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| author | mheinzl |
|---|---|
| date | Wed, 27 Feb 2019 04:50:56 -0500 |
| parents | 9919024d7778 |
| children | 9e384b0741f1 |
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#!/usr/bin/env python # Hamming distance analysis of SSCSs # # Author: Monika Heinzl, Johannes-Kepler University Linz (Austria) # Contact: monika.heinzl@edumail.at # # Takes at least one TABULAR file with tags before the alignment to the SSCS and optionally a second TABULAR file as input. # The program produces a plot which shows a histogram of Hamming distances separated after family sizes, # a family size distribution separated after Hamming distances for all (sample_size=0) or a given sample of SSCSs or SSCSs, which form a DCS. # In additon, the tool produces HD and FSD plots for the difference between the HDs of both parts of the tags and for the chimeric reads # and finally a CSV file with the data of the plots. # It is also possible to perform the HD analysis with shortened tags with given sizes as input. # The tool can run on a certain number of processors, which can be defined by the user. # USAGE: python hd.py --inputFile filename --inputName1 filename --sample_size int / # --only_DCS True --FamilySize3 True --subset_tag True --nproc int --minFS int --maxFS int --nr_above_bars True/False --output_pdf outputfile_name_pdf --output_tabular outputfile_name_tabular --output_chimeras_tabular outputfile_name_chimeras_tabular import argparse import itertools import operator import sys from collections import Counter, defaultdict from functools import partial from multiprocessing.pool import Pool import matplotlib.pyplot as plt import numpy from matplotlib.backends.backend_pdf import PdfPages plt.switch_backend('agg') def plotFSDwithHD2(familySizeList1, maximumXFS, minimumXFS, originalCounts, title_file1, subtitle, pdf, relative=False, diff=True): if diff is False: colors = ["#e6194b", "#3cb44b", "#ffe119", "#0082c8", "#f58231", "#911eb4"] labels = ["HD=1", "HD=2", "HD=3", "HD=4", "HD=5-8", "HD>8"] else: colors = ["#93A6AB", "#403C14", "#731E41", "#BAB591", "#085B6F", "#E8AA35", "#726C66"] if relative is True: labels = ["d=0", "d=0.1", "d=0.2", "d=0.3", "d=0.4", "d=0.5-0.8", "d>0.8"] else: labels = ["d=0", "d=1", "d=2", "d=3", "d=4", "d=5-8", "d>8"] fig = plt.figure(figsize=(6, 7)) ax = fig.add_subplot(111) plt.subplots_adjust(bottom=0.1) p1 = numpy.bincount(numpy.concatenate((familySizeList1))) maximumY = numpy.amax(p1) if len(range(minimumXFS, maximumXFS)) == 0: range1 = range(minimumXFS - 1, minimumXFS + 2) else: range1 = range(0, maximumXFS + 2) counts = plt.hist(familySizeList1, label=labels, color=colors, stacked=True, rwidth=0.8, alpha=1, align="left", edgecolor="None", bins=range1) plt.legend(loc='upper right', fontsize=14, frameon=True, bbox_to_anchor=(1.45, 1)) # plt.title(title_file1, fontsize=12) plt.suptitle(subtitle, y=1, x=0.5, fontsize=14) plt.xlabel("Family size", fontsize=14) plt.ylabel("Absolute Frequency", fontsize=14) ticks = numpy.arange(0, maximumXFS + 1, 1) ticks1 = map(str, ticks) if maximumXFS >= 20: ticks1[len(ticks1) - 1] = ">=20" plt.xticks(numpy.array(ticks), ticks1) [l.set_visible(False) for (i, l) in enumerate(ax.get_xticklabels()) if i % 5 != 0] plt.xlim((0, maximumXFS + 1)) if len(numpy.concatenate(familySizeList1)) != 0: plt.ylim((0, max(numpy.bincount(numpy.concatenate(familySizeList1))) * 1.1)) plt.ylim((0, maximumY * 1.2)) legend = "\nfamily size: \nabsolute frequency: \nrelative frequency: " plt.text(0.15, -0.08, legend, size=12, transform=plt.gcf().transFigure) count = numpy.bincount(originalCounts) # original counts if max(originalCounts) >= 20: max_count = ">= 20" else: max_count = max(originalCounts) legend1 = "{}\n{}\n{:.5f}".format(max_count, count[len(count) - 1], float(count[len(count) - 1]) / sum(count)) plt.text(0.5, -0.08, legend1, size=12, transform=plt.gcf().transFigure) legend3 = "singletons\n{:,}\n{:.5f}".format(int(counts[0][len(counts[0]) - 1][1]), float(counts[0][len(counts[0]) - 1][1]) / sum(counts[0][len(counts[0]) - 1])) plt.text(0.7, -0.08, legend3, transform=plt.gcf().transFigure, size=12) plt.grid(b=True, which='major', color='#424242', linestyle=':') pdf.savefig(fig, bbox_inches="tight") plt.close("all") def plotHDwithFSD(list1, maximumX, minimumX, subtitle, lenTags, title_file1, pdf, xlabel, relative=False, nr_above_bars=True, nr_unique_chimeras=0, len_sample=0): if relative is True: step = 0.1 else: step = 1 fig = plt.figure(figsize=(6, 8)) plt.subplots_adjust(bottom=0.1) con_list1 = numpy.concatenate(list1) p1 = numpy.array([v for k, v in sorted(Counter(con_list1).iteritems())]) maximumY = numpy.amax(p1) if relative is True: # relative difference bin1 = numpy.arange(-1, maximumX + 0.2, 0.1) else: bin1 = maximumX + 1 counts = plt.hist(list1, bins=bin1, edgecolor='black', linewidth=1, label=["FS=1", "FS=2", "FS=3", "FS=4", "FS=5-10", "FS>10"], rwidth=0.8, color=["#808080", "#FFFFCC", "#FFBF00", "#DF0101", "#0431B4", "#86B404"], stacked=True, alpha=1, align="left", range=(0, maximumX + 1)) plt.legend(loc='upper right', fontsize=14, frameon=True, bbox_to_anchor=(1.45, 1)) bins = counts[1] # width of bins counts = numpy.array(map(int, counts[0][5])) plt.suptitle(subtitle, y=1, x=0.5, fontsize=14) # plt.title(title_file1, fontsize=12) plt.xlabel(xlabel, fontsize=14) plt.ylabel("Absolute Frequency", fontsize=14) plt.grid(b=True, which='major', color='#424242', linestyle=':') plt.axis((minimumX - step, maximumX + step, 0, numpy.amax(counts) + sum(counts) * 0.1)) plt.xticks(numpy.arange(0, maximumX + step, step)) plt.ylim((0, maximumY * 1.2)) if nr_above_bars is True: bin_centers = -0.4 * numpy.diff(bins) + bins[:-1] for x_label, label in zip(counts, bin_centers): # labels for values if x_label == 0: continue else: plt.annotate("{:,}\n{:.3f}".format(x_label, float(x_label) / sum(counts), 1), xy=(label, x_label + len(con_list1) * 0.01), xycoords="data", color="#000066", fontsize=10) legend = "sample size= {:,} against {:,}".format(sum(counts), lenTags) plt.text(0.14, -0.01, legend, size=12, transform=plt.gcf().transFigure) if nr_unique_chimeras != 0 and len_sample != 0: if relative == True: legend = "nr. of unique chimeric tags= {:,} ({:.5f}) (rel.diff=1)".format(nr_unique_chimeras, int(nr_unique_chimeras) / float(len_sample)) else: legend = "nr. of unique chimeric tags= {:,} ({:.5f})".format(nr_unique_chimeras, int(nr_unique_chimeras) / float(len_sample)) plt.text(0.14, -0.05, legend, size=12, transform=plt.gcf().transFigure) pdf.savefig(fig, bbox_inches="tight") plt.close("all") plt.clf() def plotHDwithinSeq_Sum2(sum1, sum1min, sum2, sum2min, min_value, lenTags, title_file1, pdf): fig = plt.figure(figsize=(6, 8)) plt.subplots_adjust(bottom=0.1) ham_partial = [sum1, sum1min, sum2, sum2min, numpy.array(min_value)] # new hd within tags maximumX = numpy.amax(numpy.concatenate(ham_partial)) minimumX = numpy.amin(numpy.concatenate(ham_partial)) maximumY = numpy.amax(numpy.array(numpy.concatenate(map(lambda x: numpy.bincount(x), ham_partial)))) if len(range(minimumX, maximumX)) == 0: range1 = minimumX else: range1 = range(minimumX, maximumX + 2) plt.hist(ham_partial, align="left", rwidth=0.8, stacked=False, label=[ "HD a", "HD b'", "HD b", "HD a'", "HD a+b"], bins=range1, color=["#58ACFA", "#0404B4", "#FE642E", "#B40431", "#585858"], edgecolor='black', linewidth=1) plt.legend(loc='upper right', fontsize=14, frameon=True, bbox_to_anchor=(1.55, 1)) plt.suptitle('Hamming distances within tags', fontsize=14) # plt.title(title_file1, fontsize=12) plt.xlabel("HD", fontsize=14) plt.ylabel("Absolute Frequency", fontsize=14) plt.grid(b=True, which='major', color='#424242', linestyle=':') plt.axis((minimumX - 1, maximumX + 1, 0, maximumY * 1.2)) plt.xticks(numpy.arange(0, maximumX + 1, 1.0)) # plt.ylim(0, maximumY * 1.2) legend = "sample size= {:,} against {:,}".format(len(numpy.concatenate(ham_partial)), lenTags) plt.text(0.14, -0.01, legend, size=12, transform=plt.gcf().transFigure) pdf.savefig(fig, bbox_inches="tight") plt.close("all") plt.clf() def createTableFSD2(list1, diff=True): selfAB = numpy.concatenate(list1) uniqueFS = numpy.unique(selfAB) nr = numpy.arange(0, len(uniqueFS), 1) if diff is False: count = numpy.zeros((len(uniqueFS), 6)) else: count = numpy.zeros((len(uniqueFS), 7)) state = 1 for i in list1: counts = list(Counter(i).items()) hd = [item[0] for item in counts] c = [item[1] for item in counts] table = numpy.column_stack((hd, c)) if len(table) == 0: state = state + 1 continue else: if state == 1: for i, l in zip(uniqueFS, nr): for j in table: if j[0] == uniqueFS[l]: count[l, 0] = j[1] if state == 2: for i, l in zip(uniqueFS, nr): for j in table: if j[0] == uniqueFS[l]: count[l, 1] = j[1] if state == 3: for i, l in zip(uniqueFS, nr): for j in table: if j[0] == uniqueFS[l]: count[l, 2] = j[1] if state == 4: for i, l in zip(uniqueFS, nr): for j in table: if j[0] == uniqueFS[l]: count[l, 3] = j[1] if state == 5: for i, l in zip(uniqueFS, nr): for j in table: if j[0] == uniqueFS[l]: count[l, 4] = j[1] if state == 6: for i, l in zip(uniqueFS, nr): for j in table: if j[0] == uniqueFS[l]: count[l, 5] = j[1] if state == 7: for i, l in zip(uniqueFS, nr): for j in table: if j[0] == uniqueFS[l]: count[l, 6] = j[1] state = state + 1 sumRow = count.sum(axis=1) sumCol = count.sum(axis=0) uniqueFS = uniqueFS.astype(str) if uniqueFS[len(uniqueFS) - 1] == "20": uniqueFS[len(uniqueFS) - 1] = ">20" first = ["FS={}".format(i) for i in uniqueFS] final = numpy.column_stack((first, count, sumRow)) return (final, sumCol) def createFileFSD2(summary, sumCol, overallSum, output_file, name, sep, rel=False, diff=True): output_file.write(name) output_file.write("\n") if