def run(args):
options = args.parse_args()
if len(options.sam_file) == 0:
error("Missing the SAM file, use -s or --sam option.")
else:
options.sam_file = options.sam_file.split(',')
for s in options.sam_file:
if not os.path.isfile(s):
error("Can't open the SAM file: " + s)
sys.exit(1)
if len(options.ref_file) == 0:
error(
"Missing the reference genome fasta file, use -r or --ref option.")
else:
if not os.path.isfile(options.ref_file):
error("Can't open the ref file: " + options.ref_file)
if len(options.samtools) != 0:
if options.samtools[-1] != '/':
options.samtools += '/'
if len(options.name) == 0:
error("Missing the output file name, use -n or --name options.")
sam_inf = options.sam_file
ref_file = options.ref_file
bsm = options.bsm
s_path = options.samtools
name = options.name
dige_site = options.dige_site
remove_overlap = options.remove_overlap
not_mapping = options.not_mapping
info("Get the all parameter!!")
#check the input mapping files
sam_format, read_inf = check.check_mapping_file_flag(sam_inf[0], s_path)
pre_flag = read_inf.readline().split('\t')[1]
if 'p' in pre_flag:
single_on = False
info("The input mapping files are paired-end sequencing!")
else:
single_on = True
info("The input mapping files are single-end sequencing!")
#get reference information
ref = GR.get_ref(ref_file)
##scan MspI site and trim the end-repaired C
dige_dict, all_reads, all_mapping_bp, not_mapping_reads, filter_not_mapping_reads, filter_MspI_endrepair_bp, filter_remove_overlap_bp = parser_trim_sambam(
sam_inf, ref, bsm, s_path, dige_site, single_on, remove_overlap,
not_mapping, name)
##produce MspI Mbias plot
RR.generator(dige_dict, single_on, name)
##produce the filter report
report(all_reads, all_mapping_bp, not_mapping_reads,
filter_not_mapping_reads, filter_MspI_endrepair_bp,
filter_remove_overlap_bp, single_on, name)
def run(args):
options = args.parse_args()
if len(options.sam_file) == 0:
error("Missing the SAM file, use -s or --sam option.")
else:
options.sam_file = options.sam_file.split(',')
for s in options.sam_file:
if not os.path.isfile(s):
error("Can't open the SAM file: " + s)
sys.exit(1)
if len(options.ref_file) == 0:
error("Missing the reference genome fasta file, use -r or --ref option.")
else:
if not os.path.isfile(options.ref_file):
error("Can't open the ref file: " + options.ref_file)
if len(options.samtools) != 0:
if options.samtools[-1] != '/':
options.samtools += '/'
if len(options.name) == 0:
error("Missing the output file name, use -n or --name options.")
sam_inf = options.sam_file
ref_file = options.ref_file
bsm = options.bsm
s_path = options.samtools
name = options.name
dige_site = options.dige_site
remove_overlap = options.remove_overlap
not_mapping = options.not_mapping
info("Get the all parameter!!")
#check the input mapping files
sam_format, read_inf = check.check_mapping_file_flag(sam_inf[0], s_path)
pre_flag = read_inf.readline().split('\t')[1]
if 'p' in pre_flag:
single_on = False
info("The input mapping files are paired-end sequencing!")
else:
single_on = True
info("The input mapping files are single-end sequencing!")
#get reference information
ref = GR.get_ref(ref_file)
##scan MspI site and trim the end-repaired C
dige_dict, all_reads, all_mapping_bp, not_mapping_reads, filter_not_mapping_reads, filter_MspI_endrepair_bp, filter_remove_overlap_bp = parser_trim_sambam(
sam_inf, ref, bsm, s_path, dige_site, single_on, remove_overlap, not_mapping, name)
##produce MspI Mbias plot
RR.generator(dige_dict, single_on, name)
##produce the filter report
report(all_reads, all_mapping_bp, not_mapping_reads, filter_not_mapping_reads, filter_MspI_endrepair_bp,
filter_remove_overlap_bp, single_on, name)
def run(args):
"""
Alternative module: Use the strategy in Bis-SNP to trim 5' bisulfite conversion failures
"""
options = args.parse_args()
if len(options.sam_file) == 0:
error("Missing the SAM file, use -s or --sam option.")
