def write_remap_bam_pe(data_dir="test_data",
bam_filename="test_data/test.remap.bam"):
sam_lines = [
# Read pair expected to map 2 times and maps to correct location 2 times
"SRR1658224.34085432.16052611-16052734.1.2 163 chr22 16052611 12 101M = 16052734 224 TGGAGACATAAAATGAGGCATATCTGACCTCCACTTCCAAAAACATCTGAGATAGGTCTCAGTTAATTAAGAAAGTTTGTTCTGCCTAGTTTAAGGACATG CCCFFFFFHHHHHJJJJJJJJJJJJJJJIJJJJJJJJJJJJJJJJJIJJIHIJJJJEHIJJJHJJJJJJJJJJJJ=DHHHHHFFFFFFEEEEEEDDCDDDC AS:i:-11 XS:i:-17 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:7G44C48 YS:i:0 YT:Z:CP",
"SRR1658224.34085432.16052611-16052734.1.2 83 chr22 16052734 12 101M = 16052611 -224 TCCTGACAGCATGTGCCCAAGGTGGTCAGGATACAGCTTGCTTCTATATATTTTAGGGAGAAAATACATCAGCCTGTAAACAAAAAATTAAATTCTAAGGT DDDDDDDDDDDDDDEDEEEFFFFHHFHHIIFIIJJJJIJJJJJJJJJJIIJJJIIIJIJIJJJJIFIIIJJIJJJJJJJIIJJJJJJJHHHHHFFFFFCCC AS:i:0 XS:i:-12 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:101 YS:i:-11 YT:Z:CP",
"SRR1658224.34085432.16052611-16052734.2.2 163 chr22 16052611 12 101M = 16052734 224 TGGAGACATAAAATGAGGCATATCTGACCTCCACTTCCAAAAACATCTGAGATAGGTCTCAGTTAATTAAGAAAGTTTGTTCTGCCTAGTTTAAGGACATG CCCFFFFFHHHHHJJJJJJJJJJJJJJJIJJJJJJJJJJJJJJJJJIJJIHIJJJJEHIJJJHJJJJJJJJJJJJ=DHHHHHFFFFFFEEEEEEDDCDDDC AS:i:-11 XS:i:-17 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:7G44C48 YS:i:0 YT:Z:CP",
"SRR1658224.34085432.16052611-16052734.2.2 83 chr22 16052734 12 101M = 16052611 -224 TCCTGACAGCATGTGCCCAAGGTGGTCAGGATACAGCTTGCTTCTATATATTTTAGGGAGAAAATACATCAGCCTGTAAACAAAAAATTAAATTCTAAGGT DDDDDDDDDDDDDDEDEEEFFFFHHFHHIIFIIJJJJIJJJJJJJJJJIIJJJIIIJIJIJJJJIFIIIJJIJJJJJJJIIJJJJJJJHHHHHFFFFFCCC AS:i:0 XS:i:-12 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:101 YS:i:-11 YT:Z:CP",
# Read pair expected to map 2 times, but only maps 1 time
"SRR1658224.34975561.16071944-16072163.2.2 99 chr22 16071944 12 101M = 16072163 320 ATTTATTTATTTATTTATTATTGGGACAGAGTCTCACTCTGTCCCCCAGACTGGAGTCCAGTGACATGATCTCAGCTCACTGCAACCTCTGCCTCGTGGGT CCCFFFFFHHHHHJJJJJJJJJJJJIJJJJIEHIJJJJJJJIIJJJJJIJJJJJJJJJJIJHIJIJJJJIJJJJJHHHHHHFFFFFECEEEEDDDDDDBBD AS:i:-5 XS:i:-22 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:89C11 YS:i:0 YT:Z:CP",
"SRR1658224.34975561.16071944-16072163.2.2 147 chr22 16072163 12 101M = 16071944 -320 GTCTCAAACTTCTGACCTCAGGTGATCCACCCACCTCGACCTCCCAAAGTGCTGGGATTACAGGCACTAGGTCCCTAAATTAGAGCCATATTCTTTAATGT DDBCDEDCDCCDCC?DDDDDDDBACBDA<FFB:6HIIJIIJIIJJJJJJJJJJJJIJJIHJJJJJIJJJJJJJJJJJJJJJJJJJJJJHHHGGFFFFFCCC AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:101 YS:i:-5 YT:Z:CP",
# Read pair expected to map 2 times, but only 1/2 of 2nd pair maps back to same location
"SRR1658224.7462188.16235410-16235625.1.2 163 chr22 16235410 17 101M = 16235625 316 AGATAATTGTCTTATTTTTTTAAAAAAAGAGTAACTTTATATTATGGAATTCATAATATTTGAGACTATAATGCATGACATAAATAGTATAAAGGAGAGAG CC@FFFFFHHHHHJJJJJJJJJJJJJJJJIJBGIJJJJJJJJJJJJJIJIFIJJJJJJJJJHHHHGFFFFFFEEEEDEEDDDDDEED@CFFFEDDD?ABB? AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:101 YS:i:-5 YT:Z:CP",
"SRR1658224.7462188.16235410-16235625.1.2 83 chr22 16235625 17 101M = 16235410 -316 TTCAAAAGATGGTATATGCATTAATATTTTCATACAACTTCCAGCTTTTGTTTTTCTTCATTTAATTTTATTTATTTATTTATTTTTGAGATGGAGTCTCG CBDDDDECEEDEFFFDFFFHHHHHHHJJIIJJIHIHFHGHJJJJJJJGJJJJJIJJJIIJJJJJJJJJJJJJJJJJJJJJJJJJJJJJHHHHHFFFDFCCC AS:i:-5 XS:i:-39 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:15G85 YS:i:0 YT:Z:CP",
"SRR1658224.7462188.16235410-16235625.2.2 163 chr22 16235410 17 101M * 0 0 AGATAATTGTCTTATTTTTTTAAAAAAAGAGTAACTTTATATTATGGAATTCATAATATTTGAGACTATAATGCATGACATAAATAGTATAAAGGAGAGAG CC@FFFFFHHHHHJJJJJJJJJJJJJJJJIJBGIJJJJJJJJJJJJJIJIFIJJJJJJJJJHHHHGFFFFFFEEEEDEEDDDDDEED@CFFFEDDD?ABB? AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:101 YS:i:-5 YT:Z:CP",