diff is False: output_file.write("{}HD=1{}HD=2{}HD=3{}HD=4{}HD=5-8{}HD>8{}sum{}\n".format(sep, sep, sep, sep, sep, sep, sep, sep)) else: if rel is False: output_file.write("{}diff=0{}diff=1{}diff=2{}diff=3{}diff=4{}diff=5-8{}diff>8{}sum{}\n".format(sep, sep, sep, sep, sep, sep, sep, sep, sep)) else: output_file.write("{}diff=0{}diff=0.1{}diff=0.2{}diff=0.3{}diff=0.4{}diff=0.5-0.8{}diff>0.8{}sum{}\n".format(sep, sep, sep, sep, sep, sep, sep, sep, sep)) for item in summary: for nr in item: if "FS" not in nr and "diff" not in nr: nr = nr.astype(float) nr = nr.astype(int) output_file.write("{}{}".format(nr, sep)) output_file.write("\n") output_file.write("sum{}".format(sep)) sumCol = map(int, sumCol) for el in sumCol: output_file.write("{}{}".format(el, sep)) output_file.write("{}{}".format(overallSum.astype(int), sep)) output_file.write("\n\n") def createTableHD(list1, row_label): selfAB = numpy.concatenate(list1) uniqueHD = numpy.unique(selfAB) nr = numpy.arange(0, len(uniqueHD), 1) count = numpy.zeros((len(uniqueHD), 6)) state = 1 for i in list1: counts = list(Counter(i).items()) hd = [item[0] for item in counts] c = [item[1] for item in counts] table = numpy.column_stack((hd, c)) if len(table) == 0: state = state + 1 continue else: if state == 1: for i, l in zip(uniqueHD, nr): for j in table: if j[0] == uniqueHD[l]: count[l, 0] = j[1] if state == 2: for i, l in zip(uniqueHD, nr): for j in table: if j[0] == uniqueHD[l]: count[l, 1] = j[1] if state == 3: for i, l in zip(uniqueHD, nr): for j in table: if j[0] == uniqueHD[l]: count[l, 2] = j[1] if state == 4: for i, l in zip(uniqueHD, nr): for j in table: if j[0] == uniqueHD[l]: count[l, 3] = j[1] if state == 5: for i, l in zip(uniqueHD, nr): for j in table: if j[0] == uniqueHD[l]: count[l, 4] = j[1] if state == 6: for i, l in zip(uniqueHD, nr): for j in table: if j[0] == uniqueHD[l]: count[l, 5] = j[1] state = state + 1 sumRow = count.sum(axis=1) sumCol = count.sum(axis=0) first = ["{}{}".format(row_label, i) for i in uniqueHD] final = numpy.column_stack((first, count, sumRow)) return (final, sumCol) def createTableHDwithTags(list1): selfAB = numpy.concatenate(list1) uniqueHD = numpy.unique(selfAB) nr = numpy.arange(0, len(uniqueHD), 1) count = numpy.zeros((len(uniqueHD), 5)) state = 1 for i in list1: counts = list(Counter(i).items()) hd = [item[0] for item in counts] c = [item[1] for item in counts] table = numpy.column_stack((hd, c)) if len(table) == 0: state = state + 1 continue else: if state == 1: for i, l in zip(uniqueHD, nr): for j in table: if j[0] == uniqueHD[l]: count[l, 0] = j[1] if state == 2: for i, l in zip(uniqueHD, nr): for j in table: if j[0] == uniqueHD[l]: count[l, 1] = j[1] if state == 3: for i, l in zip(uniqueHD, nr): for j in table: if j[0] == uniqueHD[l]: count[l, 2] = j[1] if state == 4: for i, l in zip(uniqueHD, nr): for j in table: if j[0] == uniqueHD[l]: count[l, 3] = j[1] if state == 5: for i, l in zip(uniqueHD, nr): for j in table: if j[0] == uniqueHD[l]: count[l, 4] = j[1] state = state + 1 sumRow = count.sum(axis=1) sumCol = count.sum(axis=0) first = ["HD={}".format(i) for i in uniqueHD] final = numpy.column_stack((first, count, sumRow)) return (final, sumCol) def createFileHD(summary, sumCol, overallSum, output_file, name, sep): output_file.write(name) output_file.write("\n") output_file.write("{}FS=1{}FS=2{}FS=3{}FS=4{}FS=5-10{}FS>10{}sum{}\n".format(sep, sep, sep, sep, sep, sep, sep, sep)) for item in summary: for nr in item: if "HD" not in nr and "diff" not in nr: nr = nr.astype(float) nr = nr.astype(int) output_file.write("{}{}".format(nr, sep)) output_file.write("\n") output_file.write("sum{}".format(sep)) sumCol = map(int, sumCol) for el in sumCol: output_file.write("{}{}".format(el, sep)) output_file.write("{}{}".format(overallSum.astype(int), sep)) output_file.write("\n\n") def createFileHDwithinTag(summary, sumCol, overallSum, output_file, name, sep): output_file.write(name) output_file.write("\n") output_file.write("{}HD a{}HD b'{}HD b{}HD a'{}HD a+b{}sum{}\n".format(sep, sep, sep, sep, sep, sep, sep)) for item in summary: for nr in item: if "HD" not in nr: nr = nr.astype(float) nr = nr.astype(int) output_file.write("{}{}".format(nr, sep)) output_file.write("\n") output_file.write("sum{}".format(sep)) sumCol = map(int, sumCol) for el in sumCol: output_file.write("{}{}".format(el, sep)) output_file.write("{}{}".format(overallSum.astype(int), sep)) output_file.write("\n\n") def hamming(array1, array2): res = 99 * numpy.ones(len(array1)) i = 0 array2 = numpy.unique(array2) # remove duplicate sequences to decrease running time for a in array1: dist = numpy.array([sum(itertools.imap(operator.ne, a, b)) for b in array2]) # fastest res[i] = numpy.amin(dist[dist > 0]) # pick min distance greater than zero # print(i) i += 1 return res def hamming_difference(array1, array2, mate_b): array2 = numpy.unique(array2) # remove duplicate sequences to decrease running time array1_half = numpy.array([i[0:(len(i)) / 2] for i in array1]) # mate1 part1 array1_half2 = numpy.array([i[len(i) / 2:len(i)] for i in array1]) # mate1 part 2 array2_half = numpy.array([i[0:(len(i)) / 2] for i in array2]) # mate2 part1 array2_half2 = numpy.array([i[len(i) / 2:len(i)] for i in array2]) # mate2 part2 # diff11 = 999 * numpy.ones(len(array2)) # relativeDiffList = 999 * numpy.ones(len(array2)) # ham1 = 999 * numpy.ones(len(array2)) # ham2 = 999 * numpy.ones(len(array2)) # min_valueList = 999 * numpy.ones(len(array2)) # min_tagsList = 999 * numpy.ones(len(array2)) # diff11_zeros = 999 * numpy.ones(len(array2)) # min_tagsList_zeros = 999 * numpy.ones(len(array2)) diff11 = [] relativeDiffList = [] ham1 = [] ham2 = [] ham1min = [] ham2min = [] min_valueList = [] min_tagsList = [] diff11_zeros = [] min_tagsList_zeros = [] max_tag_list = [] i = 0 # counter, only used to see how many HDs of tags were already calculated if mate_b is False: # HD calculation for all a's half1_mate1 = array1_half half2_mate1 = array1_half2 half1_mate2 = array2_half half2_mate2 = array2_half2 elif mate_b is True: # HD calculation for all b's half1_mate1 = array1_half2 half2_mate1 = array1_half half1_mate2 = array2_half2 half2_mate2 = array2_half for a, b, tag in zip(half1_mate1, half2_mate1, array1): # exclude identical tag from array2, to prevent comparison to itself sameTag = numpy.where(array2 == tag)[0] indexArray2 = numpy.arange(0, len(array2), 1) index_withoutSame = numpy.delete(indexArray2, sameTag) # delete identical tag from the data # all tags without identical tag array2_half_withoutSame = half1_mate2[index_withoutSame] array2_half2_withoutSame = half2_mate2[index_withoutSame] array2_withoutSame = array2[index_withoutSame] # whole tag (=not splitted into 2 halfs) dist = numpy.array([sum(itertools.imap(operator.ne, a, c)) for c in array2_half_withoutSame]) # calculate HD of "a" in the tag to all "a's" or "b" in the tag to all "b's" min_index = numpy.where(dist == dist.min())[0] # get index of min HD min_value = dist[min_index] # get minimum HDs min_tag_half2 = array2_half2_withoutSame[min_index] # get all "b's" of the tag or all "a's" of the tag with minimum HD min_tag_array2 = array2_withoutSame[min_index] # get whole tag with min HD dist_second_half = numpy.array([sum(itertools.imap(operator.ne, b, e)) for e in min_tag_half2]) # calculate HD of "b" to all "b's" or "a" to all "a's" dist2 = [dist_second_half.max()] min_value = [dist.min()] max_index = numpy.where(dist_second_half == dist_second_half.max())[0] # get index of max HD max_tag = min_tag_array2[max_index] for d, d2 in zip(min_value, dist2): if mate_b is True: # half2, corrects the variable of the HD from both halfs if it is a or b ham2.append(d) ham2min.append(d2) else: # half1, corrects the variable of the HD from both halfs if it is a or b ham1.append(d) ham1min.append(d2) min_valueList.append(d + d2) min_tagsList.append(tag) difference1 = abs(d - d2) diff11.append(difference1) rel_difference = round(float(difference1) / (d + d2), 1) relativeDiffList.append(rel_difference) # tags which have identical parts: if d == 0 or d2 == 0: min_tagsList_zeros.append(numpy.array(tag)) difference1_zeros = abs(d - d2) # hd of non-identical part diff11_zeros.append(difference1_zeros) max_tag_list.append(numpy.array(max_tag)) i += 1 # print(i) # diff11 = [st for st in diff11 if st != 999] # ham1 = [st for st in ham1 if st != 999] # ham2 = [st for st in ham2 if st != 999] # min_valueList = [st for st in min_valueList if st != 999] # min_tagsList = [st for st in min_tagsList if st != 999] # relativeDiffList = [st for st in relativeDiffList if st != 999] # diff11_zeros = [st for st in diff11_zeros if st != 999] # min_tagsList_zeros = [st for st in min_tagsList_zeros if st != 999] return ([diff11, ham1, ham2, min_valueList, min_tagsList, relativeDiffList, diff11_zeros, min_tagsList_zeros, ham1min, ham2min, max_tag_list]) def readFileReferenceFree(file): with open(file, 'r') as dest_f: data_array = numpy.genfromtxt(dest_f, skip_header=0, delimiter='\t', comments='#', dtype='string') integers = numpy.array(data_array[:, 0]).astype(int) return(integers, data_array) def hammingDistanceWithFS(fs, ham): fs = numpy.asarray(fs) maximum = max(ham) minimum = min(ham) ham = numpy.asarray(ham) singletons = numpy.where(fs == 1)[0] data = ham[singletons] hd2 = numpy.where(fs == 2)[0] data2 = ham[hd2] hd3 = numpy.where(fs == 3)[0] data3 = ham[hd3] hd4 = numpy.where(fs == 4)[0] data4 = ham[hd4] hd5 = numpy.where((fs >= 5) & (fs <= 10))[0] data5 = ham[hd5] hd6 = numpy.where(fs > 10)[0] data6 = ham[hd6] list1 = [data, data2, data3, data4, data5, data6] return(list1, maximum, minimum) def