else:
options.sam_file = options.sam_file.split(',')
for s in options.sam_file:
if not os.path.isfile(s):
error("Can't open the SAM file: " + s)
sys.exit(1)
if len(options.ref_file) == 0:
error(
"Missing the reference genome fasta file, use -r or --ref option.")
else:
if not os.path.isfile(options.ref_file):
error("Can't open the ref file: " + options.ref_file)
if len(options.samtools) != 0:
if options.samtools[-1] != '/':
options.samtools += '/'
if len(options.name) == 0:
error("Missing the output file name, use -n or --name options.")
sam_inf = options.sam_file
ref_file = options.ref_file
bsm = options.bsm
s_path = options.samtools
name = options.name
remove_overlap = options.remove_overlap
filter_dup = options.filter_dup
p_poisson = options.p_poisson
gsize = options.gsize
not_mapping = options.not_mapping
info("Get the all parameter!!")
#check the input mapping files
sam_format, read_inf = check.check_mapping_file_flag(sam_inf[0], s_path)
pre_flag = read_inf.readline().split('\t')[1]
if 'p' in pre_flag:
single_on = False
info("The input mapping files are paired-end sequencing!")
else:
single_on = True
info("The input mapping files are single-end sequencing!")
loc_dict = {}
if filter_dup:
## if filter_up is TRUE, the duplicate reads will be assessed and shown in Dup_dis.pdf
info("The filter_dup has been set True.")
info("Assess the duplicate reads...")
for sam in sam_inf:
#check the input mapping files
sam_format, read_inf = check.check_mapping_file(sam, s_path)
if single_on:
for read in read_inf:
loc_dict = LI.Loc_single(read, loc_dict, bsm)
else:
for read in read_inf:
loc_dict = LI.Loc_paired(read, loc_dict, bsm)
max_cov = DR.duplicate_report(loc_dict, gsize, p_poisson, name)
info('Get the duplicate reads distribution!')
#get reference information
ref = GR.get_ref(ref_file)
trim_position = []
filter_duplicate_reads = 0
filter_nonuniform_trim_bp = 0
filter_nonuniform_trim_bp_CG = 0
filter_remove_overlap_bp = 0
filter_not_mapping_reads = 0
all_reads = 0
not_mapping_reads = 0
all_mapping_bp = 0
##filter the 5' bisulfite failure
for sam in sam_inf:
out_sam = sam[:-4] + '_' + name + '_filter.sam'
out = open(out_sam, 'w')
#check the input mapping files
record_mate = {}
sam_format, read_inf = check.check_mapping_file_header(sam, s_path)
for read in read_inf:
#for sam header
if read.startswith('@'):
out.write(read)
continue
else:
all_reads += 1 ##record the read number (2013-06-20)
#Get the read information for trimming
#If the read isn't unique mapping, we will get a empty list ([]).
#In: single unique mapping read Out: [flag,strand,chr,pos,CIGAR,seq,score]
#In: paired unique mapping read Out: [flag,strand,chr,pos1,CIGAR,pos2,insert,seq,score]
read_info = RI(read, bsm)
read_info = read_info.extract_information()
if len(read_info) == 0:
not_mapping_reads += 1
if not_mapping: #keep the not_unique mapping reads (or not paired mapping)
out.write(read)
else:
filter_not_mapping_reads += 1 ##record the not mapping read number (2013-06-20)
continue
if len(
loc_dict
) > 0: #the --filter_dup has been set True, have to remove duplicate reads
duplicate, loc_dict = DF(read_info, loc_dict, max_cov,
single_on)
else:
duplicate = False
if single_on:
all_mapping_bp += len(
read_info[5]
) ##record the mapping read basepair (2013-06-20)
else:
all_mapping_bp += len(
read_info[7]
) ##record the mapping read basepair (2013-06-20)
record_mate, trim_position, filter_nonuniform_trim_bp_CG, filter_duplicate_reads, filter_remove_overlap_bp = NF.nonuniform_filter(
read, out, read_info, ref, remove_overlap, duplicate,
single_on, record_mate, trim_position,
filter_nonuniform_trim_bp_CG, filter_duplicate_reads,
filter_remove_overlap_bp)
out.close()
del record_mate
NR.nonuniform_generator(trim_position, name)
for i in range(len(trim_position)):
filter_nonuniform_trim_bp += i * trim_position[i]
##produce the filter report
info('Produce the report file...')
