def bwaal():
log.warning(
'[Alignment][bwaal] - Currently not available for Windows, sorry.')
sys.exit(1)
bwa_ext_dir = os.path.join(work_dir, out_dir, 'bwa_alignments')
if not os.path.exists(bwa_ext_dir):
os.makedirs(bwa_ext_dir)
bam_bwa_file = os.path.join(bwa_ext_dir, (prefix + '.bam'))
if not os.path.exists(bam_bwa_file):
if stats_trigger in ['y', 'yes']:
log.debug('[Alignment][bwaal] - bwa mem -x ont2d -t %s %s %s' %
(th, ref, fast_Q_file))
bwaline = subprocess.Popen([
'lib\BWA\bwa.exe', 'mem', '-x', 'ont2d', '-t',
str(th),
str(ref),
str(fast_Q_file)
],
stdout=subprocess.PIPE)
PairDict = sam_parser(bwaline, bwa_ext_dir)
else:
sam_bwa_file = os.path.join(bwa_ext_dir, (prefix + '.sam'))
log.debug(
'[Alignment][bwaal] - bwa mem -x ont2d -t %s %s %s > %s' %
(th, ref, fast_Q_file, sam_bwa_file))
bwaline = subprocess.Popen([
'bwa', 'mem', '-x', 'ont2d', '-t',
str(th),
str(ref),
str(fast_Q_file), '>',
str(sam_bwa_file)
],
stdout=subprocess.PIPE)
outputfilebam = os.path.join(bwa_ext_dir,
(prefix + '.tmp.bam'))
log.debug(
'[Alignment][bwaal] - samtools view -Sb -@ %s %s -o %s' %
(th, sam_bwa_file, outputfilebam))
pysam.view("-Sb",
"-@%s" % str(th),
sam_bwa_file,
"-o%s" % outputfilebam,
catch_stdout=False)
os.remove(sam_bwa_file)
pysam.sort(outputfilebam,
"-o%s" % bam_bwa_file,
catch_stdout=False)
log.debug('[Alignment][bwaal] - samtools index %s -@%s' %
(bam_bwa_file, str(th)))
pysam.index(bam_bwa_file, "-@%s" % str(th), catch_stdout=False)
else:
log.warning('[Alignment][bwaal] - file %s already exists!' %
bam_bwa_file)
try:
shutil.move(bwa_ext_dir, os.path.join(work_dir, out_dir))
except shutil.Error:
log.error("Unable to move %s" % bwa_ext_dir)
def ngmlral():
ngmlr_ext_dir = os.path.join(work_dir, 'ngmlr_alignments')
if not os.path.exists(ngmlr_ext_dir):
os.makedirs(ngmlr_ext_dir)
bam_ngmlr_file = os.path.join(ngmlr_ext_dir, (prefix + '.bam'))
if not os.path.exists(bam_ngmlr_file):
if stats_trigger in ['y', 'yes']:
log.debug('[Alignment][ngmlral] - ngmlr -t %s -r %s -q %s -x ont' %
(th, ref, fast_Q_file))
ngmlrline = subprocess.Popen([
'ngmlr', '-t',
str(th), '-r',
str(ref), '-q',
str(fast_Q_file), '-x ont'
],
stdout=subprocess.PIPE)
PairDict = sam_parser(ngmlrline, ngmlr_ext_dir)
else:
sam_nglmr_file = os.path.join(ngmlr_ext_dir, (prefix + '.sam'))
log.debug(
'[Alignment][ngmlral] - ngmlr -t %s -r %s -q %s -o %s -x ont' %
(th, ref, fast_Q_file, sam_ngmlr_file))
ngmlrline = subprocess.Popen([
'ngmlr', '-t',
str(th), '-r',
str(ref), '-q',
str(fast_Q_file), '-o',
str(sam_ngmlr_file), '-x ont'
],
stdout=subprocess.PIPE).wait()
outputfilebam = os.path.join(ngmlr_ext_dir, (prefix + '.tmp.bam'))
log.debug(
'[Alignment][ngmlral] - samtools view -Sb -@ %s %s -o %s' %
(th, sam_nglmr_file, outputfilebam))
pysam.view("-Sb",
"-@%s" % str(th),
sam_nglmr_file,
"-o%s" % outputfilebam,
catch_stdout=False)
os.remove(sam_nglmr_file)
pysam.sort(outputfilebam,
"-o%s" % bam_ngmlr_file,
catch_stdout=False)
log.debug('[Alignment][ngmlral] - samtools index %s -@%s' %
(bam_ngmlr_file, str(th)))
pysam.index(bam_ngmlr_file, "-@%s" % str(th), catch_stdout=False)
os.remove(outputfilebam)
else:
log.warning('[Alignment][ngmlral] - file %s already exists!' %
bam_ngmlr_file)