# Read pair expected to map 2 times, but 1 pair maps to wrong location
"SRR1658224.31153145.16235410-16235625.1.2 163 chr22 16235410 17 101M = 16235625 316 AGATAATTGTCTTATTTTTTTAAAAAAAGAGTAACTTTATATTATGGAATTCATAATATTTGAGACTATAATGCATGACATAAATAGTATAAAGGAGAGAG CCCFFFFFHHHHHJJJJJJJJJJJJJJJJIJFHIJJJJJJJJJJJIJIJJFHIJJJJJJJJHHHHHFFFFFFEDEEEEEDDDDDEED@DEEEEDDDDDDB2 AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:101 YS:i:-2 YT:Z:CP",
"SRR1658224.31153145.16235410-16235625.1.2 83 chr22 16235625 17 101M = 16235410 -316 TTCAAAAGATGGTATGTGCATTAATATTTTCATACAACTTCCAGTTTTTGTTTTTCTTCATTTAATTTTATTTATTTATTTATTTTTGAGATGGAGTCTCG DDDDDDDDEEEEEEFFFFFFHHHHGHHJJIJJJIIJIJIHJHF@(JJJJJJJJJJJJIIIIJJJJJJJIJJJJJJJJJJJJJJJJJJJHHHHHFFFDFCCC AS:i:-2 XS:i:-36 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:44C56 YS:i:0 YT:Z:CP",
"SRR1658224.31153145.16235410-16235625.2.2 163 chr22 18235410 17 101M = 16235625 316 AGATAATTGTCTTATTTTTTTAAAAAAAGAGTAACTTTATATTATGGAATTCATAATATTTGAGACTATAATGCATGACATAAATAGTATAAAGGAGAGAG CCCFFFFFHHHHHJJJJJJJJJJJJJJJJIJFHIJJJJJJJJJJJIJIJJFHIJJJJJJJJHHHHHFFFFFFEDEEEEEDDDDDEED@DEEEEDDDDDDB2 AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:101 YS:i:-2 YT:Z:CP",
"SRR1658224.31153145.16235410-16235625.2.2 83 chr22 18235625 17 101M = 16235410 -316 TTCAAAAGATGGTATGTGCATTAATATTTTCATACAACTTCCAGTTTTTGTTTTTCTTCATTTAATTTTATTTATTTATTTATTTTTGAGATGGAGTCTCG DDDDDDDDEEEEEEFFFFFFHHHHGHHJJIJJJIIJIJIHJHF@(JJJJJJJJJJJJIIIIJJJJJJJIJJJJJJJJJJJJJJJJJJJHHHHHFFFDFCCC AS:i:-2 XS:i:-36 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:44C56 YS:i:0 YT:Z:CP",
# Read pair expected to map 2 times, but does not map at all
# "SRR1658224.25014179"
# Read pairs expected to map 1 times, with read-pairs interleaved
"readpair1.100-200.1.2 163 chr22 100 12 101M = 200 201 TGGAGACATAAAATGAGGCATATCTGACCTCCACTTCCAAAAACATCTGAGATAGGTCTCAGTTAATTAAGAAAGTTTGTTCTGCCTAGTTTAAGGACATG CCCFFFFFHHHHHJJJJJJJJJJJJJJJIJJJJJJJJJJJJJJJJJIJJIHIJJJJEHIJJJHJJJJJJJJJJJJ=DHHHHHFFFFFFEEEEEEDDCDDDC AS:i:-11 XS:i:-17 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:7G44C48 YS:i:0 YT:Z:CP",
"readpair2.150-250.1.2 163 chr22 150 12 101M = 250 201 TGGAGACATAAAATGAGGCATATCTGACCTCCACTTCCAAAAACATCTGAGATAGGTCTCAGTTAATTAAGAAAGTTTGTTCTGCCTAGTTTAAGGACATG CCCFFFFFHHHHHJJJJJJJJJJJJJJJIJJJJJJJJJJJJJJJJJIJJIHIJJJJEHIJJJHJJJJJJJJJJJJ=DHHHHHFFFFFFEEEEEEDDCDDDC AS:i:-11 XS:i:-17 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:7G44C48 YS:i:0 YT:Z:CP",
"readpair1.100-200.1.2 83 chr22 200 12 101M = 100 -201 TCCTGACAGCATGTGCCCAAGGTGGTCAGGATACAGCTTGCTTCTATATATTTTAGGGAGAAAATACATCAGCCTGTAAACAAAAAATTAAATTCTAAGGT DDDDDDDDDDDDDDEDEEEFFFFHHFHHIIFIIJJJJIJJJJJJJJJJIIJJJIIIJIJIJJJJIFIIIJJIJJJJJJJIIJJJJJJJHHHHHFFFFFCCC AS:i:0 XS:i:-12 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:101 YS:i:-11 YT:Z:CP",
"readpair2.150-250.1.2 163 chr22 250 12 101M = 150 -201 TGGAGACATAAAATGAGGCATATCTGACCTCCACTTCCAAAAACATCTGAGATAGGTCTCAGTTAATTAAGAAAGTTTGTTCTGCCTAGTTTAAGGACATG CCCFFFFFHHHHHJJJJJJJJJJJJJJJIJJJJJJJJJJJJJJJJJIJJIHIJJJJEHIJJJHJJJJJJJJJJJJ=DHHHHHFFFFFFEEEEEEDDCDDDC AS:i:-11 XS:i:-17 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:7G44C48 YS:i:0 YT:Z:CP",
"readpair1.100-200.2.2 163 chr22 100 12 101M = 200 201 TGGAGACATAAAATGAGGCATATCTGACCTCCACTTCCAAAAACATCTGAGATAGGTCTCAGTTAATTAAGAAAGTTTGTTCTGCCTAGTTTAAGGACATG CCCFFFFFHHHHHJJJJJJJJJJJJJJJIJJJJJJJJJJJJJJJJJIJJIHIJJJJEHIJJJHJJJJJJJJJJJJ=DHHHHHFFFFFFEEEEEEDDCDDDC AS:i:-11 XS:i:-17 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:7G44C48 YS:i:0 YT:Z:CP",