report_out = open(name + "_BSeQC_nonuniform_filter_report.txt", 'w')
report_out.write('Total reads: %d\n' % all_reads)
if single_on:
report_out.write('Not unique mapping reads: %d(%.2f%s all reads)\n' %
(not_mapping_reads,
float(not_mapping_reads) / all_reads * 100, "%"))
report_out.write(
'Unique mapping reads: %d(%.2f%s all reads)\n' %
((all_reads - not_mapping_reads),
float(all_reads - not_mapping_reads) / all_reads * 100, "%"))
report_out.write(
'Skip not unique mapping reads: %d(%.2f%s all reads)\n' %
(filter_not_mapping_reads,
float(filter_not_mapping_reads) / all_reads * 100, "%"))
report_out.write('In unique mapping reads:\n')
report_out.write('All unique mapping basepairs: %d\n' % all_mapping_bp)
report_out.write(
'Filter Duplicate reads: %d(%.2f%s of unique mapping reads)\n' %
(filter_duplicate_reads, float(filter_duplicate_reads) /
(all_reads - not_mapping_reads) * 100, "%"))
report_out.write(
"Filter 5' nonconversion basepairs: %d(%.2f%s of unique mapping basepairs)\n"
% (filter_nonuniform_trim_bp,
float(filter_nonuniform_trim_bp) / all_mapping_bp * 100, "%"))
report_out.write(
"Filter 5' nonconversion CpG basepairs: %d(%.2f%s of unique mapping basepairs)\n"
%
(filter_nonuniform_trim_bp_CG,
float(filter_nonuniform_trim_bp_CG) / all_mapping_bp * 100, "%"))
else:
report_out.write('Not unique paired mapping reads: %d(%.2f%s)\n' %
(not_mapping_reads,
float(not_mapping_reads) / all_reads * 100, "%"))
report_out.write(
'Unique paired mapping reads: %d(%.2f%s)\n' %
((all_reads - not_mapping_reads),
float(all_reads - not_mapping_reads) / all_reads * 100, "%"))
report_out.write(
'Skip not paired unique mapping reads: %d(%.2f%s)\n' %
(filter_not_mapping_reads,
float(filter_not_mapping_reads) / all_reads * 100, "%"))
report_out.write('In unique paired mapping reads:\n')
report_out.write('All unique paired mapping basepairs: %d\n' %
all_mapping_bp)
report_out.write(
'Filter Duplicate reads: %d(%.2f%s of unique paired mapping reads)\n'
% (filter_duplicate_reads, float(filter_duplicate_reads) /
(all_reads - not_mapping_reads * 100), "%"))
report_out.write(
"Filter 5' nonconversion basepairs: %d(%.2f%s of unique mapping basepairs)\n"
% (filter_nonuniform_trim_bp,
float(filter_nonuniform_trim_bp) / all_mapping_bp * 100, "%"))
report_out.write(
"Filter 5' nonconversion CpG basepairs: %d(%.2f%s of unique mapping basepairs)\n"
%
(filter_nonuniform_trim_bp_CG,
float(filter_nonuniform_trim_bp_CG) / all_mapping_bp * 100, "%"))
report_out.write(
'Filter overlapped basepairs: %d(%.2f%s of unique paired mapping basepairs)\n'
% (filter_remove_overlap_bp,
float(filter_remove_overlap_bp) / all_mapping_bp * 100, "%"))
report_out.close()
info('Get the report file!')
def run(args):
options = args.parse_args()
if len(options.sam_file) == 0:
error("Missing the SAM file, use -s or --sam option.")
else:
options.sam_file = options.sam_file.split(',')
for s in options.sam_file:
if not os.path.isfile(s):
error("Can't open the SAM file: " + s)
sys.exit(1)
if len(options.ref_file) == 0:
error(
"Missing the reference genome fasta file, use -r or --ref option.")
