| Previous changeset 14:0412ae182f38 (2016-04-15) Next changeset 16:8dae9fdd2afe (2016-04-15) |
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pieplot_macs/pieplots_macs.py |
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| diff -r 0412ae182f38 -r 4ec317901ac3 pieplot_macs/pieplots_macs.py --- a/pieplot_macs/pieplots_macs.py Fri Apr 15 11:31:29 2016 -0400 +++ b/pieplot_macs/pieplots_macs.py Fri Apr 15 11:46:20 2016 -0400 |
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| @@ -26,11 +26,11 @@ import pandas as pd from argparse import ArgumentParser -def map_peaks(gene,peak,outfile,macsFlag): +def map_peaks(gene, peak, outfile, macsFlag): genefile = open(gene, 'r') peakfile = open(peak, 'r') - types = {'promoter':0, 'after':0, 'intron':0, 'exon': 0} + types = {'promoter':0, 'after':0, 'intron':0, 'exon':0} #read mapped gene file, store closest map for each peak peaks={} #{chrom:{peakStart:[dist, type]}} @@ -46,7 +46,6 @@ maptype = words[14] if maptype == 'gene': maptype = words[15] - else: try: start = int(words[3]) @@ -58,7 +57,6 @@ print 'there probably were not enough columns in the genefile' pass - if chrom not in peaks: #new chrom peaks[chrom] = {start:[dist,maptype]} @@ -102,10 +100,10 @@ plt.pie(fracs, labels=labels) #, autopct='%1.1f%%') #Export data frame with all the counts - indexDataFrame = ['exon','intron','promoter','intergenic','after'] - df = pd.DataFrame(data=fracs, index=indexDataFrame) - dfFileName = outfile.replace("pdf","csv") - df.to_csv(dfFileName, sep=',') + # indexDataFrame = ['exon','intron','promoter','intergenic','after'] + # df = pd.DataFrame(data=fracs, index=indexDataFrame) + # dfFileName = outfile.replace("pdf","csv") + # df.to_csv(dfFileName, sep=',') #plt.title('MACS peaks in %s'%(name)) plt.figtext(.5, .1, 'Total: %i'%totalpks, ha='center') fig.savefig(outfile) |