"readpair2.150-250.2.2 163 chr22 150 12 101M = 250 201 TGGAGACATAAAATGAGGCATATCTGACCTCCACTTCCAAAAACATCTGAGATAGGTCTCAGTTAATTAAGAAAGTTTGTTCTGCCTAGTTTAAGGACATG CCCFFFFFHHHHHJJJJJJJJJJJJJJJIJJJJJJJJJJJJJJJJJIJJIHIJJJJEHIJJJHJJJJJJJJJJJJ=DHHHHHFFFFFFEEEEEEDDCDDDC AS:i:-11 XS:i:-17 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:7G44C48 YS:i:0 YT:Z:CP",
"readpair1.100-200.2.2 83 chr22 200 12 101M = 100 -201 TCCTGACAGCATGTGCCCAAGGTGGTCAGGATACAGCTTGCTTCTATATATTTTAGGGAGAAAATACATCAGCCTGTAAACAAAAAATTAAATTCTAAGGT DDDDDDDDDDDDDDEDEEEFFFFHHFHHIIFIIJJJJIJJJJJJJJJJIIJJJIIIJIJIJJJJIFIIIJJIJJJJJJJIIJJJJJJJHHHHHFFFFFCCC AS:i:0 XS:i:-12 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:101 YS:i:-11 YT:Z:CP",
"readpair2.150-250.2.2 163 chr22 250 12 101M = 150 -201 TGGAGACATAAAATGAGGCATATCTGACCTCCACTTCCAAAAACATCTGAGATAGGTCTCAGTTAATTAAGAAAGTTTGTTCTGCCTAGTTTAAGGACATG CCCFFFFFHHHHHJJJJJJJJJJJJJJJIJJJJJJJJJJJJJJJJJIJJIHIJJJJEHIJJJHJJJJJJJJJJJJ=DHHHHHFFFFFFEEEEEEDDCDDDC AS:i:-11 XS:i:-17 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:7G44C48 YS:i:0 YT:Z:CP"
]
if not os.path.exists(data_dir):
os.makedirs(data_dir)
# write temporary file in SAM format, before converting to BAM
sam_filename = data_dir + "/tmp.sam"
f = open(sam_filename, "wt")
write_sam_header(f)
for line in sam_lines:
f.write(line + "\n")
f.close()
# write to temp bam file
tmp_bam_filename = data_dir + "/tmp.bam"
subprocess.check_call("samtools view -b %s > %s" %
(sam_filename, tmp_bam_filename),
shell=True)
# sort the temp bam file
util.sort_bam(tmp_bam_filename, data_dir + "/tmp")
# remove temp bam
os.remove(tmp_bam_filename)
# rename sorted bam to output bam filename
os.rename(data_dir + "/tmp.sort.bam", bam_filename)
def write_remap_bam_pe(sam_lines, data_dir="test_data", bam_filename="test_data/test.remap.bam"):
if not os.path.exists(data_dir):
os.makedirs(data_dir)
# write temporary file in SAM format, before converting to BAM
sam_filename = data_dir + "/tmp.sam"
f = open(sam_filename, "wt")
write_sam_header(f)
for line in sam_lines:
f.write(line + "\n")
f.close()
# write to temp bam file
tmp_bam_filename = data_dir + "/tmp.bam"
subprocess.check_call("samtools view -b %s > %s" % (sam_filename, tmp_bam_filename), shell=True)
# sort the temp bam file
util.sort_bam(tmp_bam_filename, data_dir + "/tmp")
# remove temp bam
os.remove(tmp_bam_filename)
# rename sorted bam to output bam filename
os.rename(data_dir + "/tmp.sort.bam", bam_filename)
def __init__(self,
bam_filename,
is_sorted,
is_paired,
output_dir=None,
snp_dir=None,
snp_tab_filename=None,
snp_index_filename=None,
haplotype_filename=None,
samples=None):
# flag indicating whether reads are paired-end
self.is_paired = is_paired
# prefix for output files
self.prefix = None
# name of input BAM filename
self.bam_filename = bam_filename
# name of sorted input bam_filename
# (new file is created if input file is not
# already sorted)
self.bam_sort_filename = None
# pysam file handle for input BAM
self.input_bam = None
# name of output keep and to.remap BAM files
self.keep_filename = None
self.remap_filename = None
# pysam file handles for output BAM filenames
self.keep_bam = None
self.remap_bam = None
# name of output fastq files
self.fastq_single_filename = None
self.fastq1_filename = None
self.fastq2_filename = None
self.fastq1 = None
self.fastq2 = None
self.fastq_single = None
# name of directory to read SNPs from
self.snp_dir = snp_dir
# paths to HDF5 files to read SNP info from
self.snp_tab_filename = snp_tab_filename
self.snp_index_filename = snp_index_filename