familySizeDistributionWithHD(fs, ham, diff=False, rel=True): hammingDistances = numpy.unique(ham) fs = numpy.asarray(fs) ham = numpy.asarray(ham) bigFamilies2 = numpy.where(fs > 19)[0] if len(bigFamilies2) != 0: fs[bigFamilies2] = 20 maximum = max(fs) minimum = min(fs) if diff is True: hd0 = numpy.where(ham == 0)[0] data0 = fs[hd0] if rel is True: hd1 = numpy.where(ham == 0.1)[0] else: hd1 = numpy.where(ham == 1)[0] data = fs[hd1] if rel is True: hd2 = numpy.where(ham == 0.2)[0] else: hd2 = numpy.where(ham == 2)[0] data2 = fs[hd2] if rel is True: hd3 = numpy.where(ham == 0.3)[0] else: hd3 = numpy.where(ham == 3)[0] data3 = fs[hd3] if rel is True: hd4 = numpy.where(ham == 0.4)[0] else: hd4 = numpy.where(ham == 4)[0] data4 = fs[hd4] if rel is True: hd5 = numpy.where((ham >= 0.5) & (ham <= 0.8))[0] else: hd5 = numpy.where((ham >= 5) & (ham <= 8))[0] data5 = fs[hd5] if rel is True: hd6 = numpy.where(ham > 0.8)[0] else: hd6 = numpy.where(ham > 8)[0] data6 = fs[hd6] if diff is True: list1 = [data0, data, data2, data3, data4, data5, data6] else: list1 = [data, data2, data3, data4, data5, data6] return(list1, hammingDistances, maximum, minimum) def make_argparser(): parser = argparse.ArgumentParser(description='Hamming distance analysis of duplex sequencing data') parser.add_argument('--inputFile', help='Tabular File with three columns: ab or ba, tag and family size.') parser.add_argument('--inputName1') parser.add_argument('--sample_size', default=1000, type=int, help='Sample size of Hamming distance analysis.') parser.add_argument('--subset_tag', default=0, type=int, help='The tag is shortened to the given number.') parser.add_argument('--nproc', default=4, type=int, help='The tool runs with the given number of processors.') parser.add_argument('--only_DCS', action="store_false", help='Only tags of the DCSs are included in the HD analysis') parser.add_argument('--minFS', default=1, type=int, help='Only tags, which have a family size greater or equal than specified, are included in the HD analysis') parser.add_argument('--maxFS', default=0, type=int, help='Only tags, which have a family size smaller or equal than specified, are included in the HD analysis') parser.add_argument('--nr_above_bars', action="store_true", help='If no, values above bars in the histrograms are removed') parser.add_argument('--output_tabular', default="data.tabular", type=str, help='Name of the tabular file.') parser.add_argument('--output_pdf', default="data.pdf", type=str, help='Name of the pdf file.') parser.add_argument('--output_chimeras_tabular', default="data_chimeras.tabular", type=str, help='Name of the tabular file with all chimeric tags.') return parser def Hamming_Distance_Analysis(argv): parser = make_argparser() args = parser.parse_args(argv[1:]) file1 = args.inputFile name1 = args.inputName1 index_size = args.sample_size title_savedFile_pdf = args.output_pdf title_savedFile_csv = args.output_tabular output_chimeras_tabular = args.output_chimeras_tabular sep = "\t" onlyDuplicates = args.only_DCS minFS = args.minFS maxFS = args.maxFS nr_above_bars = args.nr_above_bars subset = args.subset_tag nproc = args.nproc # input checks if index_size < 0: print("index_size is a negative integer.") exit(2) if nproc <= 0: print("nproc is smaller or equal zero") exit(3) if subset < 0: print("subset_tag is smaller or equal zero.") exit(5) # PLOT plt.rcParams['axes.facecolor'] = "E0E0E0" # grey background color plt.rcParams['xtick.labelsize'] = 14 plt.rcParams['ytick.labelsize'] = 14 plt.rcParams['patch.edgecolor'] = "#000000" plt.rc('figure', figsize=(11.69, 8.27)) # A4 format name1 = name1.split(".tabular")[0] with open(title_savedFile_csv, "w") as output_file, PdfPages(title_savedFile_pdf) as pdf: print("dataset: ", name1) integers, data_array = readFileReferenceFree(file1) data_array = numpy.array(data_array) print("total nr of tags:", len(data_array)) n = [i for i, x in enumerate(data_array[:, 1]) if "N" in x] if len(n) != 0: # delete tags with N in the tag from data print("nr of tags with N's within tag:", len(n), float(len(n)) / len(data_array)) index_whole_array = numpy.arange(0, len(data_array), 1) index_withoutN_inTag = numpy.delete(index_whole_array, n) data_array = data_array[index_withoutN_inTag, :] integers = integers[index_withoutN_inTag] print("total nr of tags without Ns:", len(data_array)) data_array_whole_dataset = data_array int_f = numpy.array(data_array[:, 0]).astype(int) data_array = data_array[numpy.where(int_f >= minFS)] integers = integers[integers >= minFS] # select family size for tags if maxFS > 0: int_f2 = numpy.array(data_array[:, 0]).astype(int) data_array = data_array[numpy.where(int_f2 <= maxFS)] integers = integers[integers <= maxFS] print("min FS", min(integers)) print("max FS", max(integers)) tags = data_array[:, 