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 __call__(self, parser, namespace, values, option_string=None):
prospective_dir = values
if not os.path.isdir(prospective_dir):
log.error(
"readable_dir:{0} is not a directory".format(prospective_dir))
sys.exit(1)
if os.access(prospective_dir, os.R_OK):
setattr(namespace, self.dest, prospective_dir)
else:
log.error(
"readable_dir:{0} is not a directory".format(prospective_dir))
sys.exit(1)
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 HeatTrigger2(html_file_2):
log.debug("Triggering stats report...")
try:
fh = file(html_file_2, 'r')
except IOError:
e = sys.exc_info()
tb = traceback.format_exception(*e)
log.error(
"No such file or directory!\n\033[36m##################################\n\033[93m%s\033[32m%s\033[93m%s\033[36m##################################\n\033[0m" % (
tb[0], tb[1], tb[2]))
sys.exit(1)
subject = fh.read()
fh.close()
Idpattern = '(?<=\<div id=")(.*?)"'
try:
FileId = re.search(Idpattern, subject).group(1)
except:
e = sys.exc_info()
tb = traceback.format_exception(*e)
log.error(
"Can't find ID in html file!\n\033[36m##################################\n\033[93m%s\033[32m%s\033[93m%s\033[36m##################################\n\033[0m" % (
tb[0], tb[1], tb[2]))
sys.exit(1)
FixLine = "<script type = 'text/javascript'>var graph = document.getElementById('%(FileId)s');graph.on('plotly_hover', function(data){var divname = data.points.map(function(d){return (d.data.name)});if(divname == 'ReadsPerHour' || divname == 'BasesPerHour' || divname == 'MeanReadLengthPerHour'){if(data.xvals){Plotly.Fx.hover(graph, {xval:data.xvals[0] }, ['x5y', 'x5y3','x5y5']);}}});</script>" % locals()
SubLine = FixLine + '</body></html>'
pattern = re.compile('</body></html>')
result = pattern.sub(SubLine, subject)
f_out = file(html_file_2, 'w')
f_out.write(result)
f_out.close()
try:
shutil.move(html_file_2, os.path.join(work_dir, out_dir))
except shutil.Error:
log.error("Unable to move %s" % html_file_2)
def HeatTrigger(html_file):
log.debug("Triggering heatmaps...")
try:
fh = file(html_file, 'r')
except IOError:
e = sys.exc_info()
tb = traceback.format_exception(*e)
log.error(
"No such file or directory!\n\033[36m##################################\n\033[93m%s\033[32m%s\033[93m%s\033[36m##################################\n\033[0m" % (
tb[0], tb[1], tb[2]))
sys.exit(1)
subject = fh.read()
fh.close()
Idpattern = '(?<=\<div id=")(.*?)"'
try:
FileId = re.search(Idpattern, subject).group(1)
except:
e = sys.exc_info()
tb = traceback.format_exception(*e)
log.error(
"Can't find ID in html file!\n\033[36m##################################\n\033[93m%s\033[32m%s\033[93m%s\033[36m##################################\n\033[0m" % (
tb[0], tb[1], tb[2]))
sys.exit(1)
if summary_flag == False:
FixLine = "<script type='text/javascript'>var gd = document.getElementById('%(FileId)s');gd.on('plotly_click', function(data){var infotext = data.points.map(function(d){return (d.text)});var divname = data.points.map(function(d){return (d.data.name)}); var chan = data.points.map(function(d){return (d.text.split(' ')[1].replace('<br', ''))}); if(divname == 'ReadNHeat' || divname == 'BaseNHeat'){function range(start, stop, step){var a=[start], b=start;while(b<stop){b+=step;a.push(b)}return a;};var editindeces=range(10*(chan-1), 10*chan, 1); editindeces.pop(); var numeroPerguntas = 5122; var anyBoxesChecked = new Array(numeroPerguntas).fill(false); for (i in editindeces) { idx = parseInt(editindeces[i]); anyBoxesChecked[idx]=true}; var Newtitle = {title: infotext.toString()}; if (gd.data[0].visible === true) {var hv=[true, false]} else {var hv=[false, true]}; var exit = hv.concat(anyBoxesChecked); var update = {'visible': exit}; Plotly.update(gd ,update, Newtitle);};});gd.on('plotly_hover', function(data){var divname = data.points.map(function(d){return (d.data.name)});if(divname == 'Pore1' || divname == 'Pore2' || divname == 'Pore3' || divname == 'Pore4'){if(data.xvals){Plotly.Fx.hover(gd, {xval:data.xvals[0] }, ['x3y2', 'x3y3']);}}});</script>" % locals()