self.haplotype_filename = haplotype_filename
if self.snp_tab_filename:
self.snp_tab_h5 = tables.openFile(snp_tab_filename, "r")
self.snp_index_h5 = tables.openFile(snp_index_filename, "r")
self.hap_h5 = tables.openFile(haplotype_filename, "r")
else:
self.snp_tab_h5 = None
self.snp_index_h5 = None
self.hap_h5 = None
# separate input directory and bam filename
tokens = self.bam_filename.split("/")
bam_dir = "/".join(tokens[:-1])
filename = tokens[-1]
if output_dir is None:
# if no output dir specified, use same directory as input
# bam file
output_dir = bam_dir
else:
if output_dir.endswith("/"):
# strip trailing '/' from output dir name
output_dir = output_dir[:-1]
name_split = filename.split(".")
if len(name_split) > 1:
self.prefix = output_dir + "/" + ".".join(name_split[:-1])
else:
self.prefix = output_dir + "/" + name_split[0]
# TODO: could allow names of output files to be specified
# on command line rather than appending name to prefix
sys.stderr.write("prefix: %s\n" % self.prefix)
if not is_sorted:
util.sort_bam(self.bam_filename, self.prefix)
self.bam_sort_filename = self.prefix + ".sort.bam"
else:
self.bam_sort_filename = self.bam_filename
self.keep_filename = self.prefix + ".keep.bam"
self.remap_filename = self.prefix + ".to.remap.bam"
sys.stderr.write("reading reads from:\n %s\n" %
self.bam_sort_filename)
sys.stderr.write("writing output files to:\n")
if self.is_paired:
self.fastq1_filename = self.prefix + ".remap.fq1.gz"
self.fastq2_filename = self.prefix + ".remap.fq2.gz"
self.fastq1 = gzip.open(self.fastq1_filename, "wb")
self.fastq2 = gzip.open(self.fastq2_filename, "wb")
self.fastq_single_filename = self.prefix + ".remap.single.fq.gz"
self.fastq_single = gzip.open(self.fastq_single_filename, "wb")
sys.stderr.write(" %s\n %s\n %s\n" %
(self.fastq1_filename, self.fastq2_filename,
self.fastq_single_filename))
else:
self.fastq_single_filename = self.prefix + ".remap.fq.gz"
self.fastq_single = gzip.open(self.fastq_single_filename, "wb")
sys.stderr.write(" %s\n" % (self.fastq_single_filename))
self.input_bam = pysam.Samfile(self.bam_sort_filename, "rb")
self.keep_bam = pysam.Samfile(self.keep_filename,
"wb",
template=self.input_bam)
self.remap_bam = pysam.Samfile(self.remap_filename,
"wb",
template=self.input_bam)
sys.stderr.write(" %s\n %s\n" %
(self.keep_filename, self.remap_filename))
def __init__(self,
bam_filename,
is_sorted,
is_paired,
output_dir=None,
snp_dir=None):
# flag indicating whether reads are paired-end
self.is_paired = is_paired
# prefix for output files
self.prefix = None
# name of input BAM filename
self.bam_filename = bam_filename
# name of sorted input bam_filename
# (new file is created if input file is not
# already sorted)
self.bam_sort_filename = None
# pysam file handle for input BAM
self.input_bam = None
# name of output file to check initial imbalance
self.initial_AI_filename = None
# file handles for output pickle filename
#self.initial_AI_pickle = None
self.initial_AI_txt = None
# name of output fastq files
self.fastq_single_filename = None
self.fastq1_filename = None
self.fastq2_filename = None
self.fastq1 = None
self.fastq2 = None
self.fastq_single = None
# name of directory to read SNPs from
self.snp_dir = snp_dir
# separate input directory and bam filename
tokens = self.bam_filename.split("/")
bam_dir = "/".join(tokens[:-1])
filename = tokens[-1]
if output_dir is None:
# if no output dir specified, use same directory as input
# bam file
output_dir = bam_dir
else:
if output_dir.endswith("/"):
# strip trailing '/' from output dir name
output_dir = output_dir[:-1]
name_split = filename.split(".")
