def make_index_and_hash(data_folder, adaID, VERBOSE=0, summary=True):
'''Make index and hash files for reference or consensus'''
if VERBOSE:
print 'Making index and hash files: adaID', adaID
# 1. Make genome index file for reference
if os.path.isfile(get_reference_premap_index_filename(data_folder, adaID, ext=True)):
os.remove(get_reference_premap_index_filename(data_folder, adaID, ext=True))
stdout = sp.check_output([stampy_bin,
'--species="HIV"',
'--overwrite',
'-G', get_reference_premap_index_filename(data_folder, adaID, ext=False),
get_reference_premap_filename(data_folder, adaID),
],
stderr=sp.STDOUT)
if VERBOSE:
print 'Built index: '+adaID
# 2. Build a hash file for reference
if os.path.isfile(get_reference_premap_hash_filename(data_folder, adaID, ext=True)):
os.remove(get_reference_premap_hash_filename(data_folder, adaID, ext=True))
stdout = sp.check_output([stampy_bin,
'--overwrite',
'-g', get_reference_premap_index_filename(data_folder, adaID, ext=False),
'-H', get_reference_premap_hash_filename(data_folder, adaID, ext=False),
],
stderr=sp.STDOUT)
if VERBOSE:
print 'Built hash: '+adaID
if summary:
with open(get_premap_summary_filename(data_folder, adaID), 'a') as f:
f.write('\n')
f.write('Stampy index and hash written.')
f.write('\n')
def make_index_and_hash(data_folder, adaID, VERBOSE=0, summary=True):
'''Make index and hash files for reference or consensus'''
if VERBOSE:
print 'Making index and hash files: adaID', adaID
# 1. Make genome index file for reference
if os.path.isfile(
get_reference_premap_index_filename(data_folder, adaID, ext=True)):
os.remove(
get_reference_premap_index_filename(data_folder, adaID, ext=True))
stdout = sp.check_output([
stampy_bin,
'--species="HIV"',
'--overwrite',
'-G',
get_reference_premap_index_filename(data_folder, adaID, ext=False),
get_reference_premap_filename(data_folder, adaID),
],
stderr=sp.STDOUT)
if VERBOSE:
print 'Built index: ' + adaID
# 2. Build a hash file for reference
if os.path.isfile(
get_reference_premap_hash_filename(data_folder, adaID, ext=True)):
os.remove(
get_reference_premap_hash_filename(data_folder, adaID, ext=True))
stdout = sp.check_output([
stampy_bin,
'--overwrite',
'-g',
get_reference_premap_index_filename(data_folder, adaID, ext=False),
'-H',
get_reference_premap_hash_filename(data_folder, adaID, ext=False),
],
stderr=sp.STDOUT)
if VERBOSE:
print 'Built hash: ' + adaID
if summary:
with open(get_premap_summary_filename(data_folder, adaID), 'a') as f:
f.write('\n')
f.write('Stampy index and hash written.')