else:
FixLine = "<script type='text/javascript'>var gd = document.getElementById('%(FileId)s');gd.on('plotly_click', function(data){var infotext = data.points.map(function(d){return (d.text)});var divname = data.points.map(function(d){return (d.data.name)}); var chan = data.points.map(function(d){return (d.text.split(' ')[1].replace('<br', ''))}); if(divname == 'ReadNHeat' || divname == 'BaseNHeat'){function range(start, stop, step){var a=[start], b=start;while(b<stop){b+=step;a.push(b)}return a;};var editindeces=range(4*(chan-1), 4*chan, 1); editindeces.pop(); var numeroPerguntas = 2050; var anyBoxesChecked = new Array(numeroPerguntas).fill(false); for (i in editindeces) { idx = parseInt(editindeces[i]); anyBoxesChecked[idx]=true}; var Newtitle = {title: infotext.toString()}; if (gd.data[0].visible === true) {var hv=[true, false]} else {var hv=[false, true]}; var exit = hv.concat(anyBoxesChecked); var update = {'visible': exit}; Plotly.update(gd ,update, Newtitle);};});gd.on('plotly_hover', function(data){var divname = data.points.map(function(d){return (d.data.name)});if(divname == 'Channel'){if(data.xvals){Plotly.Fx.hover(gd, {xval:data.xvals[0] }, ['x3y2', 'x3y3']);}}});</script>" % locals()
SubLine = FixLine + '</body></html>'
pattern = re.compile('</body></html>')
result = pattern.sub(SubLine, subject)
f_out = file(html_file, 'w')
f_out.write(result)
f_out.close()
try:
shutil.move(html_file, os.path.join(work_dir, out_dir))
except shutil.Error:
log.error("Unable to move %s" % html_file)
def run(argsin):
ldir = tempfile.mkdtemp()
atexit.register(lambda dir=ldir: shutil.rmtree(ldir))
parser = argparse.ArgumentParser(
add_help=False,
prog='fastqgen',
usage='''\r \n
________________
| |
| ##### |
| ## ## |
| ##### |
| ## ##### |
| ## ## ## |
| ##### |
| ## |
| ## |
|________________|
PyPore
FastQGen
usage: %(prog)s [-i <input_directory>] [-l <my_label>] [options]''',
epilog='''
PyPore. Written by Roberto Semeraro, Department of Clinical and Sperimental Medicine,
University of Florence. For bug report or suggestion write to [email protected]''',
formatter_class=argparse.RawDescriptionHelpFormatter,
)
g = parser.add_argument_group(
title='mandatory arguments',
description=
'''-i, --input_directory path to the file folder
-l, --label label for fastq file
''')
g.add_argument('-i',
'--input_directory',
action=readable_dir,
default=ldir,
help=argparse.SUPPRESS)
g.add_argument('-l',
'--label',
action='store',
metavar='',
help=argparse.SUPPRESS)
f = parser.add_argument_group(
title='options',
description=
'''-f, --fail_reads avoid skipping of fail reads [no]
-o, --output_dir if omitted, generates a results
directory in the current position
-n, --threads_number number of processing threads [1]
-v, --verbose increase verbosity: 0 = warnings only, 1 = info,
2 = debug, 3 = debug on terminal. Default is no
verbosity. No number means info
-h, --help show this help message and exit
''')
f.add_argument('-f',
'--fail_reads',
action="store",
nargs='*',
default=['n'],
metavar='',
help=argparse.SUPPRESS,
choices=['y', 'n', 'yes', 'no'])
f.add_argument('-o',
'--output_dir',
action="store",
nargs=1,
metavar='',
help=argparse.SUPPRESS)
f.add_argument('-n',
'--threads_number',
action="store",
type=int,
default=1,
metavar='',
help=argparse.SUPPRESS)
f.add_argument('-h', '--help', action="help", help=argparse.SUPPRESS)
f.add_argument('-v',
'--verbose',
const=1,
default=1,
type=int,
nargs="?",
help=argparse.SUPPRESS,
choices=range(0, 4))
try:
args = parser.parse_args(argsin)
if not args.input_directory or not args.label:
parser.print_help()
log.error('Missing mandatory arguments!')