else:
if not os.path.isfile(options.ref_file):
error("Can't open the ref file: " + options.ref_file)
if len(options.samtools) != 0:
if options.samtools[-1] != '/':
options.samtools += '/'
if len(options.name) == 0:
error("Missing the output file name, use -n or --name options.")
if len(options.trim_file) != 0 and not os.path.isfile(options.trim_file):
error("Can't open the ref file: " + options.trim_file)
options.read_length = options.read_length.split(',')
sam_inf = options.sam_file
ref_file = options.ref_file
bsm = options.bsm
s_path = options.samtools
name = options.name
read_l = options.read_length
auto = options.automatically
pvalue = options.pvalue
drift = options.drift
trim_file = options.trim_file
remove_overlap = options.remove_overlap
filter_dup = options.filter_dup
p_poisson = options.p_poisson
gsize = options.gsize
not_mapping = options.not_mapping
info("Get the all parameter!!")
#check the input mapping files
sam_format, read_inf = check.check_mapping_file_flag(sam_inf[0], s_path)
pre_flag = read_inf.readline().split('\t')[1]
if 'p' in pre_flag:
single_on = False
info("The input mapping files are paired-end sequencing!")
else:
single_on = True
info("The input mapping files are single-end sequencing!")
if filter_dup:
## if filter_up is TRUE, the duplicate reads will be assessed and shown in Dup_dis.pdf
## and the loc_dict & max_cov will be used in the trimming step
if len(trim_file) != 0:
info(
"The trimming file has been defined. But the filter_dup has been set True."
)
info("QC_report will just generate Dup distribution!!")
info(
"And the user defined trimming file will be used in the trimming step!!"
)
else:
info("The filter_dup has been set True.")
info(
"QC_report not only includes Mbias plot, Mbias table and trimming file, but also Dup distribution."
)
QC_report_MD = QR.QC_Report_Mbias_Dup(sam_inf, ref_file, bsm, s_path,
name, read_l, single_on, pvalue,
drift, trim_file, p_poisson,
gsize)
strand_t, loc_dict, max_cov = QC_report_MD.generator()
else:
if len(trim_file) != 0:
info("The trimming file has been defined. So Ignore the ")
info(
"The filter_dup has been set False!! QC_report only includes Mbias plot, Mbias table and trimming file."
)
info(
"And ignore the collection of the location information for removing duplicate reads!!"
)
QC_report_M = QR.QC_Report_Mias(sam_inf, ref_file, bsm, s_path, name,
read_l, single_on, pvalue, drift,
trim_file)
strand_t = QC_report_M.generator()
#no duplicate location information
loc_dict = {}
max_cov = 10000
if ((auto or filter_dup) and single_on) or (
(auto or filter_dup or remove_overlap) and not single_on):
## for single-end: qc_filter Mbias or filter duplicate reads
## for paired-end: qc_filter Mbias, keep one copy of the overlapping segment, or filter duplicate reads
info("Start to filter read...")
if auto:
info("Automatically trim Mbias...")
else:
info("--auto has been set %s ! Ignore trimming Mbias!!" % auto)
if filter_dup:
info("Filter duplicate reads...")
else:
info(
"--filter_dup has been set %s ! Ignore removing duplicate reads!!"
% filter_dup)
if remove_overlap and not single_on:
info("Keep one copy of the overlapping segment...")
if not remove_overlap and not single_on:
info(
"--remove_overlap has been set %s ! Ignore removing one copy of the overlapping segment!!"
% remove_overlap)
if not_mapping:
info("Keep the not_unique mapping reads!")
else:
info("Remove the not_unique mapping reads!!")
QF.filter_sam(sam_inf, ref_file, bsm, strand_t, read_l, single_on,
name, s_path, auto, remove_overlap, loc_dict, max_cov,
not_mapping)
info("Get the filtered SAM file!")
else:
if single_on:
info("Skip the trimming Mbias and removing duplicate reads!!")
info("Not BSeQC filter report!!")
else:
info(
"Skip the trimming Mbias, removing duplicate reads and removing one copy of the overlapping segment!!"