f.write('\n')
def premap_stampy(data_folder,
adaID,
VERBOSE=0,
threads=1,
summary=True,
maxreads=-1,
subsrate=0.05,
gapopen=40,
gapextend=3):
'''Call stampy for actual mapping'''
if VERBOSE:
print 'Premapping: adaID ', adaID
if summary:
summary_filename = get_premap_summary_filename(data_folder, adaID)
# Stampy can handle both gzipped and uncompressed fastq inputs
input_filenames = get_read_filenames(data_folder, adaID, gzip=True)
if not os.path.isfile(input_filenames[0]):
input_filenames = get_read_filenames(data_folder, adaID, gzip=False)
if not all(map(os.path.isfile, input_filenames)):
raise OSError('Input files for mapping not found: ' +
input_filenames[0])
# parallelize if requested
if threads == 1:
call_list = [
stampy_bin,
'--overwrite',
'-g',
get_reference_premap_index_filename(data_folder, adaID, ext=False),
'-h',
get_reference_premap_hash_filename(data_folder, adaID, ext=False),
'-o',
get_premapped_filename(data_folder, adaID, type='sam'),
'--insertsize=450',
'--insertsd=100',
'--substitutionrate=' + str(subsrate),
'--gapopen=' + str(gapopen),
'--gapextend=' + str(gapextend),
]
if maxreads > 0:
call_list.append('--numrecords=' + str(maxreads))
call_list.extend(['-M'] + input_filenames)
call_list = map(str, call_list)
if VERBOSE >= 2:
print ' '.join(call_list)
sp.call(call_list)
if summary:
with open(get_premap_summary_filename(data_folder, adaID),
'a') as f:
f.write('\nStampy premapped (single thread).\n')
# Convert to compressed BAM
convert_sam_to_bam(
get_premapped_filename(data_folder, adaID, type='bam'))
if summary:
with open(summary_filename, 'a') as f:
f.write('\nSAM file converted to compressed BAM: '+\
get_premapped_filename(data_folder, adaID, type='bam')+'\n')
else:
# Multithreading works as follows: call qsub + stampy, monitor the process
# IDs with qstat at regular intervals, and finally merge results with pysam
output_file_parts = [
get_premapped_filename(data_folder,
adaID,
type='bam',
part=(j + 1)) for j in xrange(threads)
]
# Submit map script
jobs_done = np.zeros(threads, bool)
job_IDs = np.zeros(threads, 'S30')
# Submit map call
import hivwholeseq
JOBDIR = hivwholeseq.__path__[0].rstrip('/') + '/'
JOBLOGOUT = JOBDIR + 'logout'
JOBLOGERR = JOBDIR + 'logerr'
cluster_time = ['23:59:59', '1:59:59']
vmem = '8G'
for j in xrange(threads):
call_list = [
'qsub', '-cwd', '-b', 'y', '-S', '/bin/bash', '-o', JOBLOGOUT,
'-e', JOBLOGERR, '-N', adaID + ' p' + str(j + 1), '-l',
'h_rt=' + cluster_time[threads >= 30], '-l', 'h_vmem=' + vmem,
stampy_bin, '--overwrite', '-g',
get_reference_premap_index_filename(
data_folder, adaID, ext=False), '-h',
get_reference_premap_hash_filename(
data_folder, adaID, ext=False), '-o',
get_premapped_filename(
data_folder, adaID, type='sam', part=(j + 1)),
'--processpart=' + str(j + 1) + '/' + str(threads),
'--insertsize=450', '--insertsd=100', '--substitutionrate=' +
str(subsrate), '--gapopen=' + str(gapopen),
'--gapextend=' + str(gapextend), '-M'
] + input_filenames
call_list = map(str, call_list)
if VERBOSE >= 2:
print ' '.join(call_list)
job_ID = sp.check_output(call_list)
job_ID = job_ID.split()[2]
job_IDs[j] = job_ID
# Monitor output
time_wait = 10 # secs
while not jobs_done.all():
# Sleep some time
time.sleep(time_wait)
# Get the output of qstat to check the status of jobs
qstat_output = sp.check_output(['qstat'])
qstat_output = qstat_output.split(
'\n')[:-1] # The last is an empty line
if VERBOSE >= 3:
print qstat_output
if len(qstat_output) < 3:
jobs_done[:] = True
break
else:
qstat_output = [line.split()[0] for line in qstat_output[2:]]
time_wait = 10 # secs
for j in xrange(threads):
if jobs_done[j]:
continue
if job_IDs[j] not in qstat_output:
# Convert to BAM for merging
if VERBOSE >= 1:
print 'Convert premapped reads to BAM for merging: adaID '+\
adaID+', part '+str(j+1)+ ' of '+ \
str(threads)
convert_sam_to_bam(output_file_parts[j])
# We do not need to wait if we did the conversion (it takes
# longer than some secs)
time_wait = 0
jobs_done[j] = True
if summary:
with open(summary_filename, 'a') as f:
f.write('Stampy premapped (' + str(threads) + ' threads).\n')
# Concatenate output files
if VERBOSE >= 1:
print 'Concatenate premapped reads: adaID ' + adaID + '...',
output_filename = get_premapped_filename(data_folder,
adaID,
type='bam',
unsorted=True)
pysam.cat('-o', output_filename, *output_file_parts)
if VERBOSE >= 1:
print 'done.'
