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| #!/usr/bin/env python3 | ||
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| """ | ||
| Name: ngsqc_plot.py | ||
| Created by: Tovah Markowitz | ||
| Date: 1/3/19 | ||
| Purpose: To take a number of NGSQC_report.txt files and convert into a figure. | ||
| Currently designed to work in case where all files have been moved from their original | ||
| subdirectories and the filename includes information of about the source data. All input | ||
| files must be in the noted directory (not recursive), end with ".NGSQC_report.txt", and | ||
| contain 'ext'. Output figures are named based upon 'ext'. | ||
| """ | ||
|
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| ########################################## | ||
| # Modules | ||
| import matplotlib | ||
| matplotlib.use('Agg') | ||
| import optparse | ||
| import os | ||
| import re | ||
| import matplotlib.pyplot as plt | ||
|
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| ########################################## | ||
| # Functions | ||
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| def read_ngsqc(ngsqcFile): | ||
| """Purpose: read in ngsqc file and extract similarity QCi data | ||
| """ | ||
| f = open(ngsqcFile, 'r') | ||
| ngsqc = f.readlines() | ||
| f.close() | ||
| ngsqc2 = [[],[]] | ||
| for i in range( len(ngsqc) ): | ||
| if re.search( "<", ngsqc[i] ): | ||
| tmp = ngsqc[i].strip() | ||
| tmp2 = re.search( "RCI < (.*)%: (.*)", tmp ) | ||
| ngsqc2[0].append(float(tmp2.group(1))) | ||
| ngsqc2[1].append(float(tmp2.group(2))) | ||
| return ngsqc2 | ||
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| def create_plot(ngsqcAll, ext, outfileName): | ||
| """ save data as a figure. | ||
| s90 is subsampling 90% and S50 is subsampling 50%. | ||
| RCI (Read count intensity) | ||
| """ | ||
| for ind in ngsqcAll: | ||
| plt.plot(ind[1][0],ind[1][1],'.-',label=ind[0]) | ||
| plt.xlabel('percent RCI difference') | ||
| plt.ylabel('Similarity QCi (s90/s50)') | ||
| plt.title(ext) | ||
| plt.legend() | ||
| # plt.show() | ||
| plt.savefig(outfileName) | ||
| plt.close("all") | ||
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| def all_ngsqc(directory, ext): | ||
| """ To get the ngsqc data for all NGSQC_report.txt files within a single folder | ||
| assumes that all files have been moved from their original subdirectories and | ||
| filename include information about the source of the data | ||
| """ | ||
| files = os.listdir(directory) | ||
| files2 = [ file for file in files if re.search("NGSQC_report.txt",file) ] | ||
| files3 = [ file for file in files if re.search(ext,file) ] | ||
| ngsqcAll = [ ] | ||
| regex = r"(.*)." + re.escape(ext) + r".NGSQC_report.txt" | ||
| for file in files3: | ||
| tmp = re.search(regex,file) | ||
| ngsqcAll.append([ tmp.group(1), read_ngsqc(directory + "/" + file) ]) | ||
| return ngsqcAll | ||
|
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| def name_outimage(directory, ext, group): | ||
| """this version uses ext to create the output file name | ||
| """ | ||
| if group == "": | ||
| outfileName = directory + "/NGSQC." + ext + ".pdf" | ||
| else: | ||
| outfileName = directory + "/" + group + ".NGSQC." + ext + ".pdf" | ||
| return outfileName | ||
|
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| ############################################# | ||
| # Main | ||
|
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| def main(): | ||
| desc=""" | ||
| To take a number of NGSQC_report.txt files and convert into a figure. | ||
| Currently designed to work in case where all files have been moved from their original | ||
| subdirectories and the filename includes information of about the source data. All input | ||
| files must be in the noted directory (not recursive), end with ".NGSQC_report.txt", and | ||
| contain 'ext'. Output figures are named based upon 'ext'. | ||
| """ | ||
|
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| parser = optparse.OptionParser(description=desc) | ||
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| parser.add_option('-d', dest='directory', default='', help='The name of the directory \ | ||
| with the NGSQC_report.txt files.') | ||
| parser.add_option('-e', dest='ext', default='', help='The string found in all \ | ||
| NGSQC_report.txt files. This string must be directly before ".NGSQC_report.txt".') | ||
| parser.add_option('-g', dest='group', default='', help='Any additional naming to add \ | ||
| the output file name.') | ||
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| (options,args) = parser.parse_args() | ||
| directory = options.directory | ||
| ext = options.ext | ||
| group = options.group | ||
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| outfileName = name_outimage(directory, ext, group) | ||
| ngsqcAll = all_ngsqc(directory, ext) | ||
| create_plot(ngsqcAll, ext, outfileName) | ||
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| #dir='/Users/markowitzte/Desktop/ngsqc' | ||
| #ext="sorted.Q5MDD" | ||
|
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| if __name__ == '__main__': | ||
| main() | ||
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