def convert_to_fasta(self, fasta_file_prefix):
"""converts BAM file reads into a Fasta file of reads"""
fasta_conversion_cmd = [
'java', '-jar', constant.PICARD + "picard.jar",
"SamFormatConverter"
]
fasta_conversion_cmd.append("INPUT=" + self.file)
samfile_name = self.file.replace('.bam', '.sam')
fasta_conversion_cmd.append("OUTPUT=" + samfile_name)
rc = RunCommand(fasta_conversion_cmd)
print fasta_conversion_cmd
out = rc.run_command()
print out
#convert sam file into fasta file of reads
sam_file = open(samfile_name, 'r')
fasta_file_name = fasta_file_prefix + '.fasta'
fasta_file = open(fasta_file_name, 'w')
for line in sam_file:
if line[0] != '@':
fields = line.split('\t')
name = fields[0]
seq = fields[9]
fasta_file.write('>')
fasta_file.write(name)
fasta_file.write('\n')
fasta_file.write(seq)
fasta_file.write('\n')
fasta_file.close()
return fasta_file_name
def sort_bam(self):
cmd = [
constant.SAMTOOLS, "sort",
self.get_input_file(),
self.get_output_file()
]
rc = RunCommand(cmd)
out = rc.run_command()
return 1
def align_with_GPU(self): result = self.modeldir + "out.ali" print(os.getcwd()) print self.unaligned_seq print result gpas = RunCommand(["./gpas/gpas -sm gpas/data/substitution_matrices/BLOSUM62.txt -a nwg -i ", self.unaligned_seq ," -o ", result]) gpas.run() self.gpas_aligned_file = result self.convert_gpas_to_fasta()
def is_mapped(self):
cmd = None
if self.__is_sam_format():
cmd = ["grep", "^@", self.get_input_file()]
elif self.__is_bam_format():
cmd = [constant.SAMTOOLS, "view", "-H", self.get_input_file()]
else:
return 0
rc = RunCommand(cmd)
out = rc.run_command()
return self.__check_headers(out)
def convert_to_unmapped_bam(self, java_heap='32G'):
direction = self.__get_direction()
if not direction or direction == 'FR':
cmd = self.__build_command(java_heap)
if cmd:
rc = RunCommand(cmd)
out = rc.run_command()
else:
if self.is_mapped and not os.path.exists(self.get_output_file(
)) and self.get_output_file() != self.get_input_file():
os.symlink(self.get_input_file(), self.get_output_file())
return 1
else:
fq_return_code, fastqs = self.convert_to_fastq(java_heap)
fq = FastqFile(fastqs, None, None, self.__get_direction(),
self.get_output_file())
fq_return_code = fq.convert_to_unmapped_bam(java_heap)
self.__remove_fastq_files(fastqs)
return fq_return_code
def __check_gi_list(self, gi_list):
tmp_gi_list = []
for gi in gi_list:
if not self.__have_gi_info(gi):
tmp_gi_list.append(gi)
if tmp_gi_list:
try:
tmp_gi_file = 'tmp.gi_list'
out = open(tmp_gi_file, 'w')
except:
print "Can't open tmp gi list file, " + tmp_gi_file
sys.exit(-1)
for i in tmp_gi_list:
out.write(i + '\n')
out.close()
command = self.__build_command(tmp_gi_file)
if command:
rc = RunCommand(command)
cmd_data = rc.run_command(1, 0).split('\n')
self.__populate_blast_hit_info(cmd_data)
else:
print "Unable to create blastdbcmd. Exiting."
