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neksa / mutagene

Python library and package for mutational analysis
https://www.ncbi.nlm.nih.gov/projects/mutagene/
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Issues with motif_doc.rst #44

Closed shandy79 closed 4 years ago

shandy79 commented 4 years ago

There appear to be syntactic issues with motif_doc.rst along with formatting, numbering, and other issues. In addition, the documentation should be reviewed for accuracy and completeness.

shandy79 commented 4 years ago

Example 5.1: After updating my command to use -s "A" instead of -s "=", I get the following output, which doesn't match what is in motif_doc.rst (docs branch).

sample  mutagen motif   strand  enrichment      mut_min mut_max odds_ratio      pvalue  qvalue
TCGA-50-6593-01A-11D-1753-08    C>T in CpG      [C>T]G  any strand      2.11727 10      18      2.42666 0.00169896      0.0118927
shandy79 commented 4 years ago

Example 5.3: After updating my command to use -s "T" instead of -s "+", I get the following output, which doesn't match what is in motif_doc.rst (docs branch).

sample  mutagen motif   strand  enrichment      mut_min mut_max odds_ratio      pvalue  qvalue
TCGA-50-6593-01A-11D-1753-08    C>T in CpG      [C>T]G  transcribed     2.54733 7       10      3.12042 0.00451764      0.0316235
shandy79 commented 4 years ago

Example 5.4: After updating my command to use -s "TNA" instead of -s "+-=" and adding the -f 'VCF' flag, I get the following output, which doesn't match what is in motif_doc.rst (docs branch).

sample  mutagen motif   strand  enrichment      mut_min mut_max odds_ratio      pvalue  qvalue
VCF     C>T in CpG      [C>T]G  non-transcribed 4.24964 1882    2460    7.50456 0       0
VCF     C>T in CpG      [C>T]G  any strand      4.21114 3670    4812    7.38992 0       0
VCF     C>T in CpG      [C>T]G  transcribed     4.17202 1789    2352    7.27413 0       0
VCF     APOBEC3G        C[C>K]R any strand      1.45802 721     2292    1.56628 1.17349e-74     6.16082e-74
VCF     APOBEC3G        C[C>K]R non-transcribed 1.49104 393     1193    1.61104 3.05357e-44     1.2825e-43
VCF     APOBEC3G        C[C>K]R transcribed     1.42365 328     1099    1.52034 9.7673e-33      3.41855e-32
VCF     Pol Eta W[A>T]  transcribed     1.13727 24      194     1.24465 0.0130597       0.0391791