Mercurial > repos > mheinzl > hd
changeset 14:883e6381ba29 draft
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 38f5c032262361131c645812dd3dc639be6a5f4e
| author | mheinzl |
|---|---|
| date | Wed, 23 May 2018 14:14:10 -0400 |
| parents | 5b0a95f205ad |
| children | cf7874bb4934 |
| files | hd.py hd.xml |
| diffstat | 2 files changed, 88 insertions(+), 63 deletions(-) [+] |
line wrap: on
line diff
--- a/hd.py Tue May 15 14:23:10 2018 -0400 +++ b/hd.py Wed May 23 14:14:10 2018 -0400 @@ -14,7 +14,7 @@ # The tool can run on a certain number of processors, which can be defined by the user. # USAGE: python HDnew6_1Plot_FINAL.py --inputFile filename --inputName1 filename --inputFile2 filename2 --inputName2 filename2 --sample_size int/0 --sep "characterWhichSeparatesCSVFile" / -# --only_DCS True --FamilySize3 True --subset_tag True --nproc int --output_csv outptufile_name_csv --output_pdf outptufile_name_pdf +# --only_DCS True --FamilySize3 True --subset_tag True --nproc int --minFS int --maxFS int --nr_above_bars True/False--output_csv outptufile_name_csv --output_pdf outptufile_name_pdf import numpy import itertools @@ -92,7 +92,7 @@ plt.close("all") def plotHDwithFSD(list1,maximumX,minimumX, subtitle, lenTags, title_file1,pdf, - xlabel,relative=False): + xlabel,relative=False, nr_above_bars = True): if relative is True: step = 0.1 else: @@ -130,15 +130,16 @@ plt.ylim((0, maximumY * 1.2)) - 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) - + 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) @@ -146,11 +147,13 @@ plt.close("all") plt.clf() -def plotHDwithinSeq_Sum2(sum1, sum2,min_value, lenTags, title_file1, pdf): +def plotHDwithinSeq_Sum2(sum1, sum2,sum1min, sum2min, min_value, lenTags, title_file1, pdf): fig = plt.figure(figsize=(6, 8)) plt.subplots_adjust(bottom=0.1) - ham = [sum1, sum2,numpy.array(min_value)] # new hd within tags + #ham = [sum1, sum2,numpy.array(min_value)] # new hd within tags + ham = [sum1, sum2, sum1min, sum2min, numpy.array(min_value)] # new hd within tags + maximumX = numpy.amax(numpy.concatenate(ham)) minimumX = numpy.amin(numpy.concatenate(ham)) @@ -162,12 +165,15 @@ range1 = range(minimumX, maximumX + 2) counts = plt.hist(ham, align="left", rwidth=0.8, stacked=False, - label=[ "HD a", "HD b","HD a+b"], - bins=range1, color=[ "#58ACFA", "#FA5858","#585858"], edgecolor='black', linewidth=1) + # label=[ "HD a", "HD b","HD a+b"], + label=[ "HD a","HD b'", "HD b", "HD a'", "HD a+b"], + #bins=range1, color=[ "#58ACFA", "#FA5858","#585858"], + 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("Hamming Distance", fontsize=14) + plt.xlabel("HD", fontsize=14) plt.ylabel("Absolute Frequency", fontsize=14) plt.grid(b=True, which='major', color='#424242', linestyle=':') @@ -448,6 +454,8 @@ relativeDiffList = [] ham1 = [] ham2 = [] + ham1min = [] + ham2min = [] min_valueList = [] min_tagsList = [] diff11_zeros = [] @@ -488,13 +496,18 @@ if mate_b is True: # half2, corrects the variable of the HD from both halfs if it is a or b d = d_2 d2 = d_1 + ham2.append(d) + ham2min.append(d2) else: # half1, corrects the variable of the HD from both halfs if it is a or b d = d_1 d2 = d_2 + ham1.append(d) + ham1min.append(d2) + min_valueList.append(d + d2) min_tagsList.append(tag) - ham1.append(d) - ham2.append(d2) + # ham1.append(d) + # ham2.append(d2) difference1 = abs(d - d2) diff11.append(difference1) rel_difference = round(float(difference1) / (d + d2), 1) @@ -517,7 +530,7 @@ #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]) + return ([diff11, ham1, ham2, min_valueList, min_tagsList, relativeDiffList, diff11_zeros, min_tagsList_zeros, ham1min, ham2min]) def readFileReferenceFree(file): with open(file, 'r') as dest_f: @@ -632,7 +645,9 @@ 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", # default=False, type=bool, + help='If no, values above bars in the histrograms are removed') + parser.add_argument('--output_csv', default="data.csv", type=str, help='Name of the csv file.') parser.add_argument('--output_pdf', default="data.pdf", type=str, @@ -665,6 +680,8 @@ onlyDuplicates = args.only_DCS minFS = args.minFS maxFS = args.maxFS + nr_above_bars = args.nr_above_bars + subset = args.subset_tag nproc = args.nproc @@ -817,7 +834,10 @@ 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) # with open("HD_within tag_{}.txt".format(app_f), "w") as output_file2: # for d, s1, s2, hd, rel_d, tag in zip(diff, HDhalf1, HDhalf2, minHDs, rel_Diff, minHD_tags): # output_file2.write( @@ -870,44 +890,46 @@ familySizeList1_diff_zeros, hammingDistances_diff_zeros, maximumXFS_diff_zeros, minimumXFS_diff_zeros = familySizeDistributionWithHD( lst_minHD_tags_zeros, diff_zeros, diff=False, rel=False) - ########################## Plot HD within tags ######################################################## - ###################################################################################################################### - plotHDwithinSeq_Sum2(HDhalf1, HDhalf2, minHDs, pdf=pdf, lenTags=lenTags, title_file1=name_file) - ##################################################################################################################### ################## 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=name_file, - lenTags=lenTags,xlabel="Hamming distance") + lenTags=lenTags,xlabel="HD", nr_above_bars=nr_above_bars) - ########################## Plot FSD with separation after HD ############################################### - ######################################################################################################################## + ########################## 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=name_file, diff=False) - ########################## Plot difference between HD's separated after FSD ########################################## - ######################################################################################################################## + ########################## Plot HD within tags ######################################################## + ###################################################################################################################### + # plotHDwithinSeq_Sum2(HDhalf1, HDhalf2, minHDs, pdf=pdf, lenTags=lenTags, title_file1=name_file) + plotHDwithinSeq_Sum2(HDhalf1, HDhalf2, HDhalf1min, HDhalf2min, minHDs, pdf=pdf, lenTags=lenTags, title_file1=name_file) + + + ########################## Plot difference between HD's separated after FSD #################################### + ###################################################################################################################### plotHDwithFSD(listDifference1, maximumXDifference, minimumXDifference, pdf=pdf, subtitle="Delta Hamming distance within tags", title_file1=name_file, lenTags=lenTags, - xlabel="absolute delta Hamming distance", relative=False) + xlabel="absolute delta HD", relative=False, nr_above_bars=nr_above_bars) plotHDwithFSD(listRelDifference1, maximumXRelDifference, minimumXRelDifference, pdf=pdf, - subtitle="Relative delta Hamming distances within tags", + subtitle="Chimera Analysis: relative delta Hamming distances", title_file1=name_file, lenTags=lenTags, - xlabel="relative delta Hamming distance", relative=True) + xlabel="relative delta HD", relative=True, nr_above_bars=nr_above_bars) #################### Plot FSD separated after difference between HD's ##################################### ######################################################################################################################## - 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, originalCounts=quant) + # 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, originalCounts=quant) - 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) + # 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) # plots for chimeric reads @@ -915,13 +937,13 @@ ## HD plotHDwithFSD(listDifference1_zeros, maximumXDifference_zeros, minimumXDifference_zeros, pdf=pdf, subtitle="Hamming distance of the non-identical half of chimeras", - title_file1=name_file, lenTags=lenTags,xlabel="Hamming distance", relative=False) + title_file1=name_file, lenTags=lenTags,xlabel="HD", relative=False, nr_above_bars=nr_above_bars) ## FSD - plotFSDwithHD2(familySizeList1_diff_zeros, maximumXFS_diff_zeros, minimumXFS_diff_zeros, - 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) + # plotFSDwithHD2(familySizeList1_diff_zeros, maximumXFS_diff_zeros, minimumXFS_diff_zeros, + # 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) ### print all data to a CSV file #### HD #### @@ -946,11 +968,11 @@ ## FSD # absolute difference - summary19, sumCol19 = createTableFSD2(familySizeList1_diff) - overallSum19 = sum(sumCol19) + # summary19, sumCol19 = createTableFSD2(familySizeList1_diff) + # overallSum19 = sum(sumCol19) # relative difference - summary21, sumCol21 = createTableFSD2(familySizeList1_reldiff) - overallSum21 = sum(sumCol21) + # summary21, sumCol21 = createTableFSD2(familySizeList1_reldiff) + # overallSum21 = sum(sumCol21) # chimeric reads if len(minHD_tags_zeros) != 0: @@ -958,8 +980,8 @@ summary15, sumCol15 = createTableHD(listDifference1_zeros, "diff=") overallSum15 = sum(sumCol15) # absolute difference and tags where at least one half has HD=0 - summary23, sumCol23 = createTableFSD2(familySizeList1_diff_zeros, diff=False) - overallSum23 = sum(sumCol23) + # summary23, sumCol23 = createTableFSD2(familySizeList1_diff_zeros, diff=False) + # overallSum23 = sum(sumCol23) output_file.write("{}\n".format(name_file)) output_file.write("number of tags per file{}{:,} (from {:,}) against {:,}\n\n".format(sep, len( @@ -994,23 +1016,23 @@ createFileHD(summary11, sumCol11, overallSum11, output_file, "Absolute delta Hamming distances within the tag", sep) createFileHD(summary13, sumCol13, overallSum13, output_file, - "Relative delta Hamming distances within the tag", sep) + "Chimera analysis: relative delta Hamming distances", sep) - createFileFSD2(summary19, sumCol19, overallSum19, output_file, - "Family size distribution separated by absolute delta Hamming distance", - sep) - createFileFSD2(summary21, sumCol21, overallSum21, output_file, - "Family size distribution separated by relative delta Hamming distance", - sep, rel=True) + # createFileFSD2(summary19, sumCol19, overallSum19, output_file, + # "Family size distribution separated by absolute delta Hamming distance", + # sep) + # createFileFSD2(summary21, sumCol21, overallSum21, output_file, + # "Family size distribution separated by relative delta Hamming distance", + # sep, rel=True) if len(minHD_tags_zeros) != 0: output_file.write( - "Identifiaction of chimeric reads:\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 compared.\n") + "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 compared.\n") createFileHD(summary15, sumCol15, overallSum15, output_file, "Hamming distances of non-zero half", sep) - createFileFSD2(summary23, sumCol23, overallSum23, output_file, - "Family size distribution separated by Hamming distance of non-zero half", - sep, diff=False) + # createFileFSD2(summary23, sumCol23, overallSum23, output_file, + # "Family size distribution separated by Hamming distance of non-zero half", + # sep, diff=False) output_file.write("\n")
--- a/hd.xml Tue May 15 14:23:10 2018 -0400 +++ b/hd.xml Wed May 23 14:14:10 2018 -0400 @@ -1,12 +1,13 @@ <?xml version="1.0" encoding="UTF-8"?> -<tool id="hd" name="Duplex Sequencing Analysis:" version="0.0.14"> +<tool id="hd" name="Duplex Sequencing Analysis: hd" version="0.0.15"> <requirements> <requirement type="package" version="2.7">python</requirement> <requirement type="package" version="1.4">matplotlib</requirement> </requirements> <description>Hamming distance (HD) analysis of tags</description> <command> - python2 $__tool_directory__/hd.py --inputFile "$inputFile" --inputName1 "$inputFile.name" --inputFile2 "$inputFile2" --inputName2 "$inputFile2.name" --sample_size $sampleSize --sep $separator --subset_tag $subsetTag --nproc $nproc $onlyDCS --minFS $minFS --maxFS $maxFS --output_pdf $output_pdf --output_csv $output_csv + python2 $__tool_directory__/hd.py --inputFile "$inputFile" --inputName1 "$inputFile.name" --inputFile2 "$inputFile2" --inputName2 "$inputFile2.name" --sample_size $sampleSize --sep $separator --subset_tag $subsetTag --nproc $nproc $onlyDCS --minFS $minFS --maxFS $maxFS + $nr_above_bars --output_pdf $output_pdf --output_csv $output_csv #if $inputFile2: --output_pdf2 $output_pdf2 --output_csv2 $output_csv2 #end if @@ -21,6 +22,8 @@ <param name="onlyDCS" type="boolean" label="only DCS in the analysis?" truevalue="" falsevalue="--only_DCS" checked="False" help="Only tags, which have a partner tag in the dataset, are included in the analysis."/> <param name="subsetTag" type="integer" label="shorten tag in the analysis?" value="0" help="An analysis with shorter tag length, which is specified by this parameter, is simulated. If this parameter is 0 (by default), the tag with its original length is used in the analysis."/> <param name="nproc" type="integer" label="number of processors" value="8" help="Number of processor used for computing."/> + <param name="nr_above_bars" type="boolean" label="include numbers above bars?" truevalue="" falsevalue="--nr_above_bars" checked="False" help="The absolute and relative values of the bar can be included or removed in the plot. "/> + </inputs> <outputs> <data name="output_csv" format="csv"/>