sys.exit(-1)
os.remove(tmp_gi_file)
def __init__(self, bam):
self.bam = bam
self.command = RunCommand(self.__build_command(bam))
self.flagstat_output = self.command.run_command(0).stdout.readlines()
self.stats = self.__populate_stats()
class BamFlagstat():
"""This class represents data in samtools flagstat output"""
def __init__(self, bam):
self.bam = bam
self.command = RunCommand(self.__build_command(bam))
self.flagstat_output = self.command.run_command(0).stdout.readlines()
self.stats = self.__populate_stats()
# private function to make flagstat command
def __build_command(self, bam):
return [constant.SAMTOOLS, "flagstat", bam]
# private function to parse output
def __populate_stats(self):
data = {}
qc_fail = 0
for i in self.flagstat_output:
tmp = i.rstrip('\n').split(' ')
if re.match('\+', tmp[1]):
qc_fail = tmp[2]
qc_pass = tmp[0]
key = ""
for j in range(3, int(len(tmp))):
if re.match('\(', tmp[j]):
if not re.search('mapQ', tmp[j]):
break
key += tmp[j] + "_"
else:
key += tmp[j] + "_"
key = key[:-1]
data[key] = ()
data[key] = (int(qc_pass), int(qc_fail))
return data
# private function to get the value from a particular stat
def __get_value_from_key(self, key, key_tuple):
sum = 0
for i in key_tuple:
sum += self.stats[key][i]
return sum
# private function to tell whether or not to look at
# qc_pass, qc_fail or both (default)
def __get_data_to_check(self, qc_pass=None):
if qc_pass == None:
return (0, 1)
if qc_pass == 1:
return (0, )
return (1, )
# private function to help get the right stat
def __check_helper(self, key, qc_pass=None):
return self.__get_value_from_key(key,
self.__get_data_to_check(qc_pass))
# public functions follow to get number value from each key
def num_total_reads(self, qc_pass=None):
key = 'in_total'
return self.__check_helper(key, qc_pass)
def num_paired_in_sequencing(self, qc_pass=None):
key = 'paired_in_sequencing'
return self.__check_helper(key, qc_pass)
def num_properly_paired(self, qc_pass=None):
key = 'properly_paired'
return self.__check_helper(key, qc_pass)
def num_duplicates(self, qc_pass=None):
key = 'duplicates'
return self.__check_helper(key, qc_pass)
def num_read1_seqs(self, qc_pass=None):
key = 'read1'
return self.__check_helper(key, qc_pass)
def num_read2_seqs(self, qc_pass=None):
key = 'read2'
return self.__check_helper(key, qc_pass)
def num_singletons(self, qc_pass=None):
key = 'singletons'
return self.__check_helper(key, qc_pass)
def num_mapped(self, qc_pass=None):
key = 'mapped'
return self.__check_helper(key, qc_pass)
def num_mapped_with_mate(self, qc_pass=None):
key = 'with_itself_and_mate_mapped'
return self.__check_helper(key, qc_pass)
def num_mates_mapped_to_diff_chr(self, qc_pass=None):
key = 'with_mate_mapped_to_a_different_chr'
return self.__check_helper(key, qc_pass)
def num_mates_mapped_to_diff_chr_qual(self, qc_pass=None):
key = 'with_mate_mapped_to_a_different_chr_(mapQ>=5)'
return self.__check_helper(key, qc_pass)
# public functions follow to get common %
def pct_mapped(self, qc_pass=None):
if self.is_aligned(qc_pass):
if self.num_total_reads(qc_pass) != 0:
return "%.2f" % ((float(self.num_mapped(qc_pass)) /
self.num_total_reads(qc_pass)) * 100)
return 0
def pct_properly_paired(self, qc_pass=None):
if self.is_aligned(qc_pass):
if self.num_mapped(qc_pass) != 0:
return "%.2f" % ((float(self.num_properly_paired(qc_pass)) /
self.num_mapped(qc_pass)) * 100)
return 0
def pct_aligned_with_pair(self, qc_pass=None):
if self.is_aligned(qc_pass):
if self.num_mapped(qc_pass) != 0:
return "%.2f" % ((float(self.num_mapped_with_mate(qc_pass)) /
self.num_mapped(qc_pass)) * 100)
return 0
def pct_singletons(self, qc_pass=None):
if self.is_aligned(qc_pass):
if self.num_mapped(qc_pass) != 0:
return "%.2f" % ((float(self.num_singletons(qc_pass)) /
self.num_mapped(qc_pass)) * 100)
return 0
def pct_paired_in_sequencing(self, qc_pass=None):
if self.num_total_reads(qc_pass) != 0:
return "%.2f" % ((float(self.num_paired_in_sequencing(qc_pass)) /
self.num_total_reads(qc_pass)) * 100)
return 0
def pct_duplicates(self, qc_pass=None):
if self.num_total_reads(qc_pass) != 0:
return "%.2f" % ((float(self.num_duplicates(qc_pass)) /
self.num_total_reads(qc_pass)) * 100)
return 0
def pct_chimeras(self, qc_pass=None):
if self.is_aligned(qc_pass):
if self.num_mapped(qc_pass):
return "%.2f" % (
(float(self.num_mates_mapped_to_diff_chr(qc_pass)) /
self.num_mapped(qc_pass)) * 100)
return 0
def pct_chimeras_qual(self, qc_pass=None):
if self.is_aligned(qc_pass):
if self.num_mapped(qc_pass) != 0:
return "%.2f" % (
(float(self.num_mates_mapped_to_diff_chr_qual(qc_pass)) /
self.num_mapped(qc_pass)) * 100)