sys.exit(1)
else:
ArgsReader(args)
except IOError as msg:
parser.error(str(msg))
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 sam_parser(bwastdout, out_dir):
log.info('Error estimation...')
bins = [
1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 30, 40, 50, 60, 70, 80, 90, 100,
200, 300, 400, 500, 600, 700, 800, 900, 1000, 2000, 3000, 4000,
5000, 6000, 7000, 8000, 9000, 10000, 15000, 20000, 25000, 30000,
35000, 40000, 45000, 50000, 100000, 200000, 300000, 400000, 500000,
750000, 1000000000
]
mapped_frac_size = {k: [0, 0] for k in bins}
pos_dict = {k: {} for k in arange(0, 250000000, 1000000)}
OutDict = {k: {} for k in ['M', 'I', 'D']}
header_list = []
proc_lists = {k: [] for k in range(th)}
chr_cov_dict = {}
file_list = []
fill_val = 0
Flag = True
while Flag:
line = bwastdout.stdout.readline()
Threshold = 50000
while len(proc_lists[th - 1]) <= Threshold:
proc_check_first = map(lambda x: len(proc_lists[x]),
range(th - 1))
line_counter = 0
if line.strip() == '':
Flag = False
break
if line[0] == '@':
header_list.append(line)
line = bwastdout.stdout.readline()
else:
while line_counter < len(proc_lists):
proc_lists[line_counter].append(line)
line_counter += 1
line = bwastdout.stdout.readline()
line_counter = 0
line = bwastdout.stdout.readline()
proc_check_second = map(lambda x: len(proc_lists[x]),
range(th - 1))
if all(v == 0 for v in proc_check_second) == False:
if proc_check_second == proc_check_first:
time.sleep(5)
proc_check_second = map(lambda x: len(proc_lists[x]),
range(th - 1))
if proc_check_second == proc_check_first:
break
fill_list = (
fill_val, fill_val + (th - 1) -
map(lambda x: len(proc_lists[x]), range(th - 1)).count(0))
fill_val = fill_val + (th - 1) - map(lambda x: len(proc_lists[x]),
range(th - 1)).count(0)
res_obj = error_wrap(proc_lists, header_list, fill_list)
for ro in res_obj:
p_d, OD, m_f_s, fname = ro
file_list.append(fname)
for k, v in p_d.iteritems():
if v is not {}:
for ch, l in v.iteritems():
pos_dict[k][ch] = pos_dict[k].get(ch, []) + l
for var_k, cnt in OD.iteritems():
if cnt is not {}:
for k, v in cnt.iteritems():
outdictget = OutDict.get(var_k)
if outdictget.get(int(k)) == None:
outdictget[int(k)] = v
else:
outdictget[int(k)] = [
outdictget.get(int(k))[0],
int(outdictget.get(int(k))[1]) + int(v[1]),
int(outdictget.get(int(k))[2]) + int(v[2])
]
for mfs in m_f_s:
mapped_frac_size[mfs[0]] = map(
sum, zip(mapped_frac_size[mfs[0]], mfs[1:]))
proc_lists = {k: [] for k in range(th)}
for ev in ['I', 'M', 'D']:
OutDict[ev] = dict(
zip(
sorted(OutDict[ev].keys()),
zip([sorted(OutDict[ev].keys())[0]] +
list(diff(sorted(OutDict[ev].keys()))), [
max(
zip(*map(lambda x: OutDict[ev].get(x),
sorted(OutDict[ev].keys())))[1])
if x[0] < zip(*map(lambda x: OutDict[ev].get(
x), sorted(OutDict[ev].keys())))[1].index(
max(
zip(*map(lambda x: OutDict[ev].get(x),
sorted(OutDict[ev].keys())))
[1])) else x[1]
for x in enumerate(
zip(*map(lambda x: OutDict[ev].get(x),
sorted(OutDict[ev].keys())))[1])
],
zip(*map(lambda x: OutDict[ev].get(x),
sorted(OutDict[ev].keys())))[2])))
for k, v in pos_dict.iteritems():
for k1, v1 in v.iteritems():
chr_cov_dict[str(k1)] = chr_cov_dict.get(
str(k1), []) + [(k, sum(v1) / 1000000.)]
