From 9c538be312a7301c3952b261dc004517b6e0c086 Mon Sep 17 00:00:00 2001 From: Jon Palmer Date: Wed, 31 Jul 2019 21:50:14 -0700 Subject: [PATCH] fix for #57 --- amptk/summarize_taxonomy.py | 11 +++++++---- 1 file changed, 7 insertions(+), 4 deletions(-) diff --git a/amptk/summarize_taxonomy.py b/amptk/summarize_taxonomy.py index afb1271..1bb2165 100755 --- a/amptk/summarize_taxonomy.py +++ b/amptk/summarize_taxonomy.py @@ -150,8 +150,11 @@ def main(args): otuDict[cols[0]] = {'score': score, 'domain': None, 'kingdom': None, 'phylum': None, 'class': None, 'order': None, 'family': None, 'genus': None, 'species': None} for w in tax.split(','): - level, value = w.split(':') - otuDict[cols[0]][taxLookup[level]] = value + try: + level, value = w.split(':') + otuDict[cols[0]][taxLookup[level]] = value + except ValueError: + pass #now populate sample dictionary for z,y in enumerate(cols): if z == 0 or z == len(cols)-1: @@ -181,12 +184,12 @@ def main(args): taxSummary[sampleID][taxInfo] += Count df = pd.DataFrame(taxSummary) if len(df.index.values.tolist()) == 1 and 'Unclassified' == df.index.values.tolist()[0]: - continue + continue if args.percent: df = (100. * df / df.sum()) df.transpose().to_csv(args.out+'.'+taxLevel+'.csv') if args.graphs: - drawBarGraph(df.transpose(), args.out+'.'+taxLevel+'.'+args.format, args=args) + drawBarGraph(df.transpose(), args.out+'.'+taxLevel+'.'+args.format, args=args) if __name__ == "__main__": main(sys.argv[1:])