return 0
# public function to get the stats keys; may be useful for user to peruse.
def get_keys(self):
return self.stats.keys()
# public function to see if bam is mapped or not (prevents division by 0)
def is_aligned(self, qc_pass=None):
key = 'mapped'
return self.__check_helper(key, qc_pass) != 0
def is_paired(self):
if float(self.pct_paired_in_sequencing()) > 0:
return 1
else:
return 0
def get_bam_name(self):
return self.bam
def __parenthesize(self, value):
return ' (' + str(value) + '%)'
def get_aligned_stats_table(self, qc_pass=None):
if self.is_aligned(qc_pass):
aligned_data = self.get_unaligned_stats_table(qc_pass)
aligned_data.append([
"Mapped",
str(self.num_mapped(qc_pass)) +
self.__parenthesize(self.pct_mapped(qc_pass))
])
aligned_data.append([
"Singletons",
str(self.num_singletons(qc_pass)) +
self.__parenthesize(self.pct_singletons(qc_pass))
])
aligned_data.append([
"Mapped w/ Mate",
str(self.num_mapped_with_mate(qc_pass)) +
self.__parenthesize(self.pct_aligned_with_pair(qc_pass))
])
aligned_data.append([
"Properly Paired",
str(self.num_properly_paired(qc_pass)) +
self.__parenthesize(self.pct_properly_paired(qc_pass))
])
aligned_data.append([
"Cross-chromosome",
str(self.num_mates_mapped_to_diff_chr(qc_pass)) +
self.__parenthesize(self.pct_chimeras(qc_pass))
])
aligned_data.append([
"Cross-chromosome (MQ >= 5)",
str(self.num_mates_mapped_to_diff_chr_qual(qc_pass)) +
self.__parenthesize(self.pct_chimeras_qual(qc_pass))
])
return aligned_data
return self.get_unaligned_stats_table(qc_pass)
def get_unaligned_stats_table(self, qc_pass=None):
unaligned_data = []
unaligned_data.append(["Total Reads", self.num_total_reads(qc_pass)])
unaligned_data.append([
"Paired Reads",
str(self.num_paired_in_sequencing(qc_pass)) +
self.__parenthesize(self.pct_paired_in_sequencing(qc_pass))
])
unaligned_data.append([
"Duplicates",
str(self.num_duplicates(qc_pass)) +
self.__parenthesize(self.pct_duplicates(qc_pass))
])
unaligned_data.append(["Total Read 1", self.num_read1_seqs(qc_pass)])
unaligned_data.append(["Total Read 2", self.num_read2_seqs(qc_pass)])
return unaligned_data
def align_with_muscle(self): result = self.modeldir + "seq.ali" muscle = RunCommand(["muscle -in ", self.unaligned_seq ," -out ", result]) muscle.run() self.fasta_aligned_file = result
def convert_to_unmapped_bam(self, java_heap='32G'):
cmd = self.__build_command(java_heap)
if cmd:
rc = RunCommand(cmd)
out = rc.run_command()
return 1
def __make_bam_index(self,bam):
rc = RunCommand([constant.SAMTOOLS,"index",bam])
rc.run_command()
def __get_header_info(self,bam):
cmd = self.__build_bam_header_command(bam)
rc = RunCommand(cmd)
return self.__get_lengths_from_headers(rc.run_command(0))
def convert_to_unmapped_bam(self, java_heap='32G', stringency='LENIENT'):
cmd = self.__build_command(java_heap, stringency)
if cmd:
rc = RunCommand(cmd)
out = rc.run_command()
return 1
def convert_to_fastq(self, java_heap='32G'):
cmd, fastqs = self.__build_fastq_command(java_heap)
if cmd:
rc = RunCommand(cmd)
out = rc.run_command()
return 1, fastqs
def convert_to_fastq(self, java_heap='32G', stringency='LENIENT'):
cmd, fastqs = self.__build_fastq_command(java_heap, stringency)
if cmd:
rc = RunCommand(cmd)
out = rc.run_command()
return 1, fastqs
class BamFlagstat():
"""This class represents data in samtools flagstat output"""
def __init__(self, bam):
self.bam = bam
self.command = RunCommand(self.__build_command(bam))
self.flagstat_output = self.command.run_command(0).stdout.readlines()
self.stats = self.__populate_stats()
#self.pysam_stats = self.__pysam_populate_stats()
# private function to make flagstat command
def __build_command(self, bam):
return [constant.SAMTOOLS,"flagstat",bam]
# private function to parse output
def __populate_stats(self):
data = {}
qc_fail = 0
for i in self.flagstat_output:
tmp = i.rstrip('\n').split(' ')
if re.match('\+',tmp[1]):
qc_fail = tmp[2]
qc_pass = tmp[0]
key = ""
for j in range(3,int(len(tmp))):
if re.match('\(',tmp[j]):
if not re.search('mapQ',tmp[j]):
break
key += tmp[j] + "_"
else:
key += tmp[j] + "_"
key = key[:-1]
data[key] = ()
data[key] = (int(qc_pass), int(qc_fail))