if len(name_split) > 1:
self.prefix = output_dir + "/" + ".".join(name_split[:-1])
else:
self.prefix = output_dir + "/" + name_split[0]
# create output dir if does not exist
if not os.path.exists(output_dir):
os.makedirs(output_dir)
if not is_sorted:
util.sort_bam(self.bam_filename, self.prefix)
self.bam_sort_filename = self.prefix + ".sort.bam"
else:
self.bam_sort_filename = self.bam_filename
self.initial_AI_filename = self.prefix + ".initial.AI.txt"
sys.stderr.write("reading reads from:\n %s\n" %
self.bam_sort_filename)
sys.stderr.write("writing output files to:\n")
if self.is_paired:
self.fastq1_filename = self.prefix + ".remap.fq1.gz"
self.fastq2_filename = self.prefix + ".remap.fq2.gz"
self.fastq1 = gzip.open(self.fastq1_filename, "wt")
self.fastq2 = gzip.open(self.fastq2_filename, "wt")
self.fastq_single_filename = self.prefix + ".remap.single.fq.gz"
self.fastq_single = gzip.open(self.fastq_single_filename, "wt")
sys.stderr.write(" %s\n %s\n %s\n" %
(self.fastq1_filename, self.fastq2_filename,
self.fastq_single_filename))
else:
self.fastq_single_filename = self.prefix + ".remap.fq.gz"
self.fastq_single = gzip.open(self.fastq_single_filename, "wt")
sys.stderr.write(" %s\n" % (self.fastq_single_filename))
self.input_bam = pysam.AlignmentFile(self.bam_sort_filename, "rb")
self.initial_AI_txt = open(self.initial_AI_filename, "w+")
sys.stderr.write(" %s\n " % self.initial_AI_filename)
def write_remap_bam_pe(data_dir="test_data", bam_filename="test_data/test.remap.bam"):
sam_lines = [
# Read pair expected to map 2 times and maps to correct location 2 times
"SRR1658224.34085432.16052611-16052734.1.2 163 chr22 16052611 12 101M = 16052734 224 TGGAGACATAAAATGAGGCATATCTGACCTCCACTTCCAAAAACATCTGAGATAGGTCTCAGTTAATTAAGAAAGTTTGTTCTGCCTAGTTTAAGGACATG CCCFFFFFHHHHHJJJJJJJJJJJJJJJIJJJJJJJJJJJJJJJJJIJJIHIJJJJEHIJJJHJJJJJJJJJJJJ=DHHHHHFFFFFFEEEEEEDDCDDDC AS:i:-11 XS:i:-17 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:7G44C48 YS:i:0 YT:Z:CP",
"SRR1658224.34085432.16052611-16052734.1.2 83 chr22 16052734 12 101M = 16052611 -224 TCCTGACAGCATGTGCCCAAGGTGGTCAGGATACAGCTTGCTTCTATATATTTTAGGGAGAAAATACATCAGCCTGTAAACAAAAAATTAAATTCTAAGGT DDDDDDDDDDDDDDEDEEEFFFFHHFHHIIFIIJJJJIJJJJJJJJJJIIJJJIIIJIJIJJJJIFIIIJJIJJJJJJJIIJJJJJJJHHHHHFFFFFCCC AS:i:0 XS:i:-12 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:101 YS:i:-11 YT:Z:CP",
"SRR1658224.34085432.16052611-16052734.2.2 163 chr22 16052611 12 101M = 16052734 224 TGGAGACATAAAATGAGGCATATCTGACCTCCACTTCCAAAAACATCTGAGATAGGTCTCAGTTAATTAAGAAAGTTTGTTCTGCCTAGTTTAAGGACATG CCCFFFFFHHHHHJJJJJJJJJJJJJJJIJJJJJJJJJJJJJJJJJIJJIHIJJJJEHIJJJHJJJJJJJJJJJJ=DHHHHHFFFFFFEEEEEEDDCDDDC AS:i:-11 XS:i:-17 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:7G44C48 YS:i:0 YT:Z:CP",
"SRR1658224.34085432.16052611-16052734.2.2 83 chr22 16052734 12 101M = 16052611 -224 TCCTGACAGCATGTGCCCAAGGTGGTCAGGATACAGCTTGCTTCTATATATTTTAGGGAGAAAATACATCAGCCTGTAAACAAAAAATTAAATTCTAAGGT DDDDDDDDDDDDDDEDEEEFFFFHHFHHIIFIIJJJJIJJJJJJJJJJIIJJJIIIJIJIJJJJIFIIIJJIJJJJJJJIIJJJJJJJHHHHHFFFFFCCC AS:i:0 XS:i:-12 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:101 YS:i:-11 YT:Z:CP",
# Read pair expected to map 2 times, but only maps 1 time
"SRR1658224.34975561.16071944-16072163.2.2 99 chr22 16071944 12 101M = 16072163 320 ATTTATTTATTTATTTATTATTGGGACAGAGTCTCACTCTGTCCCCCAGACTGGAGTCCAGTGACATGATCTCAGCTCACTGCAACCTCTGCCTCGTGGGT CCCFFFFFHHHHHJJJJJJJJJJJJIJJJJIEHIJJJJJJJIIJJJJJIJJJJJJJJJJIJHIJIJJJJIJJJJJHHHHHHFFFFFECEEEEDDDDDDBBD AS:i:-5 XS:i:-22 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:89C11 YS:i:0 YT:Z:CP",