if summary:
with open(summary_filename, 'a') as f:
f.write('BAM files concatenated (unsorted).\n')
# Sort the file by read names (to ensure the pair_generator)
# NOTE: we exclude the extension and the option -f because of a bug in samtools
if VERBOSE >= 1:
print 'Sort premapped reads: adaID ' + adaID
output_filename_sorted = get_premapped_filename(data_folder,
adaID,
type='bam',
unsorted=False)
pysam.sort('-n', output_filename, output_filename_sorted[:-4])
if summary:
with open(summary_filename, 'a') as f:
f.write('Joint BAM file sorted.\n')
# Reheader the file without BAM -> SAM -> BAM
if VERBOSE >= 1:
print 'Reheader premapped reads: adaID ' + adaID
header_filename = get_premapped_filename(data_folder,
adaID,
type='sam',
part=1)
pysam.reheader(header_filename, output_filename_sorted)
if summary:
with open(summary_filename, 'a') as f:
f.write('Joint BAM file reheaded.\n')
if VERBOSE >= 1:
print 'Remove temporary files: adaID ' + adaID
remove_premapped_tempfiles(data_folder, adaID, VERBOSE=VERBOSE)
if summary:
with open(summary_filename, 'a') as f:
f.write('Temp premapping files removed.\n')
f.write('\n')
def premap_stampy(data_folder,
adaID,
VERBOSE=0,
threads=1,
summary=True,
maxreads=-1,
subsrate=0.05,
gapopen=40,
gapextend=3):
'''Call stampy for actual mapping'''
if VERBOSE:
print 'Premapping: adaID ', adaID
if summary:
summary_filename = get_premap_summary_filename(data_folder, adaID)
# Stampy can handle both gzipped and uncompressed fastq inputs
input_filenames = get_read_filenames(data_folder, adaID, gzip=True)
if not os.path.isfile(input_filenames[0]):
input_filenames = get_read_filenames(data_folder, adaID, gzip=False)
if not all(map(os.path.isfile, input_filenames)):
raise OSError('Input files for mapping not found: ' +
input_filenames[0])
# parallelize if requested
if threads == 1:
call_list = [
stampy_bin,
'--overwrite',
'-g',
get_reference_premap_index_filename(data_folder, adaID, ext=False),
'-h',
get_reference_premap_hash_filename(data_folder, adaID, ext=False),
'-o',
get_premapped_filename(data_folder, adaID, type='sam'),
'--insertsize=450',
'--insertsd=100',
'--substitutionrate=' + str(subsrate),
'--gapopen=' + str(gapopen),
'--gapextend=' + str(gapextend),
]
if maxreads > 0:
call_list.append('--numrecords=' + str(maxreads))
call_list.extend(['-M'] + input_filenames)
call_list = map(str, call_list)
if VERBOSE >= 2:
print ' '.join(call_list)
sp.call(call_list)
if summary:
with open(get_premap_summary_filename(data_folder, adaID),
'a') as f:
f.write('\nStampy premapped (single thread).\n')
# Convert to compressed BAM
convert_sam_to_bam(
get_premapped_filename(data_folder, adaID, type='bam'))
if summary:
with open(summary_filename, 'a') as f:
f.write('\nSAM file converted to compressed BAM: '+\
get_premapped_filename(data_folder, adaID, type='bam')+'\n')
else:
# Multithreading works as follows: call qsub + stampy, monitor the process
# IDs with qstat at regular intervals, and finally merge results with pysam
output_file_parts = [
get_premapped_filename(
data_folder, adaID, type='bam', part=(j + 1))
for j in xrange(threads)
]
# Submit map script
jobs_done = np.zeros(threads, bool)
job_IDs = np.zeros(threads, 'S30')
# Submit map call
import hivwholeseq
JOBDIR = hivwholeseq.__path__[0].rstrip('/') + '/'
JOBLOGOUT = JOBDIR + 'logout'