return data
# Example dictionary of what data should look like
# {'properly_paired': (3726986, 101942), 'duplicates': (232520, 13824), 'read1': (2008943, 60581),
# 'singletons': (28670, 3947), 'with_mate_mapped_to_a_different_chr_(mapQ>=5)': (0, 0), 'read2': (2008906, 60530),
# 'in_total': (4017849, 121111), 'mapped': (3778676, 106985), 'paired_in_sequencing': (4017849, 121111),
# 'with_itself_and_mate_mapped': (3750006, 103038), 'with_mate_mapped_to_a_different_chr': (0, 0)}
# def __pysam_populate_stats(self):
# # need to have same keys that __populate_stats produces.
# pybam = pysam.AlignmentFile(self.bam, 'rb')
# data = {'properly_paired': (), 'duplicates': (), 'read1': (), 'singletons': (),
# 'with_mate_mapped_to_a_different_chr_(mapQ>=5)': (), 'read2': (), 'in_total': (),
# 'mapped': (), 'paired_in_sequencing': (), 'with_itself_and_mate_mapped': (),
# 'with_mate_mapped_to_a_different_chr': ()}
# #print("count>" + str(pybam.count(until_eof=True)))
# reads = pybam.fetch(until_eof=True)
# mapped_list = []
# unmapped_list = []
# for r in reads:
# r_list = str(r).split('\t')
# if '*' in r_list[6]:
# unmapped_list.append(r_list[0])
# else:
# mapped_list.append(r_list[0])
# print(len(set(mapped_list)) + len(set(unmapped_list)))
# return data
# private function to get the value from a particular stat
def __get_value_from_key(self,key,key_tuple):
sum = 0
for i in key_tuple:
sum += self.stats[key][i]
return sum
# private function to tell whether or not to look at
# qc_pass, qc_fail or both (default)
def __get_data_to_check(self,qc_pass=None):
if qc_pass == None:
return (0,1)
if qc_pass == 1:
return (0,)
return (1,)
# private function to help get the right stat
def __check_helper(self,key, qc_pass=None):
return self.__get_value_from_key(key,self.__get_data_to_check(qc_pass))
# public functions follow to get number value from each key
def num_total_reads(self,qc_pass=None):
key = 'in_total'
return self.__check_helper(key,qc_pass)
def num_paired_in_sequencing(self,qc_pass=None):
key = 'paired_in_sequencing'
return self.__check_helper(key,qc_pass)
def num_properly_paired(self,qc_pass=None):
key = 'properly_paired'
return self.__check_helper(key,qc_pass)
def num_duplicates(self,qc_pass=None):
key = 'duplicates'
return self.__check_helper(key,qc_pass)
def num_read1_seqs(self,qc_pass=None):
key = 'read1'
return self.__check_helper(key,qc_pass)
def num_read2_seqs(self,qc_pass=None):
key = 'read2'
return self.__check_helper(key,qc_pass)
def num_singletons(self,qc_pass=None):
key = 'singletons'
return self.__check_helper(key,qc_pass)
def num_mapped(self,qc_pass=None):
key = 'mapped'
return self.__check_helper(key,qc_pass)
def num_mapped_with_mate(self,qc_pass=None):
key = 'with_itself_and_mate_mapped'
return self.__check_helper(key,qc_pass)
def num_mates_mapped_to_diff_chr(self,qc_pass=None):
key = 'with_mate_mapped_to_a_different_chr'
return self.__check_helper(key,qc_pass)
def num_mates_mapped_to_diff_chr_qual(self,qc_pass=None):
key = 'with_mate_mapped_to_a_different_chr_(mapQ>=5)'
return self.__check_helper(key,qc_pass)
# public functions follow to get common %
def pct_mapped(self,qc_pass=None):
if self.is_aligned(qc_pass):
if self.num_total_reads(qc_pass) != 0:
return "%.2f" % ((float(self.num_mapped(qc_pass))/self.num_total_reads(qc_pass)) * 100)
return 0
def pct_properly_paired(self,qc_pass=None):
if self.is_aligned(qc_pass):
if self.num_mapped(qc_pass) != 0:
return "%.2f" % ((float(self.num_properly_paired(qc_pass))/self.num_mapped(qc_pass)) * 100)
return 0
def pct_aligned_with_pair(self,qc_pass=None):
if self.is_aligned(qc_pass):
if self.num_mapped(qc_pass) != 0:
return "%.2f" % ((float(self.num_mapped_with_mate(qc_pass))/self.num_mapped(qc_pass)) * 100)
return 0
def pct_singletons(self,qc_pass=None):
if self.is_aligned(qc_pass):
if self.num_mapped(qc_pass) != 0:
return "%.2f" % ((float(self.num_singletons(qc_pass))/self.num_mapped(qc_pass)) * 100)
return 0
def pct_paired_in_sequencing(self,qc_pass=None):
if self.num_total_reads(qc_pass) != 0:
return "%.2f" % ((float(self.num_paired_in_sequencing(qc_pass))/self.num_total_reads(qc_pass)) * 100)
return 0
def pct_duplicates(self,qc_pass=None):
if self.num_total_reads(qc_pass) != 0:
return "%.2f" % ((float(self.num_duplicates(qc_pass))/self.num_total_reads(qc_pass)) * 100)
return 0
def pct_chimeras(self,qc_pass=None):
if self.is_aligned(qc_pass):
if self.num_mapped(qc_pass):
return "%.2f" % ((float(self.num_mates_mapped_to_diff_chr(qc_pass))/self.num_mapped(qc_pass)) * 100)
return 0
def pct_chimeras_qual(self,qc_pass=None):
if self.is_aligned(qc_pass):
if self.num_mapped(qc_pass) != 0:
return "%.2f" % ((float(self.num_mates_mapped_to_diff_chr_qual(qc_pass))/self.num_mapped(qc_pass)) * 100)
return 0
# public function to get the stats keys; may be useful for user to peruse.
def get_keys(self):
return self.stats.keys()
# public function to see if bam is mapped or not (prevents division by 0)
def is_aligned(self,qc_pass=None):
key = 'mapped'
return self.__check_helper(key,qc_pass) != 0
def is_paired(self):
if float(self.pct_paired_in_sequencing()) > 0:
return 1
else:
return 0
def get_bam_name(self):
return self.bam
def __parenthesize(self, value):
return ' (' + str(value) + '%)'
def get_aligned_stats_table(self, qc_pass=None):
if self.is_aligned(qc_pass):
aligned_data = self.get_unaligned_stats_table(qc_pass)
aligned_data.append(["Mapped", str(self.num_mapped(qc_pass)) +
self.__parenthesize(self.pct_mapped(qc_pass))])
aligned_data.append(["Singletons", str(self.num_singletons(qc_pass)) +
self.__parenthesize(self.pct_singletons(qc_pass))])
aligned_data.append(["Mapped w/ Mate", str(self.num_mapped_with_mate(qc_pass)) +
self.__parenthesize(self.pct_aligned_with_pair(qc_pass))])
aligned_data.append(["Properly Paired", str(self.num_properly_paired(qc_pass)) +
self.__parenthesize(self.pct_properly_paired(qc_pass))])
aligned_data.append(["Cross-chromosome", str(self.num_mates_mapped_to_diff_chr(qc_pass)) +
self.__parenthesize(self.pct_chimeras(qc_pass))])
aligned_data.append(["Cross-chromosome (MQ >= 5)", str(self.num_mates_mapped_to_diff_chr_qual(qc_pass)) +
self.__parenthesize(self.pct_chimeras_qual(qc_pass))])
return aligned_data
return self.get_unaligned_stats_table(qc_pass)
def get_unaligned_stats_table(self,qc_pass=None):
unaligned_data = []
unaligned_data.append(["Total Reads", self.num_total_reads(qc_pass)])
unaligned_data.append(["Paired Reads", str(self.num_paired_in_sequencing(qc_pass)) +
self.__parenthesize(self.pct_paired_in_sequencing(qc_pass))])
unaligned_data.append(["Duplicates",str(self.num_duplicates(qc_pass)) +
self.__parenthesize(self.pct_duplicates(qc_pass))])
unaligned_data.append(["Total Read 1",self.num_read1_seqs(qc_pass)])
unaligned_data.append(["Total Read 2",self.num_read2_seqs(qc_pass)])
return unaligned_data