mapped_frac_size = [[
k[0], k[1][0], k[1][1],
round(1 - float(k[1][1]) / (float(k[1][0]) + float(k[1][1])), 3)
] for k in sorted(mapped_frac_size.iteritems())
if k[1][0] != 0 or k[1][1] != 0]
sorted_unmapfraqseq = zip(*mapped_frac_size)[3]
for ev in OutDict.keys():
for k, v in sorted(OutDict[ev].iteritems()):
OutDict[ev][k] = round(
float(v[2]) / (int(v[0]) * float(v[1])), 4)
plot_stats(OutDict, sorted_unmapfraqseq, mapped_frac_size,
chr_cov_dict, out_dir)
finalfile = os.path.join(tmpdir, (prefix + '.bam'))
bamsfile = os.path.join(out_dir, 'to_merge.txt')
file = open(bamsfile, 'w')
for line in file_list:
file.write(os.path.join(work_dir, line) + '\n')
file.close()
bammergeline = subprocess.Popen([
os.path.abspath(os.path.dirname(__file__)) +
'\SAMtools\samtools.exe', 'merge', '-cp', '-@',
str(th), '-b', bamsfile, finalfile
],
stdout=subprocess.PIPE).communicate()
for b in file_list:
os.remove(b)
os.remove(bamsfile)
log.debug('[Alignment][minimap2al] - samtools index %s' % (finalfile))
samindexline = subprocess.Popen([
os.path.abspath(os.path.dirname(__file__)) +
'\SAMtools\samtools.exe', 'index', finalfile
],
stdout=subprocess.PIPE).communicate()
for f in os.listdir(tmpdir):
try:
shutil.move(os.path.join(tmpdir, f),
os.path.join(work_dir, out_dir))
except shutil.Error:
log.error("Unable to move %s" % tmpdir, f)
shutil.rmtree(tmpdir, ignore_errors=True)
def run(argsin):
parser = argparse.ArgumentParser(
add_help=False,
prog='alignment',
usage='''\r \n
________________
| |
| ##### |
| ## ## |
| ##### |
| ## ##### |
| ## ## ## |
| ##### |
| ## |
| ## |
|________________|
PyPore
Alignment
usage: %(prog)s [-i <input.fq>] [-r <reference.fa>] [-l <my_label>] [options]''',
epilog='''
PyPore. Written by Roberto Semeraro, Department of Clinical and Sperimental Medicine,
University of Florence. For bug report or suggestion write to [email protected]''',
formatter_class=argparse.RawDescriptionHelpFormatter,
)
g = parser.add_argument_group(
title='mandatory arguments',
description=
'''-i, --inputs path to the read file (query.fq)
-r, --reference indexed reference sequence file
-l, --prefix prefix for alignment file
''')
g.add_argument('-i',
'--inputs',
action='store',
metavar='',
nargs='*',
help=argparse.SUPPRESS)
g.add_argument('-r',
'--reference',
action='store',
metavar='',
help=argparse.SUPPRESS)
g.add_argument('-l',
'--prefix',
action='store',
metavar='',
help=argparse.SUPPRESS)
f = parser.add_argument_group(
title='options',
description=
'''-a, --aligner aligment module (b = bwa, m = minimap2, n = ngmlr) [m b n]
-s, --alignment_stats generate alignment stats [no]
-o, --output_dir if omitted, generates a results directory
in the current position
-n, --threads_number number of processing threads [1]
-v, --verbose increase verbosity: 0 = only warnings, 1 = info, 2 = debug,
3 = debug on terminal. No number means info
Default is no verbosity
-h, --help show this help message and exit
''')
f.add_argument('-a',
'--aligner',
action="store",
nargs='*',
default=['m'],
metavar='',
help=argparse.SUPPRESS,
choices=['m', 'b', 'n'])
f.add_argument('-s',
'--alignment_stats',
action="store",
nargs='*',
default=['n'],
