| Previous changeset 12:5cc9b35b5a52 (2012-10-08) Next changeset 14:ddfef7773c2d (2014-05-09) |
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Commit message:
Deleted selected files |
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removed:
EMS_VariantDensityMapping.py |
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| diff -r 5cc9b35b5a52 -r 890eb4a380df EMS_VariantDensityMapping.py --- a/EMS_VariantDensityMapping.py Mon Oct 08 16:18:36 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,126 +0,0 @@ -#!/usr/bin/python - -import re -import sys -import optparse -import csv -from rpy import * - -def main(): - parser = optparse.OptionParser() - parser.add_option('-s', '--snp_vcf', dest = 'snp_vcf', action = 'store', type = 'string', default = None, help = "VCF of SNPs") - parser.add_option('-c', '--hist_color', dest = 'hist_color', action = 'store', type = 'string', default = "darkgray", help = "Color for 1Mb histograms") - parser.add_option('-y', '--ylim', dest = 'ylim', action = 'store', type = 'int', default= 100, help = "Upper limit of Y axis") - parser.add_option('-z', '--standardize', dest = 'standardize', default= 'false', help = "Standardize X-axis") - parser.add_option('-e', '--ems', dest = 'ems', default= 'false', help = "Whether EMS variants should be filtered for") - parser.add_option('-o', '--output', dest = 'plot_output', action = 'store', type = 'string', default = 'EMS_Variant_Density_Plot.pdf', help = "Output file name of plot") - (options, args) = parser.parse_args() - - - i, ii, iii, iv, v, x = parse_snp_vcf(snp_vcf = options.snp_vcf, ems=options.ems) - create_histograms(plot_output = options.plot_output, hist_color=options.hist_color, ylim=options.ylim, ems=options.ems, standardize=options.standardize, i = i, ii = ii, iii = iii, iv = iv, v = v, x = x) - -def create_histograms(plot_output = None, hist_color=None, ylim=None, ems=None, standardize=None , i = None, ii = None, iii = None, iv = None, v = None, x = None): - breaks = { 'I' : 16 , 'II' : 16, 'III' : 14, 'IV' : 18, 'V' : 21, 'X' : 18 } - - try: - r.pdf(plot_output, 8, 8) - if len(i) > 0: - plot_data(position_list = i, chr = "I", breaks = breaks["I"], hist_color=hist_color, ylim=ylim, ems=ems, standardize=standardize) - if len(ii) > 0: - plot_data(position_list = ii, chr = "II", breaks = breaks["II"], hist_color=hist_color, ylim=ylim, ems=ems, standardize=standardize) - if len(iii) > 0: - plot_data(position_list = iii, chr = "III", breaks = breaks["III"], hist_color=hist_color, ylim=ylim, ems=ems, standardize=standardize) - if len(iv) > 0: - plot_data(position_list = iv, chr = "IV", breaks = breaks["IV"], hist_color=hist_color, ylim=ylim, ems=ems, standardize=standardize) - if len(v) > 0: - plot_data(position_list = v, chr = "V", breaks = breaks["V"], hist_color=hist_color, ylim=ylim, ems=ems, standardize=standardize) - if len(x) > 0: - plot_data(position_list = x, chr = "X", breaks = breaks["X"], hist_color=hist_color, ylim=ylim, ems=ems, standardize=standardize) - r.dev_off() - except Exception as inst: - print inst - print "There was an error creating the plot pdf... Please try again" - -def parse_snp_vcf(snp_vcf = None, ems=None): - i_file = open(snp_vcf, 'rU') - reader = csv.reader(i_file, delimiter = '\t', quoting = csv.QUOTE_NONE) - - skip_headers(reader = reader, i_file = i_file) - - i_position_list = [] - ii_position_list = [] - iii_position_list = [] - iv_position_list = [] - v_position_list = [] - x_position_list = [] - - for row in reader: - chromosome = row[0].upper() - chromosome = re.sub("chr", "", chromosome, flags = re.IGNORECASE) - chromosome = re.sub("CHROMOSOME_", "", chromosome, flags = re.IGNORECASE) - - position = row[1] - ref_allele = row[3] - alt_allele = row[4] - - if (ems=='true'): - if (ref_allele =="G" or ref_allele =="C") and (alt_allele =="A" or alt_allele =="T"): - if chromosome == "I": - i_position_list.append(position) - elif chromosome == "II": - ii_position_list.append(position) - elif chromosome == "III": - iii_position_list.append(position) - elif chromosome == "IV": - iv_position_list.append(position) - elif chromosome == "V": - v_position_list.append(position) - elif chromosome == "X": - x_position_list.append(position) - elif (ems=='false'): - if chromosome == "I": - i_position_list.append(position) - elif chromosome == "II": - ii_position_list.append(position) - elif chromosome == "III": - iii_position_list.append(position) - elif chromosome == "IV": - iv_position_list.append(position) - elif chromosome == "V": - v_position_list.append(position) - elif chromosome == "X": - x_position_list.append(position) - - return i_position_list, ii_position_list, iii_position_list, iv_position_list, v_position_list, x_position_list - -def skip_headers(reader = None, i_file = None): - # count headers - comment = 0 - while reader.next()[0].startswith('#'): - comment = comment + 1 - - # skip headers - i_file.seek(0) - for i in range(0, comment): - reader.next() - -def plot_data(position_list = None, chr = None, breaks = None, hist_color=None, ylim = None, ems=None, standardize=None): - positions = ",".join(map(str, map(lambda x: float(x) / 1000000, position_list))) - positions = "c(" + positions + ")" - - if (standardize=='true'): - r("hist(" + positions + ", xlim=c(0,21), ylim=c(0, %d "%ylim +"),col='"+ hist_color + "', breaks = seq(0, as.integer( ' " + str(breaks) + " '), by=1), main = 'LG " + chr + "', ylab = 'Frequency Of SNPs', xlab = 'Location (Mb)')") - r("hist(" + positions + ", xlim=c(0,21), add=TRUE, ylim=c(0, %d "%ylim +"), col=rgb(1, 0, 0, 1), breaks = seq(0, as.integer( ' " + str(breaks) + " '), by=.5), main = 'Chr " + chr + "', ylab = 'Number Of SNPs', xlab = 'Location (Mb)')") - r("axis(1, at=seq(0, 21, by=1), labels=FALSE, tcl=-0.5)") - r("axis(1, at=seq(0, 21, by=0.5), labels=FALSE, tcl=-0.25)") - elif (standardize=='false'): - r("hist(" + positions + ", xlim=c(0,as.integer( ' " + str(breaks) + " ')), ylim=c(0, %d "%ylim +"),col='"+ hist_color + "', breaks = seq(0, as.integer( ' " + str(breaks) + " '), by=1), main = 'LG " + chr + "', ylab = 'Frequency Of SNPs', xlab = 'Location (Mb)')") - r("hist(" + positions + ", xlim=c(0,as.integer( ' " + str(breaks) + " ')), add=TRUE, ylim=c(0, %d "%ylim +"), col=rgb(1, 0, 0, 1), breaks = seq(0, as.integer( ' " + str(breaks) + " '), by=.5), main = 'Chr " + chr + "', ylab = 'Number Of SNPs', xlab = 'Location (Mb)')") - r("axis(1, at=seq(0, as.integer( ' " + str(breaks) + " '), by=1), labels=FALSE, tcl=-0.5)") - r("axis(1, at=seq(0, as.integer( ' " + str(breaks) + " '), by=0.5), labels=FALSE, tcl=-0.25)") - - - -if __name__ == "__main__": - main() |