def mping_genotyper_mp_runner(ril, bam_ref, bam_pseudo, mping2ID_0, binmap,
snpmap, bamcheck_file_ref, bamcheck_file_pseudo):
genotype = 3
l_flag = 3
r_flag = 3
ref_flag = 3
results = []
bamcheck_file_pseudo = '%s.%s.txt' % (bamcheck_file_pseudo, ril)
bamcheck_file_ref = '%s.%s.txt' % (bamcheck_file_ref, ril)
if os.path.isfile(bam_ref):
if os.path.isfile(bam_pseudo):
for mping in sorted(mping2ID_0.keys()):
#genotype: 0 ref, 1 non_ref, 3 unknown
genotype = genotyping_SNP(ril, mping2ID_0[mping], binmap,
snpmap)
l_flag, r_flag = bamcheck_ref(bam_pseudo, mping,
bamcheck_file_pseudo, ril)
ref_flag = bamcheck(bam_ref, mping2ID_0[mping],
bamcheck_file_ref, ril)
results.append([mping, genotype, l_flag, r_flag, ref_flag])
print '%s\t%s\t%s\t%s' % (ril, mping, l_flag, r_flag)
else:
print 'pseudo bam file not found for rils: RIL%s' % (ril)
else:
print 'reference bam file not found for rils: RIL%s' % (ril)
return [ril, results]
def main():
parser = argparse.ArgumentParser()
parser.add_argument('-i', '--input')
parser.add_argument('-o', '--output')
parser.add_argument('-v', dest='verbose', action='store_true')
args = parser.parse_args()
try:
len(args.input) > 0
except:
usage()
sys.exit(2)
if not args.output:
args.output = 'ping_coverage.matrix'
bams = glob.glob('%s/*.bam' %(args.input))
mping = "chr01:2640500-2640502"
bamcheck_file_ref = 'temp_bam_check_file.txt'
for bam in sorted(bams):
strain = os.path.split(bam)[1]
strain = re.sub(r'.special_ping_locus.bam', '', strain)
ref_flag = bamcheck(bam, mping, bamcheck_file_ref, strain)
#1 is insertion, 4 is excision or no insertion, 2 and 3 are not sure
print '{}\t{}'.format(strain, ref_flag)
def main():
parser = argparse.ArgumentParser()
parser.add_argument('--bam_ref')
parser.add_argument('--bam_pseudo')
parser.add_argument('--gff_ref')
parser.add_argument('--gff_pseudo')
parser.add_argument('--bin_map')
parser.add_argument('--snp_map')
parser.add_argument('--project')
parser.add_argument('-v', dest='verbose', action='store_true')
args = parser.parse_args()
try:
len(args.bam_pseudo) > 0 and len(args.bam_ref) > 0
except:
usage()
sys.exit(2)
if not args.project:
args.project = 'mPing_boundary'
if not args.gff_ref:
args.gff_ref = '../input/HEG4.ALL.mping.non-ref.gff'
if not args.gff_pseudo:
args.gff_pseudo = '../input/MSU_r7.Pseudo_mPing.gff'
if not args.bam_ref:
args.bam_ref = '../input/RILs_ALL_bam'
if not args.bam_pseudo:
args.bam_pseudo = '../input/RILs_ALL_unmapped_mping_bam'
if not args.bin_map:
args.bin_map = '../input/MPR.geno.bin'
if not args.snp_map:
args.snp_map = '../input/MPR.gene.data'
#we use mping gff from pseudogenome as key to project to everything
mping2ID_0 = defaultdict(lambda : str()) #ID_0 is the mping id from original call in HEG4, Chr1.1132977
id_mapping(args.gff_pseudo, mping2ID_0)
#bin map and snp genotype
binmap = convert_MAP(args.bin_map)
snpmap = convert_MAP_SNP(args.bin_map)
#go through RILs, for each ril determine the status of each mPing
bamcheck_file_pseudo = '%s.bamcheck_pseudo.txt' %(args.project)
bamcheck_file_ref = '%s.bamcheck_ref.txt' %(args.project)
mping_status = defaultdict(lambda : defaultdict(lambda : defaultdict(lambda : str())))
mping_status_ref = defaultdict(lambda : defaultdict(lambda : str()))
mping_bin_gt = defaultdict(lambda : defaultdict(lambda : str()))
mping_snp_gt = defaultdict(lambda : defaultdict(lambda : defaultdict(lambda : str())))