)
info("Not BSeQC filter report!!")
def run(args):
options = args.parse_args()
if len(options.sam_file) == 0:
error("Missing the SAM file, use -s or --sam option.")
else:
options.sam_file = options.sam_file.split(',')
for s in options.sam_file:
if not os.path.isfile(s):
error("Can't open the SAM file: " + s)
sys.exit(1)
if len(options.ref_file) == 0:
error("Missing the reference genome fasta file, use -r or --ref option.")
else:
if not os.path.isfile(options.ref_file):
error("Can't open the ref file: " + options.ref_file)
if len(options.samtools) != 0:
if options.samtools[-1] != '/':
options.samtools += '/'
if len(options.name) == 0:
error("Missing the output file name, use -n or --name options.")
if len(options.trim_file) != 0 and not os.path.isfile(options.trim_file):
error("Can't open the ref file: " + options.trim_file)
options.read_length = options.read_length.split(',')
sam_inf = options.sam_file
ref_file = options.ref_file
bsm = options.bsm
s_path = options.samtools
name = options.name
read_l = options.read_length
auto = options.automatically
pvalue = options.pvalue
drift = options.drift
trim_file = options.trim_file
remove_overlap = options.remove_overlap
filter_dup = options.filter_dup
p_poisson = options.p_poisson
gsize = options.gsize
not_mapping = options.not_mapping
info("Get the all parameter!!")
#check the input mapping files
sam_format, read_inf = check.check_mapping_file_flag(sam_inf[0], s_path)
pre_flag = read_inf.readline().split('\t')[1]
if 'p' in pre_flag:
single_on = False
info("The input mapping files are paired-end sequencing!")
else:
single_on = True
info("The input mapping files are single-end sequencing!")
if filter_dup:
## if filter_up is TRUE, the duplicate reads will be assessed and shown in Dup_dis.pdf
## and the loc_dict & max_cov will be used in the trimming step
if len(trim_file) != 0:
info("The trimming file has been defined. But the filter_dup has been set True.")
info("QC_report will just generate Dup distribution!!")
info("And the user defined trimming file will be used in the trimming step!!")
else:
info("The filter_dup has been set True.")
info("QC_report not only includes Mbias plot, Mbias table and trimming file, but also Dup distribution.")
QC_report_MD = QR.QC_Report_Mbias_Dup(sam_inf, ref_file, bsm, s_path, name, read_l, single_on, pvalue, drift,
trim_file,
p_poisson, gsize)
strand_t, loc_dict, max_cov = QC_report_MD.generator()
else:
if len(trim_file) != 0:
info("The trimming file has been defined. So Ignore the ")
info("The filter_dup has been set False!! QC_report only includes Mbias plot, Mbias table and trimming file.")
info("And ignore the collection of the location information for removing duplicate reads!!")
QC_report_M = QR.QC_Report_Mias(sam_inf, ref_file, bsm, s_path, name, read_l, single_on, pvalue, drift,
trim_file)
strand_t = QC_report_M.generator()
#no duplicate location information
loc_dict = {}
max_cov = 10000
if ((auto or filter_dup) and single_on) or ((auto or filter_dup or remove_overlap) and not single_on):
## for single-end: qc_filter Mbias or filter duplicate reads
## for paired-end: qc_filter Mbias, keep one copy of the overlapping segment, or filter duplicate reads
info("Start to filter read...")
if auto:
info("Automatically trim Mbias...")
else:
info("--auto has been set %s ! Ignore trimming Mbias!!" % auto)
if filter_dup:
info("Filter duplicate reads...")
else:
info("--filter_dup has been set %s ! Ignore removing duplicate reads!!" % filter_dup)
if remove_overlap and not single_on:
info("Keep one copy of the overlapping segment...")
if not remove_overlap and not single_on:
info(
"--remove_overlap has been set %s ! Ignore removing one copy of the overlapping segment!!" % remove_overlap)
if not_mapping:
info("Keep the not_unique mapping reads!")
else:
info("Remove the not_unique mapping reads!!")