metavar='',
help=argparse.SUPPRESS,
choices=['y', 'n', 'yes', 'no'])
f.add_argument('-o',
'--output_dir',
action="store",
nargs=1,
metavar='',
help=argparse.SUPPRESS)
f.add_argument('-n',
'--threads_number',
action="store",
type=int,
default=1,
metavar='',
help=argparse.SUPPRESS)
f.add_argument('-h', '--help', action="help", help=argparse.SUPPRESS)
f.add_argument('-v',
'--verbose',
const=1,
default=1,
type=int,
nargs="?",
help=argparse.SUPPRESS,
choices=range(0, 4))
try:
args = parser.parse_args(argsin)
if not args.inputs or not args.reference or not args.prefix:
parser.print_help()
log.error('Missing mandatory arguments!')
sys.exit(1)
else:
MainReader(args)
except IOError as msg:
parser.error(str(msg))
def result_plotting(ch_par):
def rngrabber(t):
try:
Value = int(Nanoline[t][0])
except:
Value = 0
return Value
def bgrabber(t):
try:
Value = int(Nanoline[t][1])
except:
Value = 0
return Value
log.info('Plotting results...')
log.debug("Preparing heatmaps...")
NanoLayout = [['1', '2', '3', '4', '5', '6', '7', '8', '40', '39', '38', '37', '36', '35', '34', '33'],
['9', '10', '11', '12', '13', '14', '15', '16', '48', '47', '46', '45', '44', '43', '42', '41'],
['17', '18', '19', '20', '21', '22', '23', '24', '56', '55', '54', '53', '52', '51', '50', '49'],
['25', '26', '27', '28', '29', '30', '31', '32', '64', '63', '62', '61', '60', '59', '58', '57'],
['449', '450', '451', '452', '453', '454', '455', '456', '488', '487', '486', '485', '484', '483',
'482',
'481'],
['457', '458', '459', '460', '461', '462', '463', '464', '496', '495', '494', '493', '492', '491',
'490',
'489'],
['465', '466', '467', '468', '469', '470', '471', '472', '504', '503', '502', '501', '500', '499',
'498',
'497'],
['473', '474', '475', '476', '477', '478', '479', '480', '512', '511', '510', '509', '508', '507',
'506',
'505'],
['385', '386', '387', '388', '389', '390', '391', '392', '424', '423', '422', '421', '420', '419',
'418',
'417'],
['393', '394', '395', '396', '397', '398', '399', '400', '432', '431', '430', '429', '428', '427',
'426',
'425'],
['401', '402', '403', '404', '405', '406', '407', '408', '440', '439', '438', '437', '436', '435',
'434',
'433'],
['409', '410', '411', '412', '413', '414', '415', '416', '448', '447', '446', '445', '444', '443',
'442',
'441'],
['321', '322', '323', '324', '325', '326', '327', '328', '360', '359', '358', '357', '356', '355',
'354',
'353'],
['329', '330', '331', '332', '333', '334', '335', '336', '368', '367', '366', '365', '364', '363',
'362',
'361'],
['337', '338', '339', '340', '341', '342', '343', '344', '376', '375', '374', '373', '372', '371',
'370',
'369'],
['345', '346', '347', '348', '349', '350', '351', '352', '384', '383', '382', '381', '380', '379',
'378',
'377'],
['257', '258', '259', '260', '261', '262', '263', '264', '296', '295', '294', '293', '292', '291',
'290',
'289'],
['265', '266', '267', '268', '269', '270', '271', '272', '304', '303', '302', '301', '300', '299',
'298',
'297'],
['273', '274', '275', '276', '277', '278', '279', '280', '312', '311', '310', '309', '308', '307',
'306',
'305'],
['281', '282', '283', '284', '285', '286', '287', '288', '320', '319', '318', '317', '316', '315',