2] seq = data_array[:, 1] if onlyDuplicates is True: # find all unique tags and get the indices for ALL tags, but only once u, index_unique, c = numpy.unique(numpy.array(seq), return_counts=True, return_index=True) d = u[c > 1] # get family sizes, tag for duplicates duplTags_double = integers[numpy.in1d(seq, d)] duplTags = duplTags_double[0::2] # ab of DCS duplTagsBA = duplTags_double[1::2] # ba of DCS duplTags_tag = tags[numpy.in1d(seq, d)][0::2] # ab duplTags_seq = seq[numpy.in1d(seq, d)][0::2] # ab - tags data_array = numpy.column_stack((duplTags, duplTags_seq)) data_array = numpy.column_stack((data_array, duplTags_tag)) integers = numpy.array(data_array[:, 0]).astype(int) print("DCS in whole dataset", len(data_array)) # HD analysis for a subset of the tag if subset > 0: tag1 = numpy.array([i[0:(len(i)) / 2] for i in data_array[:, 1]]) tag2 = numpy.array([i[len(i) / 2:len(i)] for i in data_array[:, 1]]) flanking_region_float = float((len(tag1[0]) - subset)) / 2 flanking_region = int(flanking_region_float) if flanking_region_float % 2 == 0: tag1_shorten = numpy.array([i[flanking_region:len(i) - flanking_region] for i in tag1]) tag2_shorten = numpy.array([i[flanking_region:len(i) - flanking_region] for i in tag2]) else: flanking_region_rounded = int(round(flanking_region, 1)) flanking_region_rounded_end = len(tag1[0]) - subset - flanking_region_rounded tag1_shorten = numpy.array( [i[flanking_region:len(i) - flanking_region_rounded_end] for i in tag1]) tag2_shorten = numpy.array( [i[flanking_region:len(i) - flanking_region_rounded_end] for i in tag2]) data_array_tag = numpy.array([i + j for i, j in zip(tag1_shorten, tag2_shorten)]) data_array = numpy.column_stack((data_array[:, 0], data_array_tag, data_array[:, 2])) print("length of tag:", len(data_array[0, 1])) # select sample: if no size given --> all vs. all comparison if index_size == 0: result = numpy.arange(0, len(data_array), 1) else: result = numpy.random.choice(len(integers), size=index_size, replace=False) # array of random sequences of size=index.size # unique_tags, unique_indices = numpy.unique(data_array[:, 1], return_index=True) # get only unique tags # result = numpy.random.choice(unique_indices, size=index_size, # replace=False) # array of random sequences of size=index.size # with open("index_result1_{}.pkl".format(app_f), "wb") as o: # pickle.dump(result, o, pickle.HIGHEST_PROTOCOL) # comparison random tags to whole dataset result1 = data_array[result, 1] # random tags result2 = data_array[:, 1] # all tags print("sample size:", len(result1)) # HD analysis of whole tag proc_pool = Pool(nproc) chunks_sample = numpy.array_split(result1, nproc) ham = proc_pool.map(partial(hamming, array2=result2), chunks_sample) proc_pool.close() proc_pool.join() ham = numpy.concatenate(ham).astype(int) # with open("HD_whole dataset_{}.txt".format(app_f), "w") as output_file1: # for h, tag in zip(ham, result1): # output_file1.write("{}\t{}\n".format(tag, h)) # HD analysis for chimeric reads # result2 = data_array_whole_dataset[:,1] proc_pool_b = Pool(nproc) diff_list_a = proc_pool_b.map(partial(hamming_difference, array2=result2, mate_b=False), chunks_sample) diff_list_b = proc_pool_b.map(partial(hamming_difference, array2=result2, mate_b=True), chunks_sample) proc_pool_b.close() proc_pool_b.join() diff = numpy.concatenate((numpy.concatenate([item[0] for item in diff_list_a]), numpy.concatenate([item_b[0] for item_b in diff_list_b]))).astype(int) HDhalf1 = numpy.concatenate((numpy.concatenate([item[1] for item in diff_list_a]), numpy.concatenate([item_b[1] for item_b in diff_list_b]))).astype(int) HDhalf2 = numpy.concatenate((numpy.concatenate([item[2] for item in diff_list_a]), numpy.concatenate([item_b[2] for item_b in diff_list_b]))).astype(int) minHDs = numpy.concatenate((numpy.concatenate([item[3] for item in diff_list_a]), numpy.concatenate([item_b[3] for item_b in diff_list_b]))).astype(int) minHD_tags = numpy.concatenate((numpy.concatenate([item[4] for item in diff_list_a]), numpy.concatenate([item_b[4] for item_b in diff_list_b]))) rel_Diff = numpy.concatenate((numpy.concatenate([item[5] for item in diff_list_a]), numpy.concatenate([item_b[5] for item_b in diff_list_b]))) diff_zeros = numpy.concatenate((numpy.concatenate([item[6] for item in diff_list_a]), numpy.concatenate([item_b[6] for item_b in diff_list_b]))).astype(int) minHD_tags_zeros = numpy.concatenate((numpy.concatenate([item[7] for item in diff_list_a]), numpy.concatenate([item_b[7] for item_b in diff_list_b]))) HDhalf1min = numpy.concatenate((numpy.concatenate([item[8] for item in diff_list_a]), numpy.concatenate([item_b[8] for item_b in diff_list_b]))).astype(int) HDhalf2min = numpy.concatenate((numpy.concatenate([item[9] for item in diff_list_a]), numpy.concatenate([item_b[9] for item_b in diff_list_b]))).astype(int) chimera_tags = numpy.concatenate(([item[10] for item in diff_list_a], [item_b[10] for item_b in diff_list_b])) chimera_tags = [x for x in chimera_tags if x != []] chimera_tags_new = [] for i in chimera_tags: if len(i) > 1: for t in i: chimera_tags_new.append(t) else: chimera_tags_new.extend(i) chimeras_dic = defaultdict(list) for t1, t2 in zip(minHD_tags_zeros, chimera_tags_new): chimeras_dic[t1].append(t2) lst_unique_chimeras = [] with open(output_chimeras_tabular, "w") as output_file1: unique_chimeras = numpy.unique(minHD_tags_zeros) sample_half_a = numpy.array([i[0:(len(i)) / 2] for i in unique_chimeras]) # mate1 part1 sample_half_b = numpy.array([i[len(i) / 2:len(i)] for i in unique_chimeras]) # mate1 part 2 output_file1.write("sample tag\tsimilar tag\n") for tag1, a, b in zip(unique_chimeras, sample_half_a, sample_half_b): max_tags = numpy.concatenate(chimeras_dic.get(tag1)) if tag1 in chimeras_dic.values(): continue else: lst_unique_chimeras.append(tag1) chimera_half_a = numpy.array([i[0:(len(i)) / 2] for i in max_tags]) # mate1 part1 chimera_half_b = numpy.array([i[len(i) / 2:len(i)] for i in max_tags]) # mate1 part 2 new_format = [] for i in range(len(max_tags)): if a == chimera_half_a[i]: max_tag = "*{}* {}".format(chimera_half_a[i], chimera_half_b[i]) new_format.append(max_tag) elif b == chimera_half_b[i]: max_tag = "{} *{}*".format(chimera_half_a[i], chimera_half_b[i]) new_format.append(max_tag) sample_tag = "{} {}".format(a, b) output_file1.write("{}\t{}\n".format(sample_tag, ", ".join(new_format))) output_file1.write( "This file contains all tags that were identified as chimeras as the first column and the corresponding tags which returned a Hamming distance of zero in either the first or the second half of the sample tag as the second column.\n " "The tags were separated by an empty space into their halves and the * marks the identical half.") nr_chimeric_tags = len(lst_unique_chimeras) print("nr of unique chimeras:", nr_chimeric_tags) lenTags = len(data_array) len_sample = len(result1) quant = numpy.array(data_array[result, 0]).astype(int) # family size for sample of tags seq = numpy.array(data_array[result, 1]) # tags of sample ham = numpy.asarray(ham) # HD for sample of tags if onlyDuplicates is True: # ab and ba strands of DCSs quant = numpy.concatenate((quant, duplTagsBA[result])) seq = numpy.tile(seq, 2) ham = numpy.tile(ham, 2) diff = numpy.tile(diff, 2) rel_Diff = numpy.tile(rel_Diff, 2) diff_zeros = numpy.tile(diff_zeros, 2) # prepare data for different kinds of plots # distribution of FSs separated after HD familySizeList1, hammingDistances, maximumXFS, minimumXFS = familySizeDistributionWithHD(quant, ham, rel=False) list1, maximumX, minimumX = hammingDistanceWithFS(quant, ham) # histogram of HDs separated after FS # get FS for all tags with min HD of analysis of chimeric reads # there are more tags than sample size in the plot, because one tag can have multiple minimas if onlyDuplicates: seqDic = defaultdict(list) for s, q in zip(seq, quant): seqDic[s].append(q) else: seqDic = dict(zip(seq, quant)) lst_minHD_tags = [] for i in minHD_tags: lst_minHD_tags.append(seqDic.get(i)) if onlyDuplicates: lst_minHD_tags = numpy.concatenate(([item[0] for item in lst_minHD_tags], [item_b[1] for item_b in lst_minHD_tags])).astype(int) # else: # lst_minHD_tags = numpy.concatenate(lst_minHD_tags) # histogram with absolute and relative difference between HDs of both parts of the tag listDifference1, maximumXDifference, minimumXDifference = hammingDistanceWithFS(lst_minHD_tags, diff) listRelDifference1, maximumXRelDifference, minimumXRelDifference = hammingDistanceWithFS(lst_minHD_tags, rel_Diff) # family size distribution separated after the difference between HDs of both parts of the tag # familySizeList1_diff, hammingDistances_diff, maximumXFS_diff, minimumXFS_diff = familySizeDistributionWithHD( # lst_minHD_tags, diff, diff=True, rel=False) # familySizeList1_reldiff, hammingDistances_reldiff, maximumXFS_reldiff, minimumXFS_reldiff = familySizeDistributionWithHD( # lst_minHD_tags, rel_Diff, diff=True, rel=True) # chimeric read analysis: tags which have HD=0 in one of the halfs if len(minHD_tags_zeros) != 0: lst_minHD_tags_zeros = [] for i in minHD_tags_zeros: lst_minHD_tags_zeros.append(seqDic.get(i)) # get family size for tags of chimeric reads if onlyDuplicates: lst_minHD_tags_zeros = numpy.concatenate(([item[0] for item in lst_minHD_tags_zeros], [item_b[1] for item_b in lst_minHD_tags_zeros])).astype(int) # histogram with HD of non-identical half listDifference1_zeros, maximumXDifference_zeros, minimumXDifference_zeros = hammingDistanceWithFS( lst_minHD_tags_zeros, diff_zeros) # plot Hamming Distance with Family size distribution plotHDwithFSD(list1=list1, maximumX=maximumX, minimumX=minimumX, pdf=pdf, subtitle="Hamming distance separated