#rils = [1, 2, 3, 4]
bams = glob.glob('%s/*.bam' %(args.bam_pseudo))
rils = get_rils(bams)
for ril in sorted(rils):
bam_ref = '%s/GN%s.bam' %(args.bam_ref, ril)
bam_pseudo = '%s/RIL%s.bam' %(args.bam_pseudo, ril)
print 'ril: %s, %s' %(ril, bam_pseudo)
if os.path.isfile(bam_pseudo):
for mping in sorted(mping2ID_0.keys()):
#genotype: 0 ref, 1 non_ref, 3 unknown
genotype = genotyping_SNP(ril, mping, binmap, snpmap)
l_flag, r_flag = bamcheck_ref(bam_pseudo, mping, bamcheck_file_pseudo, ril)
ref_flag = bamcheck(bam_ref, mping2ID_0[mping], bamcheck_file_ref, ril)
#print '%s\t%s\t%s\t%s' %(ril, mping, l_flag, r_flag)
mping_status[ril][mping2ID_0[mping]]['up'] = decode(l_flag)
mping_status[ril][mping2ID_0[mping]]['down'] = decode(r_flag)
mping_status_ref[ril][mping2ID_0[mping]] = decode(ref_flag)
mping_bin_gt[ril][mping2ID_0[mping]] = decode_gt(genotype)
else:
print 'bam file not found for rils: RIL%s' %(ril)
#output matrix into file
matrix_file = '%s.mping_status.matrix.txt' %(args.project)
ofile = open(matrix_file, 'w')
mping_ranked= sort_mping_chr(mping2ID_0)
#mping names
#print >> ofile, 'mPing,%s' %(','.join(mping_ranked))
mping_lines = ['mPing']
for m in mping_ranked:
mping_lines.append('%s,Genotype,Pseudo_up,Pseudo_down,Ref' %(m))
print >> ofile, ','.join(mping_lines)
#mping genotype
#mping status, matirx
for ril in sorted(mping_status.keys(), key=int):
inf_line = ['RIL%s' %(ril)]
for mping in mping_ranked:
inf_line.append(mping_bin_gt[ril][mping])
inf_line.append(mping_status[ril][mping]['up'])
inf_line.append(mping_status[ril][mping]['down'])
inf_line.append(mping_status_ref[ril][mping])
#status = '%s:%s' %(mping_status[ril][mping]['up'], mping_status[ril][mping]['down'])
#inf_line.append(status)
print >> ofile, ','.join(inf_line)
ofile.close()
#output matrix for individual mPing file
outdir = '%s_mPing' %(os.path.abspath(args.project))
if not os.path.exists(outdir):
os.mkdir(outdir)
sum_lines_matrix = defaultdict(lambda : list())
for mping in mping_ranked:
sum_gt = [0, 0, 0]
sum_ref_coverage = defaultdict(lambda : defaultdict(lambda : int()))
sum_ref_covered = defaultdict(lambda : defaultdict(lambda : int()))
sum_ref_clipped = defaultdict(lambda : defaultdict(lambda : int()))
sum_nonref_coverage = defaultdict(lambda : defaultdict(lambda : int()))
sum_nonref_covered = defaultdict(lambda : defaultdict(lambda : int()))
sum_nonref_clipped = defaultdict(lambda : defaultdict(lambda : int()))
mping_name = re.sub(r':', r'_', mping)
mping_name = re.sub(r'-', r'_', mping_name)
ofile = open('%s/%s.matrix.csv' %(outdir, mping_name), 'w')
#print >> ofile, 'RILs\tDepth(X)\tGenotype_Bin\tDistance_SNP5\tGenotype_SNP5\tDistance_SNP3\tGenotype_SNP3\tmPing_status'
print >> ofile, '%s,Genotype_Bin,Pseudo_mPing_status_up,Pseudo_mPing_status_down,Ref_mPing_status' %(mping)
for ril in sorted(mping_status.keys(), key=int):
#status in pseudo and ref genome have different results
#in pseudogenome, cover mean junction was covered by reads, which indicates insertion
#in refgenome, cover mean junction was covered by reads, which indicates no insertion or excision
#status = '%s:%s' %(mping_status[ril][mping]['up'], mping_status[ril][mping]['down'])
status_up = mping_status[ril][mping]['up']
status_down= mping_status[ril][mping]['down']
status_ref = mping_status_ref[ril][mping]