"SRR1658224.34975561.16071944-16072163.2.2 147 chr22 16072163 12 101M = 16071944 -320 GTCTCAAACTTCTGACCTCAGGTGATCCACCCACCTCGACCTCCCAAAGTGCTGGGATTACAGGCACTAGGTCCCTAAATTAGAGCCATATTCTTTAATGT DDBCDEDCDCCDCC?DDDDDDDBACBDA<FFB:6HIIJIIJIIJJJJJJJJJJJJIJJIHJJJJJIJJJJJJJJJJJJJJJJJJJJJJHHHGGFFFFFCCC AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:101 YS:i:-5 YT:Z:CP",
# Read pair expected to map 2 times, but only 1/2 of 2nd pair maps back to same location
"SRR1658224.7462188.16235410-16235625.1.2 163 chr22 16235410 17 101M = 16235625 316 AGATAATTGTCTTATTTTTTTAAAAAAAGAGTAACTTTATATTATGGAATTCATAATATTTGAGACTATAATGCATGACATAAATAGTATAAAGGAGAGAG CC@FFFFFHHHHHJJJJJJJJJJJJJJJJIJBGIJJJJJJJJJJJJJIJIFIJJJJJJJJJHHHHGFFFFFFEEEEDEEDDDDDEED@CFFFEDDD?ABB? AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:101 YS:i:-5 YT:Z:CP",
"SRR1658224.7462188.16235410-16235625.1.2 83 chr22 16235625 17 101M = 16235410 -316 TTCAAAAGATGGTATATGCATTAATATTTTCATACAACTTCCAGCTTTTGTTTTTCTTCATTTAATTTTATTTATTTATTTATTTTTGAGATGGAGTCTCG CBDDDDECEEDEFFFDFFFHHHHHHHJJIIJJIHIHFHGHJJJJJJJGJJJJJIJJJIIJJJJJJJJJJJJJJJJJJJJJJJJJJJJJHHHHHFFFDFCCC AS:i:-5 XS:i:-39 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:15G85 YS:i:0 YT:Z:CP",
"SRR1658224.7462188.16235410-16235625.2.2 163 chr22 16235410 17 101M * 0 0 AGATAATTGTCTTATTTTTTTAAAAAAAGAGTAACTTTATATTATGGAATTCATAATATTTGAGACTATAATGCATGACATAAATAGTATAAAGGAGAGAG CC@FFFFFHHHHHJJJJJJJJJJJJJJJJIJBGIJJJJJJJJJJJJJIJIFIJJJJJJJJJHHHHGFFFFFFEEEEDEEDDDDDEED@CFFFEDDD?ABB? AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:101 YS:i:-5 YT:Z:CP",
# Read pair expected to map 2 times, but 1 pair maps to wrong location
"SRR1658224.31153145.16235410-16235625.1.2 163 chr22 16235410 17 101M = 16235625 316 AGATAATTGTCTTATTTTTTTAAAAAAAGAGTAACTTTATATTATGGAATTCATAATATTTGAGACTATAATGCATGACATAAATAGTATAAAGGAGAGAG CCCFFFFFHHHHHJJJJJJJJJJJJJJJJIJFHIJJJJJJJJJJJIJIJJFHIJJJJJJJJHHHHHFFFFFFEDEEEEEDDDDDEED@DEEEEDDDDDDB2 AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:101 YS:i:-2 YT:Z:CP",
"SRR1658224.31153145.16235410-16235625.1.2 83 chr22 16235625 17 101M = 16235410 -316 TTCAAAAGATGGTATGTGCATTAATATTTTCATACAACTTCCAGTTTTTGTTTTTCTTCATTTAATTTTATTTATTTATTTATTTTTGAGATGGAGTCTCG DDDDDDDDEEEEEEFFFFFFHHHHGHHJJIJJJIIJIJIHJHF@(JJJJJJJJJJJJIIIIJJJJJJJIJJJJJJJJJJJJJJJJJJJHHHHHFFFDFCCC AS:i:-2 XS:i:-36 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:44C56 YS:i:0 YT:Z:CP",
"SRR1658224.31153145.16235410-16235625.2.2 163 chr22 18235410 17 101M = 16235625 316 AGATAATTGTCTTATTTTTTTAAAAAAAGAGTAACTTTATATTATGGAATTCATAATATTTGAGACTATAATGCATGACATAAATAGTATAAAGGAGAGAG CCCFFFFFHHHHHJJJJJJJJJJJJJJJJIJFHIJJJJJJJJJJJIJIJJFHIJJJJJJJJHHHHHFFFFFFEDEEEEEDDDDDEED@DEEEEDDDDDDB2 AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:101 YS:i:-2 YT:Z:CP",
"SRR1658224.31153145.16235410-16235625.2.2 83 chr22 18235625 17 101M = 16235410 -316 TTCAAAAGATGGTATGTGCATTAATATTTTCATACAACTTCCAGTTTTTGTTTTTCTTCATTTAATTTTATTTATTTATTTATTTTTGAGATGGAGTCTCG DDDDDDDDEEEEEEFFFFFFHHHHGHHJJIJJJIIJIJIHJHF@(JJJJJJJJJJJJIIIIJJJJJJJIJJJJJJJJJJJJJJJJJJJHHHHHFFFDFCCC AS:i:-2 XS:i:-36 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:44C56 YS:i:0 YT:Z:CP",
