Mercurial > repos > mheinzl > fsd
changeset 44:a76af7fd9fca draft
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/fsd commit 033dd7b750f68e8aa68f327d7d72bd311ddbee4e-dirty
| author | mheinzl |
|---|---|
| date | Wed, 14 Aug 2019 13:03:14 -0400 |
| parents | f72593bcc8ee |
| children | 6651e76baca1 |
| files | fsd.py fsd.xml |
| diffstat | 2 files changed, 5 insertions(+), 5 deletions(-) [+] |
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--- a/fsd.py Wed Aug 14 12:38:15 2019 -0400 +++ b/fsd.py Wed Aug 14 13:03:14 2019 -0400 @@ -551,14 +551,14 @@ plt.close() # write same information to a csv file - count = numpy.bincount(integers) # original counts of family sizes + count = numpy.bincount(data_o) # original counts of family sizes output_file.write("\nDataset:{}{}\n".format(sep, name_file)) - output_file.write("max. family size:{}{}\n".format(sep, max(integers))) + output_file.write("max. family size:{}{}\n".format(sep, max(data_o))) output_file.write("absolute frequency:{}{}\n".format(sep, count[len(count) - 1])) output_file.write("relative frequency:{}{:.3f}\n\n".format(sep, float(count[len(count) - 1]) / sum(count))) - output_file.write("median family size:{}{}\n".format(sep, numpy.median(numpy.array(integers)))) - output_file.write("mean family size:{}{}\n\n".format(sep, numpy.mean(numpy.array(integers)))) + output_file.write("median family size:{}{}\n".format(sep, numpy.median(numpy.array(data_o)))) + output_file.write("mean family size:{}{}\n\n".format(sep, numpy.mean(numpy.array(data_o)))) output_file.write("{}singletons:{}{}{}family size > 20:{}{}{}{}length of dataset:\n".format(sep, sep, sep, sep, sep, sep, sep, sep)) output_file.write("{}nr. of tags{}rel. freq of tags{}rel.freq of PE reads{}nr. of tags{}rel. freq of tags{}nr. of PE reads{}rel. freq of PE reads{}total nr. of tags{}total nr. of PE reads\n".format(sep, sep, sep, sep, sep, sep, sep, sep, sep))
--- a/fsd.xml Wed Aug 14 12:38:15 2019 -0400 +++ b/fsd.xml Wed Aug 14 13:03:14 2019 -0400 @@ -1,6 +1,6 @@ <?xml version="1.0" encoding="UTF-8"?> <!-- galaxy version 16.04 --> -<tool id="fsd" name="FSD" version="1.0.4"> +<tool id="fsd" name="FSD" version="1.0.5"> <description>: Family Size Distribution of duplex sequencing tags</description> <requirements> <requirement type="package" version="2.7">python</requirement>