try:
shutil.move(ngmlr_ext_dir, os.path.join(work_dir, out_dir))
except shutil.Error:
log.error("Unable to move %s" % ngmlr_ext_dir)
def get_content(ff):
Key4 = 'Analyses/Basecall_1D_000/BaseCalled_template/Fastq'
for f in ff:
with h5py.File(f, 'r') as f5:
try:
Fqstring = SeqIO.read(StringIO(f5[Key4][()].decode('UTF-8')),
"fastq")
yield Fqstring
except:
log.warning("File %s seems doesn't contain any sequence!" % f)
pass
def fastq_writer(tmp_dir):
finalfile = os.path.join(work_dir, (prefix + '.fastq.gz'))
file_list = os.listdir(tmp_dir)
file_list.sort(key=lambda x: int(ntpath.basename(x)[4:-9]))
with open(finalfile, 'wb') as outfile:
for infile in map(lambda x: os.path.join(tmp_dir, x), file_list):
shutil.copyfileobj(open(infile, 'rb'), outfile, 1024*1024*10)
for b in map(lambda x: os.path.join(tmp_dir, x), file_list):
try:
os.remove(b)
except Exception:
log.warning("File %s doesn't exist!" % b)
if not os.path.exists(os.path.join(work_dir, out_dir)):
os.makedirs(os.path.join(work_dir, out_dir))
try:
shutil.move(finalfile, os.path.join(work_dir, out_dir))
except shutil.Error:
log.error("Unable to move %s" % finalfile)
shutil.rmtree(tmp_dir, ignore_errors=True)
def minimap2al():
mm_ext_dir = os.path.join(work_dir, 'minimap2_alignments')
if not os.path.exists(mm_ext_dir):
os.makedirs(mm_ext_dir)
mmi_ref = os.path.splitext(ref)[0] + '.mmi'
if not os.path.exists(mmi_ref):
log.debug(
'[Alignment][minimap2al] - minimap2 -x map-ont -t %s -d %s %s' %
(th, mmi_ref, ref))
miniline = ('minimap2 -x map-ont -t', str(th), '-d', str(mmi_ref),
str(ref))
minrun = ' '.join(miniline)
subprocess.Popen(minrun, stdout=subprocess.PIPE, shell=True).wait()
bam_mm2_file = os.path.join(mm_ext_dir, (prefix + '.bam'))
if not os.path.exists(bam_mm2_file):
if stats_trigger in ['y', 'yes']:
log.debug(
'[Alignment][minimap2al] - minimap2 -ax map-ont --MD -L -t %s -R %s %s %s'
%
(th,
str('@RG\\tID:minimap2\\tLB:NxEr\\tPL:MinION\\tPU:NA\\tSM:' +
str(prefix)), str(mmi_ref), str(fast_Q_file)))
minimap2line = subprocess.Popen([
'minimap2', '-ax', 'map-ont', '--MD', '-L', '-t',
str(th), '-R',
str('@RG\\tID:minimap2\\tLB:NxEr\\tPL:MinION\\tPU:NA\\tSM:' +
str(prefix)),
str(mmi_ref),
str(fast_Q_file)
],
stdout=subprocess.PIPE)
PairDict = sam_parser(minimap2line, mm_ext_dir)
else:
sam_mm2_file = os.path.join(mm_ext_dir, (prefix + '.sam'))
log.debug(
'[Alignment][minimap2al] - minimap2 -ax map-ont --MD -L -t %s -R %s %s %s > %s'
%
(th,
str('@RG\\tID:minimap2\\tLB:NxEr\\tPL:MinION\\tPU:NA\\tSM:' +
str(prefix)), str(mmi_ref), str(fast_Q_file),
str(sam_mm2_file)))
with open(sam_mm2_file, "w") as outfile:
minimap2line = subprocess.Popen([
'minimap2', '-ax', 'map-ont', '--MD', '-L', '-t',
str(th), '-R',
str('@RG\\tID:minimap2\\tLB:NxEr\\tPL:MinION\\tPU:NA\\tSM:'
+ str(prefix)),
str(mmi_ref),
str(fast_Q_file)
],
stdout=outfile).wait()
outputfilebam = os.path.join(mm_ext_dir, (prefix + '.tmp.bam'))
log.debug(
'[Alignment][minimap2al] - samtools view -Sb -@ %s %s -o %s' %
(th, sam_mm2_file, outputfilebam))
pysam.view("-Sb",
"-@%s" % str(th),
sam_mm2_file,
"-o%s" % outputfilebam,
catch_stdout=False)
os.remove(sam_mm2_file)
pysam.sort(outputfilebam,
"-o%s" % bam_mm2_file,
catch_stdout=False)