QF.filter_sam(sam_inf, ref_file, bsm, strand_t, read_l, single_on, name, s_path, auto, remove_overlap, loc_dict, max_cov,
not_mapping)
info("Get the filtered SAM file!")
else:
if single_on:
info("Skip the trimming Mbias and removing duplicate reads!!")
info("Not BSeQC filter report!!")
else:
info("Skip the trimming Mbias, removing duplicate reads and removing one copy of the overlapping segment!!")
info("Not BSeQC filter report!!")
def run(args):
"""
Alternative module: Use the strategy in Bis-SNP to trim 5' bisulfite conversion failures
"""
options = args.parse_args()
if len(options.sam_file) == 0:
error("Missing the SAM file, use -s or --sam option.")
else:
options.sam_file = options.sam_file.split(',')
for s in options.sam_file:
if not os.path.isfile(s):
error("Can't open the SAM file: " + s)
sys.exit(1)
if len(options.ref_file) == 0:
error("Missing the reference genome fasta file, use -r or --ref option.")
else:
if not os.path.isfile(options.ref_file):
error("Can't open the ref file: " + options.ref_file)
if len(options.samtools) != 0:
if options.samtools[-1] != '/':
options.samtools += '/'
if len(options.name) == 0:
error("Missing the output file name, use -n or --name options.")
sam_inf = options.sam_file
ref_file = options.ref_file
bsm = options.bsm
s_path = options.samtools
name = options.name
remove_overlap = options.remove_overlap
filter_dup = options.filter_dup
p_poisson = options.p_poisson
gsize = options.gsize
not_mapping = options.not_mapping
info("Get the all parameter!!")
#check the input mapping files
sam_format, read_inf = check.check_mapping_file_flag(sam_inf[0], s_path)
pre_flag = read_inf.readline().split('\t')[1]
if 'p' in pre_flag:
single_on = False
info("The input mapping files are paired-end sequencing!")
else:
single_on = True
info("The input mapping files are single-end sequencing!")
loc_dict = {}
if filter_dup:
## if filter_up is TRUE, the duplicate reads will be assessed and shown in Dup_dis.pdf
info("The filter_dup has been set True.")
info("Assess the duplicate reads...")
for sam in sam_inf:
#check the input mapping files
sam_format, read_inf = check.check_mapping_file(sam, s_path)
if single_on:
for read in read_inf:
loc_dict = LI.Loc_single(read, loc_dict, bsm)
else:
for read in read_inf:
loc_dict = LI.Loc_paired(read, loc_dict, bsm)
max_cov = DR.duplicate_report(loc_dict, gsize, p_poisson, name)
info('Get the duplicate reads distribution!')
#get reference information
ref = GR.get_ref(ref_file)
trim_position = []
filter_duplicate_reads = 0
filter_nonuniform_trim_bp = 0
filter_nonuniform_trim_bp_CG = 0
filter_remove_overlap_bp = 0
filter_not_mapping_reads = 0
all_reads = 0
not_mapping_reads = 0
all_mapping_bp = 0
##filter the 5' bisulfite failure
for sam in sam_inf:
out_sam = sam[:-4] + '_' + name + '_filter.sam'
out = open(out_sam, 'w')
#check the input mapping files
record_mate = {}
sam_format, read_inf = check.check_mapping_file_header(sam, s_path)
for read in read_inf:
#for sam header
if read.startswith('@'):
out.write(read)
continue
else:
all_reads += 1 ##record the read number (2013-06-20)
#Get the read information for trimming
#If the read isn't unique mapping, we will get a empty list ([]).