# Read pair expected to map 2 times, but does not map at all
# "SRR1658224.25014179"
# Read pairs expected to map 1 times, with read-pairs interleaved
"readpair1.100-200.1.2 163 chr22 100 12 101M = 200 201 TGGAGACATAAAATGAGGCATATCTGACCTCCACTTCCAAAAACATCTGAGATAGGTCTCAGTTAATTAAGAAAGTTTGTTCTGCCTAGTTTAAGGACATG CCCFFFFFHHHHHJJJJJJJJJJJJJJJIJJJJJJJJJJJJJJJJJIJJIHIJJJJEHIJJJHJJJJJJJJJJJJ=DHHHHHFFFFFFEEEEEEDDCDDDC AS:i:-11 XS:i:-17 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:7G44C48 YS:i:0 YT:Z:CP",
"readpair2.150-250.1.2 163 chr22 150 12 101M = 250 201 TGGAGACATAAAATGAGGCATATCTGACCTCCACTTCCAAAAACATCTGAGATAGGTCTCAGTTAATTAAGAAAGTTTGTTCTGCCTAGTTTAAGGACATG CCCFFFFFHHHHHJJJJJJJJJJJJJJJIJJJJJJJJJJJJJJJJJIJJIHIJJJJEHIJJJHJJJJJJJJJJJJ=DHHHHHFFFFFFEEEEEEDDCDDDC AS:i:-11 XS:i:-17 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:7G44C48 YS:i:0 YT:Z:CP",
"readpair1.100-200.1.2 83 chr22 200 12 101M = 100 -201 TCCTGACAGCATGTGCCCAAGGTGGTCAGGATACAGCTTGCTTCTATATATTTTAGGGAGAAAATACATCAGCCTGTAAACAAAAAATTAAATTCTAAGGT DDDDDDDDDDDDDDEDEEEFFFFHHFHHIIFIIJJJJIJJJJJJJJJJIIJJJIIIJIJIJJJJIFIIIJJIJJJJJJJIIJJJJJJJHHHHHFFFFFCCC AS:i:0 XS:i:-12 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:101 YS:i:-11 YT:Z:CP",
"readpair2.150-250.1.2 163 chr22 250 12 101M = 150 -201 TGGAGACATAAAATGAGGCATATCTGACCTCCACTTCCAAAAACATCTGAGATAGGTCTCAGTTAATTAAGAAAGTTTGTTCTGCCTAGTTTAAGGACATG CCCFFFFFHHHHHJJJJJJJJJJJJJJJIJJJJJJJJJJJJJJJJJIJJIHIJJJJEHIJJJHJJJJJJJJJJJJ=DHHHHHFFFFFFEEEEEEDDCDDDC AS:i:-11 XS:i:-17 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:7G44C48 YS:i:0 YT:Z:CP",
"readpair1.100-200.2.2 163 chr22 100 12 101M = 200 201 TGGAGACATAAAATGAGGCATATCTGACCTCCACTTCCAAAAACATCTGAGATAGGTCTCAGTTAATTAAGAAAGTTTGTTCTGCCTAGTTTAAGGACATG CCCFFFFFHHHHHJJJJJJJJJJJJJJJIJJJJJJJJJJJJJJJJJIJJIHIJJJJEHIJJJHJJJJJJJJJJJJ=DHHHHHFFFFFFEEEEEEDDCDDDC AS:i:-11 XS:i:-17 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:7G44C48 YS:i:0 YT:Z:CP",
"readpair2.150-250.2.2 163 chr22 150 12 101M = 250 201 TGGAGACATAAAATGAGGCATATCTGACCTCCACTTCCAAAAACATCTGAGATAGGTCTCAGTTAATTAAGAAAGTTTGTTCTGCCTAGTTTAAGGACATG CCCFFFFFHHHHHJJJJJJJJJJJJJJJIJJJJJJJJJJJJJJJJJIJJIHIJJJJEHIJJJHJJJJJJJJJJJJ=DHHHHHFFFFFFEEEEEEDDCDDDC AS:i:-11 XS:i:-17 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:7G44C48 YS:i:0 YT:Z:CP",
"readpair1.100-200.2.2 83 chr22 200 12 101M = 100 -201 TCCTGACAGCATGTGCCCAAGGTGGTCAGGATACAGCTTGCTTCTATATATTTTAGGGAGAAAATACATCAGCCTGTAAACAAAAAATTAAATTCTAAGGT DDDDDDDDDDDDDDEDEEEFFFFHHFHHIIFIIJJJJIJJJJJJJJJJIIJJJIIIJIJIJJJJIFIIIJJIJJJJJJJIIJJJJJJJHHHHHFFFFFCCC AS:i:0 XS:i:-12 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:101 YS:i:-11 YT:Z:CP",
"readpair2.150-250.2.2 163 chr22 250 12 101M = 150 -201 TGGAGACATAAAATGAGGCATATCTGACCTCCACTTCCAAAAACATCTGAGATAGGTCTCAGTTAATTAAGAAAGTTTGTTCTGCCTAGTTTAAGGACATG CCCFFFFFHHHHHJJJJJJJJJJJJJJJIJJJJJJJJJJJJJJJJJIJJIHIJJJJEHIJJJHJJJJJJJJJJJJ=DHHHHHFFFFFFEEEEEEDDCDDDC AS:i:-11 XS:i:-17 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:7G44C48 YS:i:0 YT:Z:CP"
]
if not os.path.exists(data_dir):
os.makedirs(data_dir)
# write temporary file in SAM format, before converting to BAM
sam_filename = data_dir + "/tmp.sam"
f = open(sam_filename, "w")
write_sam_header(f)
for line in sam_lines:
f.write(line + "\n")
f.close()
# write to temp bam file
tmp_bam_filename = data_dir + "/tmp.bam"
subprocess.check_call("samtools view -b %s > %s" % (sam_filename, tmp_bam_filename), shell=True)
# sort the temp bam file
util.sort_bam(tmp_bam_filename, data_dir + "/tmp")
# remove temp bam
os.remove(tmp_bam_filename)
# rename sorted bam to output bam filename
os.rename(data_dir + "/tmp.sort.bam", bam_filename)
def __init__(self, bam_filename, is_sorted, is_paired,