'314',
'313'],
['193', '194', '195', '196', '197', '198', '199', '200', '232', '231', '230', '229', '228', '227',
'226',
'225'],
['201', '202', '203', '204', '205', '206', '207', '208', '240', '239', '238', '237', '236', '235',
'234',
'233'],
['209', '210', '211', '212', '213', '214', '215', '216', '248', '247', '246', '245', '244', '243',
'242',
'241'],
['217', '218', '219', '220', '221', '222', '223', '224', '256', '255', '254', '253', '252', '251',
'250',
'249'],
['129', '130', '131', '132', '133', '134', '135', '136', '168', '167', '166', '165', '164', '163',
'162',
'161'],
['137', '138', '139', '140', '141', '142', '143', '144', '176', '175', '174', '173', '172', '171',
'170',
'169'],
['145', '146', '147', '148', '149', '150', '151', '152', '184', '183', '182', '181', '180', '179',
'178',
'177'],
['153', '154', '155', '156', '157', '158', '159', '160', '192', '191', '190', '189', '188', '187',
'186',
'185'],
['65', '66', '67', '68', '69', '70', '71', '72', '104', '103', '102', '101', '100', '99', '98', '97'],
['73', '74', '75', '76', '77', '78', '79', '80', '112', '111', '110', '109', '108', '107', '106',
'105'],
['81', '82', '83', '84', '85', '86', '87', '88', '120', '119', '118', '117', '116', '115', '114',
'113'],
['89', '90', '91', '92', '93', '94', '95', '96', '128', '127', '126', '125', '124', '123', '122',
'121']]
NanoBasePlate = []
NanoPlate = []
for i in NanoLayout:
Nanoline = [ch_par[_] for _ in i]
Exlin = map(lambda x: rngrabber(x), range(0, len(Nanoline)))
NanoPlate.append(Exlin)
Exlin = map(lambda x: bgrabber(x), range(0, len(Nanoline)))
NanoBasePlate.append(Exlin)
owncolorscale = [[0.0, 'rgb(0,0,0)'], [0.001, 'rgb(140,81,10)'], [0.1111111111111111, 'rgb(140,81,10)'],
[0.2222222222222222, 'rgb(191,129,45)'], [0.33333333333, 'rgb(223,194,125)'],
[0.44444444444, 'rgb(254,224,139)'], [0.5555555555555555, 'rgb(246,232,195)'],
[0.6666666666666666, 'rgb(199,234,229)'], [0.7777777777777778, 'rgb(128,205,193)'],
[0.8888888888888888, 'rgb(53,151,143)'], [1.0, 'rgb(1,102,94)']]
xh = map(list, zip(*NanoLayout))
yh = map(list, zip(*NanoPlate))
zh = map(list, zip(*NanoBasePlate))
hovertext=[[] for i in range(len(xh))]
for x1, y1 in enumerate(xh):
for x2, y2 in enumerate(y1):
hovertext[x1].append('<b>CHANNEL:</b> {}<br /><b>RN:</b> {}<br /><b>BN:</b> {}'.format(y2, yh[x1][x2], zh[x1][x2]))
trace = go.Heatmap(name="ReadNHeat", z=map(list, zip(*NanoPlate)), x=range(1, 33), y=range(1, 17),
text=hovertext, hoverinfo="text", xgap=23, ygap=8, colorscale=owncolorscale,
colorbar=dict(y=0.77, len=0.470, exponentformat="SI")) # y=0.77,
trace1 = go.Heatmap(name="BaseNHeat", z=map(list, zip(*NanoBasePlate)), x=range(1, 33), y=range(1, 17),
text=hovertext, hoverinfo="text", xgap=23, ygap=8, colorscale=owncolorscale,
colorbar=dict(y=0.77, len=0.470, exponentformat="SI"), visible=False)
fig = plotly.tools.make_subplots(rows=13, cols=1, shared_xaxes=False,
specs=[[{'rowspan': 6}], [None], [None], [None], [None], [None], [None],
[{'rowspan': 2}], [None], [{'rowspan': 2}], [None], [None],
[{'rowspan': 1}]],
vertical_spacing=0.001, print_grid=False)
log.debug("Heatmaps ready!")
