Mercurial > repos > yhoogstrate > edger_with_design_matrix
comparison edgeR_Design_Matrix.py @ 10:a6ce4b7710d8 draft
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| author | yhoogstrate |
|---|---|
| date | Thu, 09 Jan 2014 05:42:44 -0500 |
| parents | 82bff7137e81 |
| children |
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| 9:82bff7137e81 | 10:a6ce4b7710d8 |
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| 160 fh.close() | 160 fh.close() |
| 161 | 161 |
| 162 if __name__=="__main__": | 162 if __name__=="__main__": |
| 163 parser = argparse.ArgumentParser(description="Create an edgeR design matrix with read-count datasets.") | 163 parser = argparse.ArgumentParser(description="Create an edgeR design matrix with read-count datasets.") |
| 164 parser.add_argument("-o","--output", help="Output file, '-' for stdout.",required=True) | 164 parser.add_argument("-o","--output", help="Output file, '-' for stdout.",required=True) |
| 165 parser.add_argument("-u","--unpaired-samples", nargs="+", help='Unpaired sample files.') | 165 parser.add_argument("-u","--unpaired-samples", nargs="*", help='Unpaired sample files.') |
| 166 parser.add_argument("-p","--paired-samples", nargs="+", help='Paired sample files: pat_x_sample_1.txt, .') | 166 parser.add_argument("-p","--paired-samples", nargs="*", help='Paired sample files: pat_x_sample_1.txt, .') |
| 167 parser.add_argument("-t","--treatments", nargs="+", help='Treatment conditions',required=True) | 167 parser.add_argument("-t","--treatments", nargs="+", help='Treatment conditions',required=True) |
| 168 parser.add_argument("-n","--sample-names", nargs="+", help='Paired sample files: pat_x_sample_1.txt:NAME .') | 168 parser.add_argument("-n","--sample-names", nargs="+", help='Paired sample files: pat_x_sample_1.txt:NAME .') |
| 169 | 169 |
| 170 args = parser.parse_args() | 170 args = parser.parse_args() |
| 171 | 171 |