Mercurial > repos > mheinzl > fsd
changeset 43:f72593bcc8ee 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 12:38:15 -0400 |
| parents | 321a4871564b |
| children | a76af7fd9fca |
| files | fsd.py fsd.xml test-data/fsd_output1.tab test-data/fsd_output2.tab |
| diffstat | 4 files changed, 25 insertions(+), 1 deletions(-) [+] |
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--- a/fsd.py Wed Aug 14 08:29:27 2019 -0400 +++ b/fsd.py Wed Aug 14 12:38:15 2019 -0400 @@ -557,6 +557,9 @@ 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("{}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)) output_file.write("{}{}{}{}{:.3f}{}{:.3f}{}{}{}{:.3f}{}{}{}{:.3f}{}{}{}{}\n\n".format(
--- a/fsd.xml Wed Aug 14 08:29:27 2019 -0400 +++ b/fsd.xml Wed Aug 14 12:38:15 2019 -0400 @@ -1,6 +1,6 @@ <?xml version="1.0" encoding="UTF-8"?> <!-- galaxy version 16.04 --> -<tool id="fsd" name="FSD" version="1.0.3"> +<tool id="fsd" name="FSD" version="1.0.4"> <description>: Family Size Distribution of duplex sequencing tags</description> <requirements> <requirement type="package" version="2.7">python</requirement>
--- a/test-data/fsd_output1.tab Wed Aug 14 08:29:27 2019 -0400 +++ b/test-data/fsd_output1.tab Wed Aug 14 12:38:15 2019 -0400 @@ -55,6 +55,9 @@ absolute frequency: 1 relative frequency: 0.009 +median family size: 1.0 +mean family size: 3.375 + singletons: family size > 20: length of dataset: 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 fsd_data1.tab 63 0.562 0.167 1 0.009 21 0.056 112 378 @@ -105,6 +108,9 @@ absolute frequency: 1 relative frequency: 0.009 +median family size: 1.0 +mean family size: 3.375 + singletons: family size > 20: length of dataset: 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 fsd_data2.tab 63 0.562 0.167 1 0.009 21 0.056 112 378 @@ -155,6 +161,9 @@ absolute frequency: 1 relative frequency: 0.009 +median family size: 1.0 +mean family size: 3.375 + singletons: family size > 20: length of dataset: 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 fsd_data3.tab 63 0.562 0.167 1 0.009 21 0.056 112 378 @@ -205,6 +214,9 @@ absolute frequency: 1 relative frequency: 0.009 +median family size: 1.0 +mean family size: 3.375 + singletons: family size > 20: length of dataset: 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 fsd_data4.tab 63 0.562 0.167 1 0.009 21 0.056 112 378
--- a/test-data/fsd_output2.tab Wed Aug 14 08:29:27 2019 -0400 +++ b/test-data/fsd_output2.tab Wed Aug 14 12:38:15 2019 -0400 @@ -55,6 +55,9 @@ absolute frequency: 1 relative frequency: 0.009 +median family size: 1.0 +mean family size: 3.375 + singletons: family size > 20: length of dataset: 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 fsd_data1.tab 63 0.562 0.167 1 0.009 21 0.056 112 378 @@ -105,6 +108,9 @@ absolute frequency: 1 relative frequency: 0.009 +median family size: 1.0 +mean family size: 3.375 + singletons: family size > 20: length of dataset: 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 fsd_data2.tab 63 0.562 0.167 1 0.009 21 0.056 112 378 @@ -155,6 +161,9 @@ absolute frequency: 1 relative frequency: 0.009 +median family size: 1.0 +mean family size: 3.375 + singletons: family size > 20: length of dataset: 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 fsd_data3.tab 63 0.562 0.167 1 0.009 21 0.056 112 378