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annotate data.py @ 0:8918de535391 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 2fc7f3c08f30e2d81dc4ad19759dfe7ba9b0a3a1
author rnateam
date Tue, 31 May 2016 05:41:03 -0400
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children a609d6dc8047
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8918de535391 planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 2fc7f3c08f30e2d81dc4ad19759dfe7ba9b0a3a1
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1 """Dataset handler."""
8918de535391 planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 2fc7f3c08f30e2d81dc4ad19759dfe7ba9b0a3a1
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8918de535391 planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 2fc7f3c08f30e2d81dc4ad19759dfe7ba9b0a3a1
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3 import numpy as np
8918de535391 planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 2fc7f3c08f30e2d81dc4ad19759dfe7ba9b0a3a1
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5 import pandas as pd
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7 from theano import config
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9 __author__ = "Gianluca Corrado"
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10 __copyright__ = "Copyright 2016, Gianluca Corrado"
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11 __license__ = "MIT"
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12 __maintainer__ = "Gianluca Corrado"
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13 __email__ = "gianluca.corrado@unitn.it"
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14 __status__ = "Production"
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17 class Dataset(object):
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18 """General dataset."""
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20 def __init__(self, fp, fr, standardize_proteins=False,
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21 standardize_rnas=False):
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22 """
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23 Constructor.
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25 Parameters
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26 ----------
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27 fp : str
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28 Protein features
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30 fr : str
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31 The name of the HDF5 file containing features for the RNAs.
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32 """
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33 self.Fp = fp.astype(config.floatX)
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35 store = pd.io.pytables.HDFStore(fr)
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36 self.Fr = store.features.astype(config.floatX)
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37 store.close()
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38
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39 def load(self):
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40 """Load dataset in memory."""
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41 raise NotImplementedError()
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44 class PredictDataset(Dataset):
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45 """Test dataset."""
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46
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47 def __init__(self, fp, fr):
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48 """
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49 Constructor.
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50
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51 Parameters
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52 ----------
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53 fp : str
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54 The name of the HDF5 file containing features for the proteins.
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56 fr : str
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57 The name of the HDF5 file containing features for the RNAs.
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58 """
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59 super(PredictDataset, self).__init__(fp, fr)
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60
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61 def load(self):
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62 """
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63 Load dataset in memory.
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64
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65 Return
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66 ------
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67 Examples to predict. For each example:
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68 - p contains the protein features,
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69 - r contains the RNA features,
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70 - p_names contains the name of the protein,
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71 - r_names contains the name of the RNA.
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72
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73 """
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74 protein_input_dim = self.Fp.shape[0]
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75 rna_input_dim = self.Fr.shape[0]
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76 num_examples = self.Fp.shape[1] * self.Fr.shape[1]
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77 p = np.zeros((num_examples, protein_input_dim)).astype(config.floatX)
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78 p_names = []
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79 r = np.zeros((num_examples, rna_input_dim)).astype(config.floatX)
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80 r_names = []
8918de535391 planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 2fc7f3c08f30e2d81dc4ad19759dfe7ba9b0a3a1
rnateam
parents:
diff changeset
81 index = 0
8918de535391 planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 2fc7f3c08f30e2d81dc4ad19759dfe7ba9b0a3a1
rnateam
parents:
diff changeset
82 for protein in self.Fp.columns:
8918de535391 planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 2fc7f3c08f30e2d81dc4ad19759dfe7ba9b0a3a1
rnateam
parents:
diff changeset
83 for rna in self.Fr.columns:
8918de535391 planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 2fc7f3c08f30e2d81dc4ad19759dfe7ba9b0a3a1
rnateam
parents:
diff changeset
84 p[index] = self.Fp[protein]
8918de535391 planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 2fc7f3c08f30e2d81dc4ad19759dfe7ba9b0a3a1
rnateam
parents:
diff changeset
85 p_names.append(protein)
8918de535391 planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 2fc7f3c08f30e2d81dc4ad19759dfe7ba9b0a3a1
rnateam
parents:
diff changeset
86 r[index] = self.Fr[rna]
8918de535391 planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 2fc7f3c08f30e2d81dc4ad19759dfe7ba9b0a3a1
rnateam
parents:
diff changeset
87 r_names.append(rna)
8918de535391 planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 2fc7f3c08f30e2d81dc4ad19759dfe7ba9b0a3a1
rnateam
parents:
diff changeset
88 index += 1
8918de535391 planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 2fc7f3c08f30e2d81dc4ad19759dfe7ba9b0a3a1
rnateam
parents:
diff changeset
89
8918de535391 planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 2fc7f3c08f30e2d81dc4ad19759dfe7ba9b0a3a1
rnateam
parents:
diff changeset
90 return (p, np.array(p_names), r, np.array(r_names))