def extract_reads_subsample(data_folder,
adaID,
fragment,
n_reads,
VERBOSE=0,
summary=True):
'''Extract a subsample of reads from the initial sample premapped'''
from hivwholeseq.utils.mapping import extract_mapped_reads_subsample
input_filename = get_divided_filename(data_folder,
adaID,
fragment,
type='bam')
output_filename = get_mapped_filename(data_folder,
adaID,
fragment,
n_iter=1,
type='bam')
n_written = extract_mapped_reads_subsample(input_filename,
output_filename,
n_reads,
VERBOSE=VERBOSE)
if summary:
with open(get_summary_fn(data_folder, adaID, fragment), 'a') as f:
f.write('\n')
f.write('Subsample of reads copied: ' + str(n_written))
f.write('\n')
def extract_reads_subsample(data_folder, adaID, fragment, n_reads, VERBOSE=0,
summary=True):
'''Extract a subsample of reads from the initial sample premapped'''
from hivwholeseq.utils.mapping import extract_mapped_reads_subsample
input_filename = get_divided_filename(data_folder, adaID, fragment, type='bam')
output_filename = get_mapped_filename(data_folder, adaID, fragment, n_iter=1, type='bam')
n_written = extract_mapped_reads_subsample(input_filename, output_filename,
n_reads, VERBOSE=VERBOSE)
if summary:
with open(get_summary_fn(data_folder, adaID, fragment), 'a') as f:
f.write('\n')
f.write('Subsample of reads copied: '+str(n_written))
f.write('\n')
def map_stampy_singlethread(sample, fragment, VERBOSE=0, n_pairs=-1,
summary=True, only_chunk=None, filtered=True):
'''Map using stampy, single thread (no cluster queueing race conditions)'''
pname = sample.patient
samplename_pat = sample['patient sample']
seq_run = sample['seq run']
data_folder = sample.sequencing_run['folder']
adaID = sample['adapter']
PCR = int(sample.PCR)
if VERBOSE:
print 'Map via stampy (single thread): '+samplename+' '+fragment
if summary:
summary_filename = get_map_initial_summary_filename(pname, samplename_pat,
samplename, fragment,
PCR=PCR)
# Specific fragment (e.g. F5 --> F5bi)
frag_spec = filter(lambda x: fragment in x, sample.regions_complete)
if not len(frag_spec):
if summary:
with open(summary_filename, 'a') as f:
f.write('Failed (specific fragment for '+fragment+'not found).\n')
raise ValueError(samplename+': fragment '+fragment+' not found.')
else:
frag_spec = frag_spec[0]
input_filename = get_input_filename(data_folder, adaID, frag_spec, type='bam',
only_chunk=only_chunk, filtered=filtered)
# NOTE: we introduced fragment nomenclature late, e.g. F3a. Check for that
if not os.path.isfile(input_filename):
if fragment == 'F3':
input_filename = input_filename.replace('F3a', 'F3')
# Check existance of input file, because stampy creates output anyway
if not os.path.isfile(input_filename):
if summary:
with open(summary_filename, 'a') as f:
f.write('Failed (input file for mapping not found).\n')
raise ValueError(samplename+', fragment '+fragment+': input file not found.')
# Extract subsample of reads if requested
if n_pairs > 0:
from hivwholeseq.utils.mapping import extract_mapped_reads_subsample
input_filename_sub = get_mapped_to_initial_filename(pname, samplename_pat,
samplename, fragment,
PCR=PCR,
type='bam')[:-4]+\
'_unmapped.bam'
n_written = extract_mapped_reads_subsample(input_filename,
input_filename_sub,
n_pairs, VERBOSE=VERBOSE)
# Get output filename
output_filename = get_mapped_to_initial_filename(pname, samplename_pat,
samplename, fragment,
PCR=PCR,
type='sam', only_chunk=only_chunk)
# Map
call_list = [stampy_bin,
'-g', get_initial_index_filename(pname, fragment, ext=False),
'-h', get_initial_hash_filename(pname, fragment, ext=False),
'-o', output_filename,
'--overwrite',
'--substitutionrate='+subsrate,
'--gapopen', stampy_gapopen,
'--gapextend', stampy_gapextend]
if stampy_sensitive:
call_list.append('--sensitive')
if n_pairs > 0:
call_list = call_list + ['-M', input_filename_sub]
else:
call_list = call_list + ['-M', input_filename]
call_list = map(str, call_list)
if VERBOSE >=2:
print ' '.join(call_list)
sp.call(call_list)
output_filename_bam = get_mapped_to_initial_filename(pname, samplename_pat,
samplename, fragment,
type='bam',
PCR=PCR,
only_chunk=only_chunk)
convert_sam_to_bam(output_filename_bam)
if summary:
with open(summary_filename, 'a') as f:
f.write('Stampy mapped (single thread).\n')
if only_chunk is None:
if VERBOSE >= 1:
print 'Remove temporary files: sample '+samplename
remove_mapped_init_tempfiles(pname, samplename_pat,
samplename, fragment,
PCR=PCR,
VERBOSE=VERBOSE, only_chunk=only_chunk)
if summary:
with open(summary_filename, 'a') as f:
f.write('Temp mapping files removed.\n')
f.write('\n')
if n_pairs > 0:
os.remove(input_filename_sub)
