Mercurial > repos > rnateam > rnacommender
annotate utils/__init__.py @ 1:79c9b4b34b63 draft default tip
planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 7ef62aa3d86abd4b911e35447646712a4628e7fe
| author | rnateam |
|---|---|
| date | Fri, 29 Jul 2016 03:27:44 -0400 |
| parents | d04fa5201f51 |
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| rev | line source |
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d04fa5201f51
planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 7ad344d108076116e702e1c1e91cea73d8fcadc4
rnateam
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1 """Util functions.""" |
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d04fa5201f51
planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 7ad344d108076116e702e1c1e91cea73d8fcadc4
rnateam
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2 |
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d04fa5201f51
planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 7ad344d108076116e702e1c1e91cea73d8fcadc4
rnateam
parents:
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3 import pandas as pd |
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d04fa5201f51
planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 7ad344d108076116e702e1c1e91cea73d8fcadc4
rnateam
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4 import cPickle |
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d04fa5201f51
planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 7ad344d108076116e702e1c1e91cea73d8fcadc4
rnateam
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5 |
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d04fa5201f51
planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 7ad344d108076116e702e1c1e91cea73d8fcadc4
rnateam
parents:
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6 __author__ = "Gianluca Corrado" |
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d04fa5201f51
planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 7ad344d108076116e702e1c1e91cea73d8fcadc4
rnateam
parents:
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7 __copyright__ = "Copyright 2016, Gianluca Corrado" |
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d04fa5201f51
planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 7ad344d108076116e702e1c1e91cea73d8fcadc4
rnateam
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8 __license__ = "MIT" |
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d04fa5201f51
planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 7ad344d108076116e702e1c1e91cea73d8fcadc4
rnateam
parents:
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9 __maintainer__ = "Gianluca Corrado" |
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d04fa5201f51
planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 7ad344d108076116e702e1c1e91cea73d8fcadc4
rnateam
parents:
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10 __email__ = "gianluca.corrado@unitn.it" |
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d04fa5201f51
planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 7ad344d108076116e702e1c1e91cea73d8fcadc4
rnateam
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11 __status__ = "Production" |
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d04fa5201f51
planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 7ad344d108076116e702e1c1e91cea73d8fcadc4
rnateam
parents:
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12 |
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d04fa5201f51
planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 7ad344d108076116e702e1c1e91cea73d8fcadc4
rnateam
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13 |
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d04fa5201f51
planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 7ad344d108076116e702e1c1e91cea73d8fcadc4
rnateam
parents:
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14 def feature_size(store_name): |
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d04fa5201f51
planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 7ad344d108076116e702e1c1e91cea73d8fcadc4
rnateam
parents:
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15 """Number of features.""" |
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d04fa5201f51
planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 7ad344d108076116e702e1c1e91cea73d8fcadc4
rnateam
parents:
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16 store = pd.io.pytables.HDFStore(store_name) |
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d04fa5201f51
planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 7ad344d108076116e702e1c1e91cea73d8fcadc4
rnateam
parents:
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17 a = store.features |
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d04fa5201f51
planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 7ad344d108076116e702e1c1e91cea73d8fcadc4
rnateam
parents:
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18 store.close() |
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d04fa5201f51
planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 7ad344d108076116e702e1c1e91cea73d8fcadc4
rnateam
parents:
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19 return a.shape[0] |
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d04fa5201f51
planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 7ad344d108076116e702e1c1e91cea73d8fcadc4
rnateam
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20 |
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d04fa5201f51
planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 7ad344d108076116e702e1c1e91cea73d8fcadc4
rnateam
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21 |
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d04fa5201f51
planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 7ad344d108076116e702e1c1e91cea73d8fcadc4
rnateam
parents:
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22 def save_serendipity_dic(y, filename): |
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d04fa5201f51
planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 7ad344d108076116e702e1c1e91cea73d8fcadc4
rnateam
parents:
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23 """Save the dictionary with the serendipity values.""" |
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d04fa5201f51
planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 7ad344d108076116e702e1c1e91cea73d8fcadc4
rnateam
parents:
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24 store = pd.io.pytables.HDFStore(y) |
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d04fa5201f51
planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 7ad344d108076116e702e1c1e91cea73d8fcadc4
rnateam
parents:
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25 mat = store.matrix |
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d04fa5201f51
planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 7ad344d108076116e702e1c1e91cea73d8fcadc4
rnateam
parents:
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26 store.close() |
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d04fa5201f51
planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 7ad344d108076116e702e1c1e91cea73d8fcadc4
rnateam
parents:
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27 n = len(mat.columns) |
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d04fa5201f51
planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 7ad344d108076116e702e1c1e91cea73d8fcadc4
rnateam
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28 ser = 1 - mat.sum(axis=1) / n |
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d04fa5201f51
planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 7ad344d108076116e702e1c1e91cea73d8fcadc4
rnateam
parents:
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29 |
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d04fa5201f51
planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 7ad344d108076116e702e1c1e91cea73d8fcadc4
rnateam
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30 f = open(filename, "w") |
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d04fa5201f51
planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 7ad344d108076116e702e1c1e91cea73d8fcadc4
rnateam
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31 cPickle.dump(ser.to_dict(), f, protocol=2) |
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d04fa5201f51
planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 7ad344d108076116e702e1c1e91cea73d8fcadc4
rnateam
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32 f.close() |
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d04fa5201f51
planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 7ad344d108076116e702e1c1e91cea73d8fcadc4
rnateam
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33 |
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d04fa5201f51
planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 7ad344d108076116e702e1c1e91cea73d8fcadc4
rnateam
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34 |
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d04fa5201f51
planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 7ad344d108076116e702e1c1e91cea73d8fcadc4
rnateam
parents:
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35 def get_serendipity_val(dic, key): |
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d04fa5201f51
planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 7ad344d108076116e702e1c1e91cea73d8fcadc4
rnateam
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36 """Return the serendipity of a RNA.""" |
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d04fa5201f51
planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 7ad344d108076116e702e1c1e91cea73d8fcadc4
rnateam
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37 # The key was in the training set |
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d04fa5201f51
planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 7ad344d108076116e702e1c1e91cea73d8fcadc4
rnateam
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38 try: |
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d04fa5201f51
planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 7ad344d108076116e702e1c1e91cea73d8fcadc4
rnateam
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39 return dic[key] |
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d04fa5201f51
planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 7ad344d108076116e702e1c1e91cea73d8fcadc4
rnateam
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40 # The key wasn't in the training set, then the serendipity is 1 |
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d04fa5201f51
planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 7ad344d108076116e702e1c1e91cea73d8fcadc4
rnateam
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41 except KeyError: |
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d04fa5201f51
planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 7ad344d108076116e702e1c1e91cea73d8fcadc4
rnateam
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42 return 1. |