log.debug('[Alignment][minimap2al] - samtools index %s -@%s' %
(bam_mm2_file, str(th)))
pysam.index(bam_mm2_file, "-@%s" % str(th), catch_stdout=False)
os.remove(outputfilebam)
else:
log.warning('[Alignment][minimap2al] - file %s already exists!' %
bam_mm2_file)
try:
shutil.move(mm_ext_dir, os.path.join(work_dir, out_dir))
except shutil.Error:
log.error("Unable to move %s" % mm_ext_dir)
def minimap2al():
mm_ext_dir = os.path.join(work_dir, out_dir, 'minimap2_alignments')
if not os.path.exists(mm_ext_dir):
os.makedirs(mm_ext_dir)
mmi_ref = os.path.splitext(ref)[0] + '.mmi'
if not os.path.exists(mmi_ref):
log.debug(
'[Alignment][minimap2al] - minimap2 -x map-ont -t %s -d %s %s'
% (th, mmi_ref, ref))
miniline = (os.path.abspath(os.path.dirname(__file__)) +
'\minimap2\minimap2.exe -x map-ont -t', str(th), '-d',
str(mmi_ref), str(ref))
minrun = ' '.join(miniline)
subprocess.Popen(minrun, stdout=subprocess.PIPE, shell=True).wait()
bam_mm2_file = os.path.join(mm_ext_dir, (prefix + '.bam'))
if not os.path.exists(bam_mm2_file):
if stats_trigger in ['y', 'yes']:
log.debug(
'[Alignment][minimap2al] - minimap2 -ax map-ont --MD -L -t %s -R %s %s %s'
%
(th,
str('@RG\\tID:minimap2\\tLB:NxEr\\tPL:MinION\\tPU:NA\\tSM:'
+ str(prefix)), str(mmi_ref), str(fast_Q_file)))
minimap2line = subprocess.Popen([
os.path.abspath(os.path.dirname(__file__)) +
'\minimap2\minimap2.exe', '-ax', 'map-ont', '--MD', '-L',
'-t',
str(th), '-R',
str('@RG\\tID:minimap2\\tLB:NxEr\\tPL:MinION\\tPU:NA\\tSM:'
+ str(prefix)),
str(mmi_ref),
str(fast_Q_file)
],
stdout=subprocess.PIPE)
PairDict = sam_parser(minimap2line, mm_ext_dir)
else:
sam_mm2_file = os.path.join(mm_ext_dir, (prefix + '.sam'))
log.debug(
'[Alignment][minimap2al] - minimap2 -ax map-ont --MD -L -t %s -R %s %s %s > %s'
%
(th,
str('@RG\\tID:minimap2\\tLB:NxEr\\tPL:MinION\\tPU:NA\\tSM:'
+ str(prefix)), str(mmi_ref), str(fast_Q_file),
str(sam_mm2_file)))
with open(sam_mm2_file, "w") as out:
minimap2line = subprocess.Popen([
os.path.abspath(os.path.dirname(__file__)) +
'\minimap2\minimap2.exe', '-ax', 'map-ont', '--MD',
'-L', '-t',
str(th), '-R',
str('@RG\\tID:minimap2\\tLB:NxEr\\tPL:MinION\\tPU:NA\\tSM:'
+ str(prefix)),
str(mmi_ref),
str(fast_Q_file)
],
stdout=out).communicate()
outputfilebam = os.path.join(mm_ext_dir, (prefix + '.tmp.bam'))
log.debug(
'[Alignment][minimap2al] - samtools view -Sb -@ %s %s -o %s'
% (th, sam_mm2_file, outputfilebam))
samviewline = subprocess.Popen(
[
os.path.abspath(os.path.dirname(__file__)) +
'\SAMtools\samtools.exe', 'view', '-Sb', '-@',
str(th), sam_mm2_file, '-o', outputfilebam
],
stdout=subprocess.PIPE).communicate()
os.remove(sam_mm2_file)
samsortline = subprocess.Popen(
[
os.path.abspath(os.path.dirname(__file__)) +
'\SAMtools\samtools.exe', 'sort', '-@',
str(th), outputfilebam, '-o', bam_mm2_file
],
stdout=subprocess.PIPE).communicate()
log.debug('[Alignment][minimap2al] - samtools index %s -@%s' %
(bam_mm2_file, str(th)))
samindexline = subprocess.Popen(
[
os.path.abspath(os.path.dirname(__file__)) +
'\SAMtools\samtools.exe', 'index', bam_mm2_file
],
stdout=subprocess.PIPE).communicate()
os.remove(outputfilebam)
else:
log.warning('[Alignment][minimap2al] - file %s already exists!' %
bam_mm2_file)