def CF_plot(args):
try:
import locale
import matplotlib
matplotlib.use('Agg')
import matplotlib.pyplot as plt
import pylab as P
from matplotlib.lines import Line2D
from matplotlib.patches import Rectangle
_ = locale.setlocale(locale.LC_ALL, '')
except:
print "[ERROR] One or more of the required modules for plotting cannot be loaded! Are matplotlib and pylab installed?"
sys.exit(0)
chr, start, stop = cf.parseLocString(args.region)
r = cf.rpkm_reader(args.input)
data = r.getExonValuesByRegion(chr,start,stop)
_ = data.smooth()
plt.gcf().clear()
fig = plt.figure(figsize=(10,5))
ax = fig.add_subplot(111)
ax.plot(data.rpkm, linewidth = 0.3, c='k')
if args.sample != 'none':
cnt = 1
coloriter = iter(['r','b','g','y'])
for sample in args.sample:
try:
color, sampleID = sample.split(":")
except:
color =coloriter.next()
sampleID = sample
ax.plot(data.getSample([sampleID]), linewidth = 1, c=color, label = sampleID)
if cnt == 1:
cf.plotRawData(ax, r.getExonValuesByRegion(chr,start,stop,sampleList=[sampleID]).getSample([sampleID]),color=color)
cnt +=1
plt.legend(prop={'size':10},frameon=False)
cf.plotGenes(ax, data)
cf.plotGenomicCoords(plt,data)
plt.xlim(0,data.shape[1])
plt.ylim(-3,3)
plt.title("%s: %s - %s" % (cf.chrInt2Str(chr),locale.format("%d",start, grouping=True),locale.format("%d",stop, grouping=True)))
plt.xlabel("Position")
plt.ylabel("SVD-ZRPKM Values")
plt.savefig(args.output)
sys.exit(0)
def CF_plot(args):
try:
import locale
import matplotlib
matplotlib.use('Agg')
import matplotlib.pyplot as plt
import pylab as P
from matplotlib.lines import Line2D
from matplotlib.patches import Rectangle
_ = locale.setlocale(locale.LC_ALL, '')
except:
print "[ERROR] One or more of the required modules for plotting cannot be loaded! Are matplotlib and pylab installed?"
sys.exit(0)
chr, start, stop = cf.parseLocString(args.region)
r = cf.rpkm_reader(args.input)
data = r.getExonValuesByRegion(chr,start,stop)
_ = data.smooth()
plt.gcf().clear()
fig = plt.figure(figsize=(10,5))
ax = fig.add_subplot(111)
ax.plot(data.rpkm, linewidth = 0.3, c='k')
if args.sample != 'none':
cnt = 1
coloriter = iter(['r','b','g','y'])
for sample in args.sample:
try:
color, sampleID = sample.split(":")
except:
color =coloriter.next()
sampleID = sample
ax.plot(data.getSample([sampleID]), linewidth = 1, c=color, label = sampleID)
if cnt == 1:
cf.plotRawData(ax, r.getExonValuesByRegion(chr,start,stop,sampleList=[sampleID]).getSample([sampleID]),color=color)
cnt +=1
plt.legend(prop={'size':10},frameon=False)
cf.plotGenes(ax, data)
cf.plotGenomicCoords(plt,data)
plt.xlim(0,data.shape[1])
plt.ylim(-3,3)
plt.title("%s: %s - %s" % (cf.chrInt2Str(chr),locale.format("%d",start, grouping=True),locale.format("%d",stop, grouping=True)))
plt.xlabel("Position")
plt.ylabel("SVD-ZRPKM Values")
plt.savefig(args.output)
sys.exit(0)
def CF_plotcalls(args):
try:
import matplotlib
matplotlib.use('Agg')
import matplotlib.pyplot as plt
import pylab as P
from matplotlib.lines import Line2D
from matplotlib.patches import Rectangle
except:
print "[ERROR] One or more of the required modules for plotting cannot be loaded! Are matplotlib and pylab installed?"
