# HG changeset patch # User mheinzl # Date 1526405462 14400 # Node ID 7adc48c8a03d334661126fa861cdef8b6f49a47d # Parent 69aa17354a6ee21d789486207defcea411a057cd planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 8d9bdadb5e154dadc455720c99700afbd9aafae9 diff -r 69aa17354a6e -r 7adc48c8a03d hd.py --- a/hd.py Tue May 15 11:27:27 2018 -0400 +++ b/hd.py Tue May 15 13:31:02 2018 -0400 @@ -30,7 +30,7 @@ from matplotlib.backends.backend_pdf import PdfPages from collections import Counter -def plotFSDwithHD2(familySizeList1,maximumXFS,minimumXFS, quant, +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"] @@ -78,9 +78,9 @@ legend = "\nmax. family size: \nabsolute frequency: \nrelative frequency: " plt.text(0.15, -0.08, legend, size=12, transform=plt.gcf().transFigure) - count = numpy.bincount(quant) # original counts + count = numpy.bincount(originalCounts) # original counts legend1 = "{}\n{}\n{:.5f}" \ - .format(max(quant), count[len(count) - 1], float(count[len(count) - 1]) / sum(count)) + .format(max(originalCounts), 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( @@ -508,14 +508,14 @@ 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] + #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]) @@ -525,28 +525,28 @@ integers = numpy.array(data_array[:, 0]).astype(int) return(integers, data_array) -def hammingDistanceWithFS(quant, ham): - quant = numpy.asarray(quant) +def hammingDistanceWithFS(fs, ham): + fs = numpy.asarray(fs) maximum = max(ham) minimum = min(ham) ham = numpy.asarray(ham) - singletons = numpy.where(quant == 1)[0] + singletons = numpy.where(fs == 1)[0] data = ham[singletons] - hd2 = numpy.where(quant == 2)[0] + hd2 = numpy.where(fs == 2)[0] data2 = ham[hd2] - hd3 = numpy.where(quant == 3)[0] + hd3 = numpy.where(fs == 3)[0] data3 = ham[hd3] - hd4 = numpy.where(quant == 4)[0] + hd4 = numpy.where(fs == 4)[0] data4 = ham[hd4] - hd5 = numpy.where((quant >= 5) & (quant <= 10))[0] + hd5 = numpy.where((fs >= 5) & (fs <= 10))[0] data5 = ham[hd5] - hd6 = numpy.where(quant > 10)[0] + hd6 = numpy.where(fs > 10)[0] data6 = ham[hd6] list1 = [data, data2, data3, data4, data5, data6] @@ -884,7 +884,7 @@ ########################## Plot FSD with separation after HD ############################################### ######################################################################################################################## plotFSDwithHD2(familySizeList1, maximumXFS, minimumXFS, - quant=quant, subtitle="Family size distribution separated by Hamming distance", + originalCounts=quant, subtitle="Family size distribution separated by Hamming distance", pdf=pdf,relative=False, title_file1=name_file, diff=False) ########################## Plot difference between HD's separated after FSD ########################################## @@ -903,9 +903,9 @@ ######################################################################################################################## plotFSDwithHD2(familySizeList1_diff, maximumXFS_diff, minimumXFS_diff, subtitle="Family size distribution separated by delta Hamming distances within the tags", - pdf=pdf,relative=False, diff=True, title_file1=name_file, quant=quant) + pdf=pdf,relative=False, diff=True, title_file1=name_file, originalCounts=quant) - plotFSDwithHD2(familySizeList1_reldiff, maximumXFS_reldiff, minimumXFS_reldiff, quant=quant, pdf=pdf, + plotFSDwithHD2(familySizeList1_reldiff, maximumXFS_reldiff, minimumXFS_reldiff, originalCounts=quant, pdf=pdf, subtitle="Family size distribution separated by delta Hamming distances within the tags", relative=True, diff=True, title_file1=name_file) @@ -919,7 +919,7 @@ ## FSD plotFSDwithHD2(familySizeList1_diff_zeros, maximumXFS_diff_zeros, minimumXFS_diff_zeros, - quant=quant, pdf=pdf, + originalCounts=quant, pdf=pdf, subtitle="Family size distribution separated by Hamming distance of the non-identical half of chimeras", relative=False, diff=False, title_file1=name_file) diff -r 69aa17354a6e -r 7adc48c8a03d hd.xml --- a/hd.xml Tue May 15 11:27:27 2018 -0400 +++ b/hd.xml Tue May 15 13:31:02 2018 -0400 @@ -1,5 +1,5 @@ - + python matplotlib