print >> ofile, 'RIL%s,%s,%s,%s,%s' %(ril, mping_bin_gt[ril][mping], status_up, status_down, status_ref)
if mping_bin_gt[ril][mping] == 'NB':
sum_gt[0] += 1
elif mping_bin_gt[ril][mping] == 'HEG4':
sum_gt[1] += 1
else:
sum_gt[2] += 1
if 1:
gt = mping_bin_gt[ril][mping]
#summary on mping status in ref mapping bam, 0 mean only one status for each mPing
if status_ref == 'covered':
sum_ref_coverage[gt][0] += 1
sum_ref_covered[gt][0] += 1
elif status_ref == 'clipped':
sum_ref_coverage[gt][0] += 1
sum_ref_clipped[gt][0] += 1
#summary on mping status in pseudo mapping bam, 0 mean upstream status and 1 mean downstream status
if mping_status[ril][mping]['up'] == 'covered':
sum_nonref_coverage[gt][0] += 1
sum_nonref_covered[gt][0] += 1
elif mping_status[ril][mping]['up'] == 'clipped':
sum_nonref_coverage[gt][0] += 1
sum_nonref_clipped[gt][0] += 1
if mping_status[ril][mping]['down'] == 'covered':
sum_nonref_coverage[gt][1] += 1
sum_nonref_covered[gt][1] += 1
elif mping_status[ril][mping]['down'] == 'clipped':
sum_nonref_coverage[gt][1] += 1
sum_nonref_clipped[gt][1] += 1
#total line, perfectage of coverage
total_gt = (sum_gt[0] + sum_gt[1])/float(sum(sum_gt))
total_up = sum_nonref_coverage['NB'][0]/float(sum(sum_gt)) + sum_nonref_coverage['HEG4'][0]/float(sum(sum_gt)) + sum_nonref_coverage['NA'][0]/float(sum(sum_gt))
total_down = sum_nonref_coverage['NB'][1]/float(sum(sum_gt)) + sum_nonref_coverage['HEG4'][1]/float(sum(sum_gt)) + sum_nonref_coverage['NA'][1]/float(sum(sum_gt))
total_ref = sum_ref_coverage['NB'][0]/float(sum(sum_gt)) + sum_ref_coverage['HEG4'][0]/float(sum(sum_gt)) + sum_ref_coverage['NA'][0]/float(sum(sum_gt))
print >> ofile, 'Total,%s,%s,%s,%s' %(total_gt, total_up, total_down, total_ref)
sum_lines_matrix['total'].append('%s,%s,%s,%s' %(total_gt, total_up, total_down, total_ref))
#NB line, covered/clipped/unknown
nb_gt = sum_gt[0]
nb_up = '%s:%s:%s' %(sum_nonref_covered['NB'][0], sum_nonref_clipped['NB'][0], sum_gt[0]-sum_nonref_covered['NB'][0]-sum_nonref_clipped['NB'][0])
nb_down = '%s:%s:%s' %(sum_nonref_covered['NB'][1], sum_nonref_clipped['NB'][1], sum_gt[0]-sum_nonref_covered['NB'][1]-sum_nonref_clipped['NB'][1])
nb_ref = '%s:%s:%s' %(sum_ref_covered['NB'][0], sum_ref_clipped['NB'][0], sum_gt[0]-sum_ref_covered['NB'][0]-sum_ref_clipped['NB'][0])
print >> ofile, 'NB,%s,%s,%s,%s' %(nb_gt, nb_up, nb_down, nb_ref)
sum_lines_matrix['nb'].append('%s,%s,%s,%s' %(nb_gt, nb_up, nb_down, nb_ref))
#HEG4 line, covered/clipped/unknown
heg4_gt = sum_gt[1]
heg4_up = '%s:%s:%s' %(sum_nonref_covered['HEG4'][0], sum_nonref_clipped['HEG4'][0], sum_gt[1]-sum_nonref_covered['HEG4'][0]-sum_nonref_clipped['HEG4'][0])
heg4_down = '%s:%s:%s' %(sum_nonref_covered['HEG4'][1], sum_nonref_clipped['HEG4'][1], sum_gt[1]-sum_nonref_covered['HEG4'][1]-sum_nonref_clipped['HEG4'][1])
heg4_ref = '%s:%s:%s' %(sum_ref_covered['HEG4'][0], sum_ref_clipped['HEG4'][0], sum_gt[1]-sum_ref_covered['HEG4'][0]-sum_ref_clipped['HEG4'][0])
print >> ofile, 'HEG4,%s,%s,%s,%s' %(heg4_gt, heg4_up, heg4_down, heg4_ref)
sum_lines_matrix['heg4'].append('%s,%s,%s,%s' %(heg4_gt, heg4_up, heg4_down, heg4_ref))
#NA line, covered/clipped/unknown
na_gt = sum_gt[2]
na_up = '%s:%s:%s' %(sum_nonref_covered['NA'][0], sum_nonref_clipped['NA'][0], sum_gt[2]-sum_nonref_covered['NA'][0]-sum_nonref_clipped['NA'][0])