sys.exit(0)
import locale
try:
_ = locale.setlocale(locale.LC_ALL, 'en_US')
except:
_ = locale.setlocale(locale.LC_ALL, '')
try:
callfile_fn = str(args.calls)
callfile_f = open(callfile_fn, mode='r')
except IOError as e:
print '[ERROR] Cannot open call file for reading: ', callfile_fn
sys.exit(0)
all_calls = []
header = callfile_f.readline()
for line in callfile_f:
sampleID, chr, start, stop, state = line.strip().split()
chr = cf.chrStr2Int(chr)
all_calls.append({
"chromosome": int(chr),
"start": int(start),
"stop": int(stop),
"sampleID": sampleID
})
r = cf.rpkm_reader(args.input)
for call in all_calls:
chr = call["chromosome"]
start = call["start"]
stop = call["stop"]
sampleID = call["sampleID"]
exons = r.getExonIDs(chr, int(start), int(stop))
window_start = max(exons[0] - args.window, 0)
window_stop = exons[-1] + args.window
data = r.getExonValuesByExons(chr, window_start, window_stop)
_ = data.smooth()
plt.gcf().clear()
fig = plt.figure(figsize=(10, 5))
ax = fig.add_subplot(111)
ax.plot(data.rpkm, linewidth=0.3, c='k')
ax.plot(data.getSample([sampleID]), linewidth=1, c='r', label=sampleID)
cf.plotRawData(ax,
r.getExonValuesByExons(chr,
window_start,
window_stop,
sampleList=[sampleID]).getSample(
[sampleID]),
color='r')
plt.legend(prop={'size': 10}, frameon=False)
cf.plotGenes(ax, data)
cf.plotGenomicCoords(plt, data)
exon_start = np.where(data.exons["start"] == start)[0][0]
exon_stop = np.where(data.exons["stop"] == stop)[0][0]
_ = ax.add_line(
matplotlib.lines.Line2D([exon_start, exon_stop], [2, 2],
color='k',
lw=6,
linestyle='-',
alpha=1,
solid_capstyle='butt'))
_ = plt.xlim(0, data.shape[1])
_ = plt.ylim(-3, 3)
plt.title(
"%s: %s - %s" %
(cf.chrInt2Str(chr), locale.format("%d", start, grouping=True),
locale.format("%d", stop, grouping=True)))
plt.xlabel("Position")
plt.ylabel("SVD-ZRPKM Values")
outfile = "%s_%d_%d_%s.png" % (cf.chrInt2Str(chr), start, stop,
sampleID)
plt.savefig(args.outputdir + "/" + outfile)
def CF_call(args):
try:
h5file_in_fn = str(args.input)
h5file_in = openFile(h5file_in_fn, mode='r')
except IOError as e:
print '[ERROR] Cannot open CoNIFER input file for reading: ', h5file_in_fn
sys.exit(0)
try:
callfile_fn = str(args.output)
callfile_f = open(callfile_fn, mode='w')
except IOError as e:
print '[ERROR] Cannot open output file for writing: ', callfile_fn
sys.exit(0)
chrs_to_process = []
for chr in h5file_in.root:
if chr._v_title not in ('probes', 'samples'):
chrs_to_process.append(chr._v_title.replace("chr", ""))
h5file_in.close()
print '[INIT] Initializing caller at threshold = %f' % (args.threshold)
r = cf.rpkm_reader(h5file_in_fn)
all_calls = []
for chr in chrs_to_process:
print '[RUNNING] Now processing chr%s' % chr
data = r.getExonValuesByRegion(chr)
#raw_data = copy.copy(data)
_ = data.smooth()
mean = np.mean(data.rpkm, axis=1)
sd = np.std(data.rpkm, axis=1)
for sample in r.getSampleList():
sample_data = data.getSample([sample]).flatten()
#sample_raw_data = raw_data.getSample([sample]).flatten()
dup_mask = sample_data >= args.threshold
del_mask = sample_data <= -1 * args.threshold
dup_bkpoints = cf.getbkpoints(
dup_mask
) #returns exon coordinates for this chromosome (numpy array coords)
del_bkpoints = cf.getbkpoints(del_mask)
dups = []
for start, stop in dup_bkpoints:
try:
new_start = np.max(
np.where(sample_data[:start] < (mean[:start] +
3 * sd[:start])))
except ValueError:
new_start = 0
try:
new_stop = stop + np.min(
np.where(sample_data[stop:] <
(mean[stop:] + 3 * sd[stop:])))
except ValueError:
new_stop = data.shape[1] - 1
dups.append({
"sampleID": sample,
"chromosome": cf.chrInt2Str(chr),
"start": data.exons[new_start]["start"],
"stop": data.exons[new_stop]["stop"],
"state": "dup"
})
dels = []
for start, stop in del_bkpoints:
try:
new_start = np.max(
np.where(sample_data[:start] > (-1 * mean[:start] -
3 * sd[:start])))
except ValueError:
new_start = 0
try:
new_stop = stop + np.min(
np.where(sample_data[stop:] >
(-1 * mean[stop:] - 3 * sd[stop:])))
except ValueError:
new_stop = data.shape[1] - 1
dels.append({
"sampleID": sample,
"chromosome": cf.chrInt2Str(chr),
"start": data.exons[new_start]["start"],
"stop": data.exons[new_stop]["stop"],
"state": "del"
})
dels = cf.mergeCalls(dels) #merges overlapping calls
dups = cf.mergeCalls(dups)
#print sampleID, len(dels), len(dups)
all_calls.extend(list(dels))
all_calls.extend(list(dups))
# print calls to file
header = ['sampleID', 'chromosome', 'start', 'stop', 'state']
callfile_f.write('\t'.join(header) + "\n")
for call in all_calls:
print "%s\t%s\t%d\t%d\t%s" % (call["sampleID"], call["chromosome"],
call["start"], call["stop"],
call["state"])
callfile_f.write("%s\t%s\t%d\t%d\t%s\n" %
(call["sampleID"], call["chromosome"], call["start"],
call["stop"], call["state"]))
sys.exit(0)
def CF_plotcalls(args):
try:
import matplotlib
matplotlib.use('Agg')
import matplotlib.pyplot as plt
import pylab as P
from matplotlib.lines import Line2D
from matplotlib.patches import Rectangle
except:
print "[ERROR] One or more of the required modules for plotting cannot be loaded! Are matplotlib and pylab installed?"
sys.exit(0)
import locale
try:
_ = locale.setlocale(locale.LC_ALL, 'en_US')
except:
_ = locale.setlocale(locale.LC_ALL, '')
try:
callfile_fn = str(args.calls)
callfile_f = open(callfile_fn, mode='r')
except IOError as e:
print '[ERROR] Cannot open call file for reading: ', callfile_fn
sys.exit(0)
all_calls = []
header = callfile_f.readline()
for line in callfile_f:
sampleID, chr, start, stop, state = line.strip().split()
chr = cf.chrStr2Int(chr)
all_calls.append({"chromosome":int(chr), "start":int(start), "stop":int(stop), "sampleID":sampleID})
r = cf.rpkm_reader(args.input)
for call in all_calls:
chr = call["chromosome"]
start = call["start"]
stop = call["stop"]
sampleID = call["sampleID"]
exons = r.getExonIDs(chr,int(start),int(stop))
window_start = max(exons[0]-args.window,0)
window_stop = exons[-1]+args.window
data = r.getExonValuesByExons(chr,window_start, window_stop)
_ = data.smooth()
plt.gcf().clear()
fig = plt.figure(figsize=(10,5))
ax = fig.add_subplot(111)
ax.plot(data.rpkm, linewidth = 0.3, c='k')
ax.plot(data.getSample([sampleID]), linewidth = 1, c='r', label = sampleID)
cf.plotRawData(ax, r.getExonValuesByExons(chr,window_start, window_stop,sampleList=[sampleID]).getSample([sampleID]),color='r')
plt.legend(prop={'size':10},frameon=False)
cf.plotGenes(ax, data)
cf.plotGenomicCoords(plt,data)
exon_start = np.where(data.exons["start"] == start)[0][0]
exon_stop = np.where(data.exons["stop"] == stop)[0][0]
