_len
ref_idx += subseq_len
sub_ref_idx += subseq_len
num_err += len(mut_indices)
elif (cigar_list[idx] == 'I'):
subseq_len = int(cigar_list[idx - 1])
if (read_idx + subseq_len > read_seq_len):
err_state = True
break
insert_str = re.sub(
r'N|n', '',
read_seq[read_idx:(read_idx +
int(cigar_list[idx - 1]))])
if (insert_str != ""):
diff_list += [
str(sub_ref_idx) + '+' +
read_seq[read_idx:(read_idx + subseq_len)]
]
read_idx += subseq_len
num_err += subseq_len
elif (cigar_list[idx] == 'D'):
subseq_len = int(cigar_list[idx - 1])
if (ref_idx + subseq_len > ref_seq_len):
err_state = True
break
for del_idx in range(subseq_len):
diff_list += [
str(sub_ref_idx + del_idx) + '-' +
ref_seq[ref_idx + del_idx]
]
ref_idx += subseq_len
sub_ref_idx += subseq_len
num_err += subseq_len
else:
#print 'Err in cigar: tag : ' + line
err_state = True
break
if ((cigar_list[-1] == '') and (not err_state)):
if (len(diff_list) == 0):
diff_list.append("*")
err_rate = (100 * num_err) / read_seq_len
if (err_rate <= self.error_rate_threshold):
ostrings.append('\t'.join([
pseudo_SR_name, fields[0], fields[1],
' '.join(diff_list), self.SR_seq, self.SR_idx_seq
]))
if len(ostrings) == 0: return None
return ostrings
def main():
parser = argparse.ArgumentParser()
parser.add_argument('--only_output_alternates',action='store_true',help='When selected, the original coordiantes are not output, and only the alternates are output')
parser.add_argument('--long_form', action='store_true',help="add an additional column to the beginning of the output indicating whether it is an original or alternate splice coordinate")
parser.add_argument('GenomeFastaFile',nargs=1,help="FILENAME Fasta format file of the reference genome")
parser.add_argument('SpliceSiteFile',nargs=1,help="FILENAME Splice Site file is in tsv format with <Left chrom> <Left coord (base-1)> <Left dir [+-]> <Right chrom> <Right coord (base-1)> <Right dir [+-]>\nWhere the coordinates indicate the base that is inside the exon proximal to the splice. Direction indicates the transcription direction on the chromosome for that side of the splice. For coordiantes 1-base means that the number 1 would be the first base of the sequence (makes sense to do it that way, right? :P)")
of = sys.stdout
args = parser.parse_args()
golds = []
with open(args.SpliceSiteFile[0]) as inf:
for line in inf:
f = line.rstrip().split()
t = {}
t['l'] = {}
t['r'] = {}
t['l']['chr'] = f[0]
t['l']['coord'] = int(f[1])
t['l']['dir'] = f[2]
t['r']['chr'] = f[3]
t['r']['coord'] = int(f[4])
t['r']['dir'] = f[5]
golds.append(t)
ref = read_fasta_into_hash(args.GenomeFastaFile[0])
lens = {}
for chr in ref:
lens[chr] = len(ref[chr])
for g in golds:
l_chrom = g['l']['chr']
r_chrom = g['r']['chr']
l_start = g['l']['coord']
r_start = g['r']['coord']
l_dir = g['l']['dir']
r_dir = g['r']['dir']
# print the main case
if not args.only_output_alternates:
startstring = ''
if args.long_form: startstring = "original\t"
of.write(startstring+l_chrom + "\t" + str(l_start) + "\t" + l_dir + "\t" + r_chrom + "\t" + str(r_start) + "\t" + r_dir+"\n")
#check upstream left
equivalent = 1
l_base = l_start
r_base = r_start
while(equivalent == 1):
left_bases = ''
right_bases = ''
if l_dir == '+':
l_base -= 1
if l_base < 1: break
left_bases = str(ref[l_chrom][l_base])
else:
l_base += 1