VisibleData = [False] * (513 * 10)
updatemenus = list([
dict(type="buttons",
active=-1,
buttons=list([
dict(label='Read Number',
method='update',
args=[{'visible': [True, False] + VisibleData},
{'annotations': trace}]),
dict(label='Base Pair Number',
method='update',
args=[{'visible': [False, True] + VisibleData},
{'annotations': trace1}]),
]),
x=-0.03,
y=0.99
)
])
fig.append_trace(trace, 1, 1)
fig.append_trace(trace1, 1, 1)
log.debug("Computing pore performance...")
ChannelsInfoList = []
X3Index = []
X4index = []
global hour_vec
hour_vec = range(48)
for c in range(1, 513):
Res, x3i, x4i = ChannelPlotter_f(c, ch_par)
ChannelsInfoList += Res
X3Index += x3i
X4index += x4i
fig.data.extend(ChannelsInfoList)
for fi in X3Index:
fig.data[fi].update({'xaxis': 'x3'})
for fi in X4index:
fig.data[fi].update({'xaxis': 'x4'})
log.debug("Plotting pore performance...")
fig['layout'].update(title='Channel Productivity', spikedistance=-1, yaxis1=dict(range=[16.5, 0.5], visible=False, fixedrange=True),
xaxis1=dict(visible=False, fixedrange=True, range=[0.5, 32.5], hoverformat='.2s'),
yaxis2=dict(fixedrange=False, title='Reads', hoverformat='.2s', anchor='x3'),
xaxis2=dict(visible=False, fixedrange=True),
xaxis3=dict(autotick=False, title='hours', range=[0, 48], showspikes=True, spikethickness=1.5,
spikemode='across', spikecolor='grey', spikedash='solid'),
yaxis3=dict(fixedrange=False, title='Base Pairs', hoverformat='.2s'),
xaxis4=dict(visible=False, fixedrange=True, range=[0, 100]),
yaxis4=dict(fixedrange=True, visible=False),
legend=dict(x=-0.062, y=0.439, yanchor='yaxis2', xanchor='right'), updatemenus=updatemenus,
barmode='stack') # y=0.450 range=[0, 1500000] range=[0, 600]
fig.layout.update({'hovermode': 'compare'})
config = {'displaylogo': False,
'modeBarButtonsToRemove': ['toImage', 'sendDataToCloud', 'zoom2d', 'pan2d', 'select2d', 'lasso2d',
'hoverClosestCartesian', 'toggleHover', 'autoScale2d']}
try:
out_html = os.path.join(work_dir, prefix + '_pore_activity_map.html')
plotly.offline.plot(fig, filename=out_html, show_link=False, auto_open=False, config=config)
except:
e = sys.exc_info()
tb = traceback.format_exception(*e)
log.error(
"Something went wrong during plotting...\n\033[36m##################################\n\033[93m%s\033[32m%s\033[93m%s\033[36m##################################\n\033[0m" % (
tb[0], tb[1], tb[2]))
sys.exit(1)
HeatTrigger(out_html)