na_down = '%s:%s:%s' %(sum_nonref_covered['NA'][1], sum_nonref_clipped['NA'][1], sum_gt[2]-sum_nonref_covered['NA'][1]-sum_nonref_clipped['NA'][1])
na_ref = '%s:%s:%s' %(sum_ref_covered['NA'][0], sum_ref_clipped['NA'][0], sum_gt[2]-sum_ref_covered['NA'][0]-sum_ref_clipped['NA'][0])
print >> ofile, 'NA,%s,%s,%s,%s' %(na_gt, na_up, na_down, na_ref)
sum_lines_matrix['na'].append('%s,%s,%s,%s' %(na_gt, na_up, na_down, na_ref))
ofile.close()
#add summary to big matrix
ofile = open(matrix_file, 'a')
print >> ofile, '%s,%s' %('Total', ','.join(sum_lines_matrix['total']))
print >> ofile, '%s,%s' %('NB', ','.join(sum_lines_matrix['nb']))
print >> ofile, '%s,%s' %('HEG4', ','.join(sum_lines_matrix['heg4']))
print >> ofile, '%s,%s' %('NA', ','.join(sum_lines_matrix['na']))
ofile.close()
def main():
parser = argparse.ArgumentParser()
parser.add_argument('--ref_gff')
parser.add_argument('--qry_gff')
parser.add_argument('--ref_bam')
parser.add_argument('--qry_bam')
parser.add_argument('--project')
parser.add_argument('-v', dest='verbose', action='store_true')
args = parser.parse_args()
try:
len(args.ref_gff) > 0 and len(args.qry_gff) > 0
except:
usage()
sys.exit(2)
if not args.project:
args.project = 'HEG4vsEG4'
#summary
shared = 0
ref_sum = defaultdict(lambda: int())
qry_sum = defaultdict(lambda: int())
#bamcheck files
bamcheck_file_ref = '%s.bamcheck.txt' % (os.path.splitext(
os.path.split(args.ref_bam)[1])[0])
bamcheck_file_qry = '%s.bamcheck.txt' % (os.path.splitext(
os.path.split(args.qry_bam)[1])[0])
#parse gff of mping file
ref_gff_dict = gff_parser(args.ref_gff)
qry_gff_dict = gff_parser(args.qry_gff)
#get mping from both strain into one dict
mpings_all = ref_gff_dict.keys()
mpings_all.extend(qry_gff_dict.keys())
mpings_all = list(set(mpings_all))
#classify shared and unique mPing, for unique mping check for footprint of excision
ofile = open('%s.mPing.Excision.table' % (args.project), 'w')
for mping in mpings_all:
if ref_gff_dict.has_key(mping) and qry_gff_dict.has_key(mping):
print >> ofile, '%s\t%s\t%s\tNA\tNA' % (mping, 1, 1)
shared += 1
elif ref_gff_dict.has_key(mping):
mping_format = '%s:%s-%s' % (ref_gff_dict[mping][0][0],
ref_gff_dict[mping][0][3],
ref_gff_dict[mping][0][4])
flag = bamcheck(args.qry_bam, mping_format, bamcheck_file_qry,
'qry')
print >> ofile, '%s\t%s\t%s\t%s\t%s' % (mping, 1, 0, flag,
decode(flag))
ref_sum['unique'] += 1
if int(flag) == 0:
ref_sum['footprint'] += 1
elif qry_gff_dict.has_key(mping):
mping_format = '%s:%s-%s' % (qry_gff_dict[mping][0][0],
qry_gff_dict[mping][0][3],
qry_gff_dict[mping][0][4])
flag = bamcheck(args.ref_bam, mping_format, bamcheck_file_ref,
'ref')
print >> ofile, '%s\t%s\t%s\t%s\t%s' % (mping, 0, 1, flag,
decode(flag))
qry_sum['unique'] += 1
if int(flag) == 0:
qry_sum['footprint'] += 1
else:
#will not happen
print >> ofile, 'NA\t0\t0\tNA\tNA'
ofile.close()
#output summary
ofile = open('%s.mPing.Excision.sum' % (args.project), 'w')
print >> ofile, 'Number of Reference mPing: %s' % (len(ref_gff_dict))
print >> ofile, 'Number of Query mPing: %s' % (len(qry_gff_dict))
print >> ofile, 'Number of Shared mPing: %s' % (shared)
print >> ofile, 'Number of unique Ref mPing: %s and %s with footprint in Qry' % (
ref_sum['unique'], ref_sum['footprint'])
print >> ofile, 'Number of unique Qry mPing: %s and %s with footprint in Ref' % (
qry_sum['unique'], qry_sum['footprint'])
ofile.close()