if l_base > lens[l_chrom]: break
left_bases = rc(str(ref[l_chrom][l_base-2]))
if r_dir == '+':
r_base -= 1
if r_base < 1: break
right_bases = str(ref[r_chrom][r_base-1])
else:
r_base += 1
if r_base > lens[r_chrom]: break
right_bases = rc(str(ref[r_chrom][r_base-1]))
if left_bases != right_bases: break
startstring = ''
if args.long_form: startstring = "alternate\t"
of.write(startstring+l_chrom + "\t" + str(l_base) + "\t" + l_dir + "\t" + r_chrom + "\t" + str(r_base) + "\t" + r_dir+"\n")
#check downstream left
equivalent = 1
l_base = l_start
r_base = r_start
while(equivalent == 1):
left_bases = ''
right_bases = ''
if l_dir == '+':
l_base += 1
if l_base > lens[l_chrom]: break
left_bases = str(ref[l_chrom][l_base-1])
else:
l_base -= 1
if l_base < 1: break
left_bases = rc(str(ref[l_chrom][l_base-1]))
if r_dir == '+':
r_base += 1
if r_base > lens[r_chrom]: break
right_bases = str(ref[r_chrom][r_base-2])
else:
r_base -= 1
if r_base > lens[r_chrom]: break
right_bases = rc(str(ref[r_chrom][r_base]))
if left_bases != right_bases: break
startstring = ''
if args.long_form: startstring = "alternate\t"
of.write(startstring+l_chrom + "\t" + str(l_base) + "\t" + l_dir + "\t" + r_chrom + "\t" + str(r_base) + "\t" + r_dir+"\n")
def do_combine_operation(best_option,left,right,read,seq,args):
#print "choice is "+str(best_option)
left_target = best_option[0]
right_target = best_option[1]
left_query = best_option[2]
right_query = best_option[3]
# store for output
q_start_array = []
t_start_array = []
block_size_array = []
left_query_start = left['qStarts'][0]
left_target_start = left['tStarts'][0]
for i in range(0,len(left['tStarts'])):
tstart = left['tStarts'][i]
tend = left['tStarts'][i]+left['blockSizes'][i]
qstart = left['qStarts'][i]
qend = left['qStarts'][i]+left['blockSizes'][i]
if left_query <= qstart+1: break
left_query_start = qstart
left_target_start = tstart
if left_query <= qend: break
q_start_array.append(qstart)
t_start_array.append(tstart)
block_size_array.append(left['blockSizes'][i])
#print "left things"
#print [left_query_start+1,left_query]
#print [left_target_start+1,left_target]
right_query_end = right['qStarts'][0]+right['blockSizes'][0]
right_target_end = right['tStarts'][0]+right['blockSizes'][0]
right_outer_index = 0
for j in range(0,len(right['tStarts'])):
tstart = right['tStarts'][j]
tend = right['tStarts'][j]+right['blockSizes'][j]
qstart = right['qStarts'][j]
qend = right['qStarts'][j]+right['blockSizes'][j]
right_outer_index = j+1
if right_query <= qstart+1: break
right_query_end = qend
right_target_end = tend
if right_query < qend: break
#print "right things"
#print [right_query+1,right_query_end]
#print [right_target+1,right_target_end]
working_read = read.upper()
if left['strand'] == '-': working_read = rc(read.upper())
pread = working_read[left_query_start:right_query_end]
tseq = seq[left_target_start:left_target].upper()+seq[right_target-1:right_target_end].upper()
res = needleman_wunsch(pread,tseq)
#print "short needleman wunsch"
#print res[0]
#print res[1]
# Fun part of making the new portion of the alignment
qindex = left_query_start
tindex = left_target_start
in_alignment = 0
alignment = None
bynumbers = None
for i in range(0,len(res[0])):
if res[0][i] == '-': #insertion in target (gap in query)
tindex += 1
in_alignment = 0