output_dir=None, snp_dir=None,
snp_tab_filename=None, snp_index_filename=None,
haplotype_filename=None, samples=None):
# flag indicating whether reads are paired-end
self.is_paired = is_paired
# prefix for output files
self.prefix = None
# name of input BAM filename
self.bam_filename = bam_filename
# name of sorted input bam_filename
# (new file is created if input file is not
# already sorted)
self.bam_sort_filename = None
# pysam file handle for input BAM
self.input_bam = None
# name of output keep and to.remap BAM files
self.keep_filename = None
self.remap_filename = None
# pysam file handles for output BAM filenames
self.keep_bam = None
self.remap_bam = None
# name of output fastq files
self.fastq_single_filename = None
self.fastq1_filename = None
self.fastq2_filename = None
self.fastq1 = None
self.fastq2 = None
self.fastq_single = None
# name of directory to read SNPs from
self.snp_dir = snp_dir
# paths to HDF5 files to read SNP info from
self.snp_tab_filename = snp_tab_filename
self.snp_index_filename = snp_index_filename
self.haplotype_filename = haplotype_filename
if self.snp_tab_filename:
self.snp_tab_h5 = tables.open_file(snp_tab_filename, "r")
self.snp_index_h5 = tables.open_file(snp_index_filename, "r")
self.hap_h5 = tables.open_file(haplotype_filename, "r")
else:
self.snp_tab_h5 = None
self.snp_index_h5 = None
self.hap_h5 = None
# separate input directory and bam filename
tokens = self.bam_filename.split("/")
bam_dir = "/".join(tokens[:-1])
filename = tokens[-1]
if output_dir is None:
# if no output dir specified, use same directory as input
# bam file
output_dir = bam_dir
else:
if output_dir.endswith("/"):
# strip trailing '/' from output dir name
output_dir = output_dir[:-1]
name_split = filename.split(".")
if len(name_split) > 1:
self.prefix = output_dir + "/" + ".".join(name_split[:-1])
else:
self.prefix = output_dir + "/" + name_split[0]
# create output dir if does not exist
if not os.path.exists(output_dir):
os.makedirs(output_dir)
# TODO: could allow names of output files to be specified
# on command line rather than appending name to prefix
sys.stderr.write("prefix: %s\n" % self.prefix)
if not is_sorted:
util.sort_bam(self.bam_filename, self.prefix)
self.bam_sort_filename = self.prefix + ".sort.bam"
else:
self.bam_sort_filename = self.bam_filename
self.keep_filename = self.prefix + ".keep.bam"
self.remap_filename = self.prefix + ".to.remap.bam"
sys.stderr.write("reading reads from:\n %s\n" %
self.bam_sort_filename)
sys.stderr.write("writing output files to:\n")
if self.is_paired:
self.fastq1_filename = self.prefix + ".remap.fq1.gz"
self.fastq2_filename = self.prefix + ".remap.fq2.gz"
self.fastq1 = gzip.open(self.fastq1_filename, "wt")
self.fastq2 = gzip.open(self.fastq2_filename, "wt")
self.fastq_single_filename = self.prefix + ".remap.single.fq.gz"
self.fastq_single = gzip.open(self.fastq_single_filename, "wt")
sys.stderr.write(" %s\n %s\n %s\n" %
(self.fastq1_filename,
self.fastq2_filename,
self.fastq_single_filename))
else:
self.fastq_single_filename = self.prefix + ".remap.fq.gz"
self.fastq_single = gzip.open(self.fastq_single_filename, "wt")
sys.stderr.write(" %s\n" % (self.fastq_single_filename))
self.input_bam = pysam.Samfile(self.bam_sort_filename, "r")
self.keep_bam = pysam.Samfile(self.keep_filename, "w",
template=self.input_bam)
self.remap_bam = pysam.Samfile(self.remap_filename, "w",
template=self.input_bam)
sys.stderr.write(" %s\n %s\n" % (self.keep_filename,
self.remap_filename))