by family size", title_file1=name1, lenTags=lenTags, xlabel="HD", nr_above_bars=nr_above_bars) # Plot FSD with separation after plotFSDwithHD2(familySizeList1, maximumXFS, minimumXFS, originalCounts=quant, subtitle="Family size distribution separated by Hamming distance", pdf=pdf, relative=False, title_file1=name1, diff=False) # Plot HD within tags plotHDwithinSeq_Sum2(HDhalf1, HDhalf1min, HDhalf2, HDhalf2min, minHDs, pdf=pdf, lenTags=lenTags, title_file1=name1) # Plot difference between HD's separated after FSD plotHDwithFSD(listDifference1, maximumXDifference, minimumXDifference, pdf=pdf, subtitle="Delta Hamming distance within tags", title_file1=name1, lenTags=lenTags, xlabel="absolute delta HD", relative=False, nr_above_bars=nr_above_bars) plotHDwithFSD(listRelDifference1, maximumXRelDifference, minimumXRelDifference, pdf=pdf, subtitle="Chimera Analysis: relative delta Hamming distances", title_file1=name1, lenTags=lenTags, xlabel="relative delta HD", relative=True, nr_above_bars=nr_above_bars, nr_unique_chimeras=nr_chimeric_tags, len_sample=len_sample) # plots for chimeric reads if len(minHD_tags_zeros) != 0: # HD plotHDwithFSD(listDifference1_zeros, maximumXDifference_zeros, minimumXDifference_zeros, pdf=pdf,subtitle="Hamming distance of the non-identical half of chimeras", title_file1=name1, lenTags=lenTags, xlabel="HD", relative=False, nr_above_bars=nr_above_bars, nr_unique_chimeras=nr_chimeric_tags, len_sample=len_sample) # print all data to a CSV file # HD summary, sumCol = createTableHD(list1, "HD=") overallSum = sum(sumCol) # sum of columns in table # FSD summary5, sumCol5 = createTableFSD2(familySizeList1, diff=False) overallSum5 = sum(sumCol5) # HD of both parts of the tag summary9, sumCol9 = createTableHDwithTags([HDhalf1, HDhalf1min, HDhalf2, HDhalf2min, numpy.array(minHDs)]) overallSum9 = sum(sumCol9) # HD # absolute difference summary11, sumCol11 = createTableHD(listDifference1, "diff=") overallSum11 = sum(sumCol11) # relative difference and all tags summary13, sumCol13 = createTableHD(listRelDifference1, "diff=") overallSum13 = sum(sumCol13) # chimeric reads if len(minHD_tags_zeros) != 0: # absolute difference and tags where at least one half has HD=0 summary15, sumCol15 = createTableHD(listDifference1_zeros, "HD=") overallSum15 = sum(sumCol15) output_file.write("{}\n".format(name1)) output_file.write("number of tags per file{}{:,} (from {:,}) against {:,}\n\n".format(sep, len( numpy.concatenate(list1)), lenTags, lenTags)) # HD createFileHD(summary, sumCol, overallSum, output_file, "Hamming distance separated by family size", sep) # FSD createFileFSD2(summary5, sumCol5, overallSum5, output_file, "Family size distribution separated by Hamming distance", sep, diff=False) # output_file.write("{}{}\n".format(sep, name1)) output_file.write("\n") max_fs = numpy.bincount(integers[result]) output_file.write("max. family size in sample:{}{}\n".format(sep, max(integers[result]))) output_file.write("absolute frequency:{}{}\n".format(sep, max_fs[len(max_fs) - 1])) output_file.write( "relative frequency:{}{}\n\n".format(sep, float(max_fs[len(max_fs) - 1]) / sum(max_fs))) # HD within tags output_file.write( "The hamming distances were calculated by comparing each half of all tags against the tag(s) with the minimum Hamming distance per half.\n" "Since this calculation was repeated, but starting with the second half to find all possible chimeras in the data, the actual number of tags in the plots differs from the sample size entered by the user.\n" "In addition, both family sizes of one tag will be included in the plots if only tags of reads that can form a DCS were allowed.\n") output_file.write("length of one part of the tag = {}\n\n".format(len(data_array[0, 1]) / 2)) createFileHDwithinTag(summary9, sumCol9, overallSum9, output_file, "Hamming distance of each half in the tag", sep) createFileHD(summary11, sumCol11, overallSum11, output_file, "Absolute delta Hamming distances within the tag", sep) createFileHD(summary13, sumCol13, overallSum13, output_file, "Chimera analysis: relative delta Hamming distances", sep) if len(minHD_tags_zeros) != 0: output_file.write( "Chimeras:\nAll tags were filtered: only those tags where at least one half is identical with the half of the min. tag are kept.\nSo the Hamming distance of the non-identical half is shown.\n") output_file.write( "Be aware that the real number of chimeric tags (where rel. diff = 1) is not shown in the plot because of the above reasons.\n") output_file.write("real number of chimeric tags{}{}{}{}\n".format(sep, nr_chimeric_tags, sep, int(nr_chimeric_tags) / float(len_sample))) createFileHD(summary15, sumCol15, overallSum15, output_file, "Hamming distances of non-zero half", sep) output_file.write("\n") if __name__ == '__main__': sys.exit(Hamming_Distance_Analysis(sys.argv))