JOBLOGERR = JOBDIR + 'logerr'
cluster_time = ['23:59:59', '1:59:59']
vmem = '8G'
for j in xrange(threads):
call_list = [
'qsub', '-cwd', '-b', 'y', '-S', '/bin/bash', '-o', JOBLOGOUT,
'-e', JOBLOGERR, '-N', adaID + ' p' + str(j + 1), '-l',
'h_rt=' + cluster_time[threads >= 30], '-l', 'h_vmem=' + vmem,
stampy_bin, '--overwrite', '-g',
get_reference_premap_index_filename(
data_folder, adaID, ext=False), '-h',
get_reference_premap_hash_filename(
data_folder, adaID, ext=False), '-o',
get_premapped_filename(
data_folder, adaID, type='sam', part=(j + 1)),
'--processpart=' + str(j + 1) + '/' + str(threads),
'--insertsize=450', '--insertsd=100', '--substitutionrate=' +
str(subsrate), '--gapopen=' + str(gapopen),
'--gapextend=' + str(gapextend), '-M'
] + input_filenames
call_list = map(str, call_list)
if VERBOSE >= 2:
print ' '.join(call_list)
job_ID = sp.check_output(call_list)
job_ID = job_ID.split()[2]
job_IDs[j] = job_ID
# Monitor output
time_wait = 10 # secs
while not jobs_done.all():
# Sleep some time
time.sleep(time_wait)
# Get the output of qstat to check the status of jobs
qstat_output = sp.check_output(['qstat'])
qstat_output = qstat_output.split(
'\n')[:-1] # The last is an empty line
if VERBOSE >= 3:
print qstat_output
if len(qstat_output) < 3:
jobs_done[:] = True
break
else:
qstat_output = [line.split()[0] for line in qstat_output[2:]]
time_wait = 10 # secs
for j in xrange(threads):
if jobs_done[j]:
continue
if job_IDs[j] not in qstat_output:
# Convert to BAM for merging
if VERBOSE >= 1:
print 'Convert premapped reads to BAM for merging: adaID '+\
adaID+', part '+str(j+1)+ ' of '+ \
str(threads)
convert_sam_to_bam(output_file_parts[j])
# We do not need to wait if we did the conversion (it takes
# longer than some secs)
time_wait = 0
jobs_done[j] = True
if summary:
with open(summary_filename, 'a') as f:
f.write('Stampy premapped (' + str(threads) + ' threads).\n')
# Concatenate output files
if VERBOSE >= 1:
print 'Concatenate premapped reads: adaID ' + adaID + '...',
output_filename = get_premapped_filename(
data_folder, adaID, type='bam', unsorted=True)
pysam.cat('-o', output_filename, *output_file_parts)
if VERBOSE >= 1:
print 'done.'
if summary:
with open(summary_filename, 'a') as f:
f.write('BAM files concatenated (unsorted).\n')
# Sort the file by read names (to ensure the pair_generator)
# NOTE: we exclude the extension and the option -f because of a bug in samtools
if VERBOSE >= 1:
print 'Sort premapped reads: adaID ' + adaID
output_filename_sorted = get_premapped_filename(
data_folder, adaID, type='bam', unsorted=False)
pysam.sort('-n', output_filename, output_filename_sorted[:-4])
if summary:
with open(summary_filename, 'a') as f:
f.write('Joint BAM file sorted.\n')
# Reheader the file without BAM -> SAM -> BAM
if VERBOSE >= 1:
print 'Reheader premapped reads: adaID ' + adaID
header_filename = get_premapped_filename(
data_folder, adaID, type='sam', part=1)
pysam.reheader(header_filename, output_filename_sorted)
if summary:
with open(summary_filename, 'a') as f:
f.write('Joint BAM file reheaded.\n')
if VERBOSE >= 1:
print 'Remove temporary files: adaID ' + adaID
remove_premapped_tempfiles(data_folder, adaID, VERBOSE=VERBOSE)
if summary:
with open(summary_filename, 'a') as f:
f.write('Temp premapping files removed.\n')
f.write('\n')