_ = ax.add_line(matplotlib.lines.Line2D([exon_start,exon_stop],[2,2],color='k',lw=6,linestyle='-',alpha=1,solid_capstyle='butt'))
_ = plt.xlim(0,data.shape[1])
_ = plt.ylim(-3,3)
plt.title("%s: %s - %s" % (cf.chrInt2Str(chr),locale.format("%d",start, grouping=True),locale.format("%d",stop, grouping=True)))
plt.xlabel("Position")
plt.ylabel("SVD-ZRPKM Values")
outfile = "%s_%d_%d_%s.png" % (cf.chrInt2Str(chr), start, stop, sampleID)
plt.savefig(args.outputdir + "/" + outfile)
def CF_call(args):
try:
h5file_in_fn = str(args.input)
h5file_in = openFile(h5file_in_fn, mode='r')
except IOError as e:
print '[ERROR] Cannot open CoNIFER input file for reading: ', h5file_in_fn
sys.exit(0)
try:
callfile_fn = str(args.output)
callfile_f = open(callfile_fn, mode='w')
except IOError as e:
print '[ERROR] Cannot open output file for writing: ', callfile_fn
sys.exit(0)
chrs_to_process = []
for chr in h5file_in.root:
if chr._v_title not in ('probes','samples'):
chrs_to_process.append(chr._v_title.replace("chr",""))
h5file_in.close()
print '[INIT] Initializing caller at threshold = %f' % (args.threshold)
r = cf.rpkm_reader(h5file_in_fn)
all_calls = []
for chr in chrs_to_process:
print '[RUNNING] Now processing chr%s' % chr
data = r.getExonValuesByRegion(chr)
#raw_data = copy.copy(data)
_ = data.smooth()
mean= np.mean(data.rpkm,axis=1)
sd = np.std(data.rpkm,axis=1)
for sample in r.getSampleList():
sample_data = data.getSample([sample]).flatten()
#sample_raw_data = raw_data.getSample([sample]).flatten()
dup_mask = sample_data >= args.threshold
del_mask = sample_data <= -1*args.threshold
dup_bkpoints = cf.getbkpoints(dup_mask) #returns exon coordinates for this chromosome (numpy array coords)
del_bkpoints = cf.getbkpoints(del_mask)
dups = []
for start,stop in dup_bkpoints:
try: new_start = np.max(np.where(sample_data[:start] < (mean[:start] + 3*sd[:start])))
except ValueError: new_start = 0
try: new_stop = stop + np.min(np.where(sample_data[stop:] < (mean[stop:] + 3*sd[stop:])))
except ValueError: new_stop = data.shape[1]-1
dups.append({"sampleID":sample,"chromosome": cf.chrInt2Str(chr), "start":data.exons[new_start]["start"], "stop": data.exons[new_stop]["stop"], "state": "dup"})
dels = []
for start,stop in del_bkpoints:
try: new_start = np.max(np.where(sample_data[:start] > (-1*mean[:start] - 3*sd[:start])))
except ValueError: new_start = 0
try: new_stop = stop + np.min(np.where(sample_data[stop:] > (-1*mean[stop:] - 3*sd[stop:])))
except ValueError: new_stop = data.shape[1]-1
dels.append({"sampleID":sample,"chromosome": cf.chrInt2Str(chr), "start":data.exons[new_start]["start"], "stop": data.exons[new_stop]["stop"], "state": "del"})
dels = cf.mergeCalls(dels) #merges overlapping calls
dups = cf.mergeCalls(dups)
#print sampleID, len(dels), len(dups)
all_calls.extend(list(dels))
all_calls.extend(list(dups))
# print calls to file
header = ['sampleID','chromosome','start','stop','state']
callfile_f.write('\t'.join(header) + "\n")
for call in all_calls:
print "%s\t%s\t%d\t%d\t%s" % (call["sampleID"], call["chromosome"], call["start"], call["stop"], call["state"])
callfile_f.write("%s\t%s\t%d\t%d\t%s\n" % (call["sampleID"], call["chromosome"], call["start"], call["stop"], call["state"]))
sys.exit(0)