#In: single unique mapping read Out: [flag,strand,chr,pos,CIGAR,seq,score]
#In: paired unique mapping read Out: [flag,strand,chr,pos1,CIGAR,pos2,insert,seq,score]
read_info = RI(read, bsm)
read_info = read_info.extract_information()
if len(read_info) == 0:
not_mapping_reads += 1
if not_mapping: #keep the not_unique mapping reads (or not paired mapping)
out.write(read)
else:
filter_not_mapping_reads += 1 ##record the not mapping read number (2013-06-20)
continue
if len(loc_dict) > 0: #the --filter_dup has been set True, have to remove duplicate reads
duplicate, loc_dict = DF(read_info, loc_dict, max_cov, single_on)
else:
duplicate = False
if single_on:
all_mapping_bp += len(read_info[5]) ##record the mapping read basepair (2013-06-20)
else:
all_mapping_bp += len(read_info[7]) ##record the mapping read basepair (2013-06-20)
record_mate, trim_position, filter_nonuniform_trim_bp_CG, filter_duplicate_reads, filter_remove_overlap_bp = NF.nonuniform_filter(read,
out,
read_info,
ref,
remove_overlap,
duplicate,
single_on,
record_mate,
trim_position,
filter_nonuniform_trim_bp_CG,
filter_duplicate_reads,
filter_remove_overlap_bp)
out.close()
del record_mate
NR.nonuniform_generator(trim_position, name)
for i in range(len(trim_position)):
filter_nonuniform_trim_bp += i * trim_position[i]
##produce the filter report
info('Produce the report file...')
report_out = open(name + "_BSeQC_nonuniform_filter_report.txt", 'w')
report_out.write('Total reads: %d\n' % all_reads)
if single_on:
report_out.write('Not unique mapping reads: %d(%.2f%s all reads)\n' % (
not_mapping_reads, float(not_mapping_reads) / all_reads * 100, "%"))
report_out.write('Unique mapping reads: %d(%.2f%s all reads)\n' % (
(all_reads - not_mapping_reads), float(all_reads - not_mapping_reads) / all_reads * 100, "%"))
report_out.write('Skip not unique mapping reads: %d(%.2f%s all reads)\n' % (
filter_not_mapping_reads, float(filter_not_mapping_reads) / all_reads * 100, "%"))
report_out.write('In unique mapping reads:\n')
report_out.write('All unique mapping basepairs: %d\n' % all_mapping_bp)
report_out.write('Filter Duplicate reads: %d(%.2f%s of unique mapping reads)\n' % (
filter_duplicate_reads, float(filter_duplicate_reads) / (all_reads - not_mapping_reads) * 100, "%"))
report_out.write("Filter 5' nonconversion basepairs: %d(%.2f%s of unique mapping basepairs)\n" % (
filter_nonuniform_trim_bp, float(filter_nonuniform_trim_bp) / all_mapping_bp * 100, "%"))
report_out.write("Filter 5' nonconversion CpG basepairs: %d(%.2f%s of unique mapping basepairs)\n" % (
filter_nonuniform_trim_bp_CG, float(filter_nonuniform_trim_bp_CG) / all_mapping_bp * 100, "%"))
else:
report_out.write('Not unique paired mapping reads: %d(%.2f%s)\n' % (
not_mapping_reads, float(not_mapping_reads) / all_reads * 100, "%"))
report_out.write('Unique paired mapping reads: %d(%.2f%s)\n' % (
(all_reads - not_mapping_reads), float(all_reads - not_mapping_reads) / all_reads * 100, "%"))
report_out.write('Skip not paired unique mapping reads: %d(%.2f%s)\n' % (
filter_not_mapping_reads, float(filter_not_mapping_reads) / all_reads * 100, "%"))
report_out.write('In unique paired mapping reads:\n')
report_out.write('All unique paired mapping basepairs: %d\n' % all_mapping_bp)
report_out.write('Filter Duplicate reads: %d(%.2f%s of unique paired mapping reads)\n' % (
filter_duplicate_reads, float(filter_duplicate_reads) / (all_reads - not_mapping_reads * 100), "%"))
report_out.write("Filter 5' nonconversion basepairs: %d(%.2f%s of unique mapping basepairs)\n" % (
filter_nonuniform_trim_bp, float(filter_nonuniform_trim_bp) / all_mapping_bp * 100, "%"))
report_out.write("Filter 5' nonconversion CpG basepairs: %d(%.2f%s of unique mapping basepairs)\n" % (
filter_nonuniform_trim_bp_CG, float(filter_nonuniform_trim_bp_CG) / all_mapping_bp * 100, "%"))
report_out.write('Filter overlapped basepairs: %d(%.2f%s of unique paired mapping basepairs)\n' % (
filter_remove_overlap_bp, float(filter_remove_overlap_bp) / all_mapping_bp * 100, "%"))
report_out.close()
info('Get the report file!')