elif res[1][i] == '-': #insertion in query (gap in target)
qindex += 1
in_alignment = 0
else: # we are in an alignment
if in_alignment == 0:
# output buffered result
if alignment:
if len(alignment[0]) > 0:
q_start_array.append(bynumbers[0])
t_start_array.append(bynumbers[1])
block_size_array.append(len(alignment[0]))
alignment = ['','']
bynumbers = [qindex,tindex,qindex,tindex]
in_alignment = 1
alignment[0] += res[0][i]
alignment[1] += res[1][i]
bynumbers[2] += 1
bynumbers[3] += 1
qindex+=1
tindex+=1
if qindex == right_query: # switch forward
#print "switch"
#print str(tindex) + "\t" + str(right_target)
#print str(qindex) + "\t" + str(right_query)
if not tindex == right_target:
in_alignment = 0
tindex = right_target
if alignment:
if len(alignment[0]) > 0:
q_start_array.append(bynumbers[0])
t_start_array.append(bynumbers[1])
block_size_array.append(len(alignment[0]))
#print bynumbers
for i in range(right_outer_index,len(right['blockSizes'])):
q_start_array.append(right['qStarts'][i])
t_start_array.append(right['tStarts'][i])
block_size_array.append(right['blockSizes'][i])
#now we can finally construct a psl line
#we won't keep track of repeats for now
matches = 0
misMatches = 0
repMatches = 0
nCount = 0
qNumInsert = 0
qBaseInsert = 0
tNumInsert = 0
tBaseInsert = 0
strand = left['strand']
qName = left['qName']
qSize = len(read)
qStart = q_start_array[0]
qEnd = q_start_array[len(q_start_array)-1]+block_size_array[len(block_size_array)-1]
tName = left['tName']
tSize = len(seq)
tStart = t_start_array[0]
tEnd = t_start_array[len(t_start_array)-1]+block_size_array[len(block_size_array)-1]
blockCount = len(block_size_array)
blockSizes = ','.join([str(x) for x in block_size_array])+','
qStarts = ','.join([str(x) for x in q_start_array])+','
tStarts = ','.join([str(x) for x in t_start_array])+','
prev_q_end = None
prev_t_end = None
for i in range(0,len(block_size_array)):
qseg = working_read[q_start_array[i]:q_start_array[i]+block_size_array[i]]
tseg = seq[t_start_array[i]:t_start_array[i]+block_size_array[i]].upper()
for j in range(0,len(qseg)):
if qseg[j] == 'N': nCount += 1
if qseg[j] == tseg[j]: matches += 1
else:
misMatches += 1
if prev_t_end:
t_dist = t_start_array[i]-prev_t_end
if t_dist > 0 and t_dist < args.min_intron_size: #we have an insert into the target and its not an intron
tNumInsert += 1
tBaseInsert += t_dist
if prev_q_end:
q_dist = q_start_array[i]-prev_q_end
if q_dist > 0:
qNumInsert += 1
qBaseInsert += q_dist
prev_q_end = q_start_array[i]+block_size_array[i]
prev_t_end = t_start_array[i]+block_size_array[i]
# now we have everything to make the line
combo_line = str(matches) + "\t" + str(misMatches) + "\t" + str(repMatches) + "\t" \
+ str(nCount) + "\t" + str(qNumInsert) + "\t" + str(qBaseInsert) + "\t" \
+ str(tNumInsert) + "\t" + str(tBaseInsert) + "\t" \
+ strand + "\t" + qName + "\t" + str(qSize) + "\t" \
+ str(qStart) + "\t" + str(qEnd) + "\t" \
+ tName + "\t" + str(tSize) + "\t" \
+ str(tStart) + "\t" + str(tEnd) + "\t" + str(blockCount) + "\t" \
+ blockSizes + "\t" + qStarts + "\t" + tStarts
#print combo_line
#print q_start_array
#print t_start_array
#print block_size_array
# print str(right['qStarts'][i])+"\t"+str(right['qStarts'][i]+right['blockSizes'][i])
# print i
return PSLBasics.line_to_entry(combo_line)
