diff --git a/src/python/bamstats.py b/src/python/bamstats.py index 4eb0d5c..6001a92 100755 --- a/src/python/bamstats.py +++ b/src/python/bamstats.py @@ -30,6 +30,7 @@ import traceback import tempfile import json +import pandas scriptDir = os.path.abspath(os.path.dirname(__file__)) sys.path.append(os.path.abspath(os.path.join(scriptDir, '..', 'lib', 'python27'))) @@ -41,15 +42,28 @@ def main(): parser = argparse.ArgumentParser("BAM Statistics") - parser.add_argument("input", nargs=1) + parser.add_argument("input", nargs="+") parser.add_argument("-o", "--output", dest="output", help="Output CSV file name") args = parser.parse_args() - bs = Tools.bamstats.bamStats(args.input[0]) - print str(bs) + + all_results = [] + for inp in args.input: + bs = Tools.bamstats.bamStats(inp) + bs["FILE"] = inp + all_results.append(bs) + + all_results = pandas.concat(all_results) + all_results.reset_index(inplace=True) + + pandas.set_option("display.width", 10000) + pandas.set_option("display.max_colwidth", 2048) + pandas.set_option("display.max_columns", 10000) + pandas.set_option("display.max_rows", 1000000) + print str(all_results) if args.output: - bs.to_csv(args.output) + all_results.to_csv(args.output) if __name__ == '__main__':