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fix >3 peaks found
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@AntoineHo
AntoineHo authored Oct 21, 2020
1 parent c69e48c commit d80f2e2
Showing 1 changed file with 78 additions and 28 deletions.
106 changes: 78 additions & 28 deletions Hap.py
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Original file line number Diff line number Diff line change
Expand Up @@ -223,46 +223,23 @@ def estimate_haploidy(args) :
peak_ratios = None
limits = {}

#
if len(peaks) > 3 : # In case 3+ peaks:
log("Found more than 3 peaks at: {}x and {}x".format("x, ".join(str(peak) for peak in peaks[:-1]), peaks[-1]))

# In case number of peaks lower than max contam is > 1
if len([peak for peak in peaks if peak < dc_args["max_contam"]]) > 1 :
# INCREASE THRESHOLD to detect peaks
log("WARNING: More than 1 contaminant peak is found")
print("HELP: Try running with --debug flag and check the histogram curve.")
print("HELP: If you estimate that there should be no contaminant peaks detected then increase the min_peak (-mp) threshold (currently {}).".format(dc_args["min_peak"]))
print("HELP: If you estimate that there should be a contaminant peak but it is not considered contaminant, then increase the max_contaminant (-mc) optional argument value (currently {}).".format(dc_args["max_contam"]))
log("Exiting...")
sys.exit(1)
elif len([peak for peak in peaks if (peak >= dc_args["max_contam"] and peak < dc_args["max_diploid"])]) > 1 : # If number of diploid peaks is > 1
log("WARNING: More than 1 diploid peak is found")
print("HELP: Try running with --debug flag and check the histogram curve.")
print("HELP: If you estimate that there should be no diploid peaks (or only one) then maybe one is a contaminant or an haploid peak try modifying the max_contaminants and max_diploid arguments (currently {} and {}).".format(dc_args["max_contam"], dc_args["max_diploid"]))
#print("NOTE: If you estimate that there should be a contaminant peak but it is not considered contaminant, then increase the max_contaminant (-mc) optional argument value (currently {}).".format(dc_args["max_contaminant"]))
log("Exiting...")
sys.exit(1)
else :
log("WARNING: More than 1 diploid peak is found")
print("HELP: Try running with --debug flag and check the histogram curve.")
log("Exiting...")
sys.exit(1)
peaks, heights, widths = check_peaks(peaks, props, widths, len(smoothed), dc_args)

elif len(peaks) == 3 : # In case 3 peaks:
if len(peaks) == 3 : # In case 3 peaks : 1 in each category
log("Found 3 peaks at: {}x, {}x and {}x".format(peaks[0], peaks[1], peaks[2]))
haplotigs_peak_ratio = round(heights[-2] / heights[-1], 3)

# For each peak height and with
for n, height, width in zip(range(3), peaks, widths) :
# For each peak pos and width
for n, pos, width in zip(range(3), peaks, widths) :
if n == 0 :
categ = "Contaminants"
elif n == 1 :
categ = "Diploid"
elif n == 2 :
break
# Store limit under the key category of the peak
limits[categ] = math.ceil(height + width)
limits[categ] = math.ceil(pos + width)

elif len(peaks) == 2 : # If only 2 peaks
log("Found 2 peaks at: {}x and {}x".format(peaks[0], peaks[1]))
Expand Down Expand Up @@ -374,6 +351,79 @@ def estimate_haploidy(args) :
sys.exit(0)


def check_peaks(peaks, props, widths, maximum_cov, dc_args) :
"""In case there are more than 3 peaks, find only the 3 highest interest peaks"""
log("Warning: detected more than 3 peaks at: {}x and {}x".format("x, ".join(str(peak) for peak in peaks[:-1]), peaks[-1]))

contaminant_peak, diploid_peak, haploid_peak = None, None, None
contaminant_height, diploid_height, haploid_height = None, None, None
contaminant_width, diploid_width, haploid_width = None, None, None

# Find highest peaks
for pos, height in zip(peaks, props["peak_heights"]) :
if pos < dc_args["max_contam"] :
if contaminant_peak == None :
contaminant_peak = pos
contaminant_height = height
elif height > contaminant_height :
contaminant_peak = pos
contaminant_height = height
else :
continue
elif pos >= dc_args["max_contam"] and pos < dc_args["max_diploid"] :
if diploid_peak == None :
diploid_peak = pos
diploid_height = height
elif height > diploid_height :
diploid_peak = pos
diploid_height = height
else :
continue
else :
if haploid_peak == None :
haploid_peak = pos
haploid_height = height
elif height > haploid_height :
haploid_peak = pos
haploid_height = height
else :
continue

# widths = general boundaries <-- may be a problem sometimes
contaminant_width = math.floor(abs(dc_args["max_contam"]-contaminant_peak)) # floor of absolute distance between contaminant boundary and highest contaminant peak
diploid_width = math.floor(abs(dc_args["max_diploid"]-diploid_peak)) # floor of absolute distance between diploid boundary and highest diploid peak
haploid_width = math.floor(abs(maximum_cov-diploid_peak)) # floor of absolute distance between haploid peak and max coverage ( == len(x) == number of bins ) from the histogram

"""
# In case number of peaks lower than max contam is > 1
if len([peak for peak in peaks if peak < dc_args["max_contam"]]) > 1 :
# INCREASE THRESHOLD to detect peaks
log("WARNING: More than 1 contaminant peak is found. Trying to use only largest found")
print("HELP: Try running with --debug flag and check the histogram curve.")
print("HELP: If you estimate that there should be no contaminant peaks detected then increase the min_peak (-mp) threshold (currently {}).".format(dc_args["min_peak"]))
print("HELP: If you estimate that there should be a contaminant peak but it is not considered contaminant, then increase the max_contaminant (-mc) optional argument value (currently {}).".format(dc_args["max_contam"]))
log("Exiting...")
sys.exit(1)
elif len([peak for peak in peaks if (peak >= dc_args["max_contam"] and peak < dc_args["max_diploid"])]) > 1 : # If number of diploid peaks is > 1
log("WARNING: More than 1 diploid peak is found")
print("HELP: Try running with --debug flag and check the histogram curve.")
print("HELP: If you estimate that there should be no diploid peaks (or only one) then maybe one is a contaminant or an haploid peak try modifying the max_contaminants and max_diploid arguments (currently {} and {}).".format(dc_args["max_contam"], dc_args["max_diploid"]))
#print("NOTE: If you estimate that there should be a contaminant peak but it is not considered contaminant, then increase the max_contaminant (-mc) optional argument value (currently {}).".format(dc_args["max_contaminant"]))
log("Exiting...")
sys.exit(1)
else :
log("WARNING: More than 1 diploid peak is found")
print("HELP: Try running with --debug flag and check the histogram curve.")
log("Exiting...")
sys.exit(1)
"""

newpeaks = [contaminant_peak, diploid_peak, haploid_peak]
newheights = [contaminant_height, diploid_height, haploid_height]
newwidths = [contaminant_width, diploid_width, haploid_width]
return newpeaks, newheights, newwidths




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