annotate data.py @ 3:ecf125a1ad73 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit fb1fc1e3a062adfb1a78cd46aafd6a6e9f1e3bab
author rnateam
date Tue, 19 Jul 2016 10:22:02 -0400
parents 8918de535391
children a609d6dc8047
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
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
1 """Dataset handler."""
8918de535391 planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 2fc7f3c08f30e2d81dc4ad19759dfe7ba9b0a3a1
rnateam
parents:
diff changeset
2
8918de535391 planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 2fc7f3c08f30e2d81dc4ad19759dfe7ba9b0a3a1
rnateam
parents:
diff changeset
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
rnateam
parents:
diff changeset
4
8918de535391 planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 2fc7f3c08f30e2d81dc4ad19759dfe7ba9b0a3a1
rnateam
parents:
diff changeset
5 import pandas as pd
8918de535391 planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 2fc7f3c08f30e2d81dc4ad19759dfe7ba9b0a3a1
rnateam
parents:
diff changeset
6
8918de535391 planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 2fc7f3c08f30e2d81dc4ad19759dfe7ba9b0a3a1
rnateam
parents:
diff changeset
7 from theano import config
8918de535391 planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 2fc7f3c08f30e2d81dc4ad19759dfe7ba9b0a3a1
rnateam
parents:
diff changeset
8
8918de535391 planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 2fc7f3c08f30e2d81dc4ad19759dfe7ba9b0a3a1
rnateam
parents:
diff changeset
9 __author__ = "Gianluca Corrado"
8918de535391 planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 2fc7f3c08f30e2d81dc4ad19759dfe7ba9b0a3a1
rnateam
parents:
diff changeset
10 __copyright__ = "Copyright 2016, Gianluca Corrado"
8918de535391 planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 2fc7f3c08f30e2d81dc4ad19759dfe7ba9b0a3a1
rnateam
parents:
diff changeset
11 __license__ = "MIT"
8918de535391 planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 2fc7f3c08f30e2d81dc4ad19759dfe7ba9b0a3a1
rnateam
parents:
diff changeset
12 __maintainer__ = "Gianluca Corrado"
8918de535391 planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 2fc7f3c08f30e2d81dc4ad19759dfe7ba9b0a3a1
rnateam
parents:
diff changeset
13 __email__ = "gianluca.corrado@unitn.it"
8918de535391 planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 2fc7f3c08f30e2d81dc4ad19759dfe7ba9b0a3a1
rnateam
parents:
diff changeset
14 __status__ = "Production"
8918de535391 planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 2fc7f3c08f30e2d81dc4ad19759dfe7ba9b0a3a1
rnateam
parents:
diff changeset
15
8918de535391 planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 2fc7f3c08f30e2d81dc4ad19759dfe7ba9b0a3a1
rnateam
parents:
diff changeset
16
8918de535391 planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 2fc7f3c08f30e2d81dc4ad19759dfe7ba9b0a3a1
rnateam
parents:
diff changeset
17 class Dataset(object):
8918de535391 planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 2fc7f3c08f30e2d81dc4ad19759dfe7ba9b0a3a1
rnateam
parents:
diff changeset
18 """General dataset."""
8918de535391 planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 2fc7f3c08f30e2d81dc4ad19759dfe7ba9b0a3a1
rnateam
parents:
diff changeset
19
8918de535391 planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 2fc7f3c08f30e2d81dc4ad19759dfe7ba9b0a3a1
rnateam
parents:
diff changeset
20 def __init__(self, fp, fr, standardize_proteins=False,
8918de535391 planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 2fc7f3c08f30e2d81dc4ad19759dfe7ba9b0a3a1
rnateam
parents:
diff changeset
21 standardize_rnas=False):
8918de535391 planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 2fc7f3c08f30e2d81dc4ad19759dfe7ba9b0a3a1
rnateam
parents:
diff changeset
22 """
8918de535391 planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 2fc7f3c08f30e2d81dc4ad19759dfe7ba9b0a3a1
rnateam
parents:
diff changeset
23 Constructor.
8918de535391 planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 2fc7f3c08f30e2d81dc4ad19759dfe7ba9b0a3a1
rnateam
parents:
diff changeset
24
8918de535391 planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 2fc7f3c08f30e2d81dc4ad19759dfe7ba9b0a3a1
rnateam
parents:
diff changeset
25 Parameters
8918de535391 planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 2fc7f3c08f30e2d81dc4ad19759dfe7ba9b0a3a1
rnateam
parents:
diff changeset
26 ----------
8918de535391 planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 2fc7f3c08f30e2d81dc4ad19759dfe7ba9b0a3a1
rnateam
parents:
diff changeset
27 fp : str
8918de535391 planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 2fc7f3c08f30e2d81dc4ad19759dfe7ba9b0a3a1
rnateam
parents:
diff changeset
28 Protein features
8918de535391 planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 2fc7f3c08f30e2d81dc4ad19759dfe7ba9b0a3a1
rnateam
parents:
diff changeset
29
8918de535391 planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 2fc7f3c08f30e2d81dc4ad19759dfe7ba9b0a3a1
rnateam
parents:
diff changeset
30 fr : str
8918de535391 planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 2fc7f3c08f30e2d81dc4ad19759dfe7ba9b0a3a1
rnateam
parents:
diff changeset
31 The name of the HDF5 file containing features for the RNAs.
8918de535391 planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 2fc7f3c08f30e2d81dc4ad19759dfe7ba9b0a3a1
rnateam
parents:
diff changeset
32 """
8918de535391 planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 2fc7f3c08f30e2d81dc4ad19759dfe7ba9b0a3a1
rnateam
parents:
diff changeset
33 self.Fp = fp.astype(config.floatX)
8918de535391 planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 2fc7f3c08f30e2d81dc4ad19759dfe7ba9b0a3a1
rnateam
parents:
diff changeset
34
8918de535391 planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 2fc7f3c08f30e2d81dc4ad19759dfe7ba9b0a3a1
rnateam
parents:
diff changeset
35 store = pd.io.pytables.HDFStore(fr)
8918de535391 planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 2fc7f3c08f30e2d81dc4ad19759dfe7ba9b0a3a1
rnateam
parents:
diff changeset
36 self.Fr = store.features.astype(config.floatX)
8918de535391 planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 2fc7f3c08f30e2d81dc4ad19759dfe7ba9b0a3a1
rnateam
parents:
diff changeset
37 store.close()
8918de535391 planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 2fc7f3c08f30e2d81dc4ad19759dfe7ba9b0a3a1
rnateam
parents:
diff changeset
38
8918de535391 planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 2fc7f3c08f30e2d81dc4ad19759dfe7ba9b0a3a1
rnateam
parents:
diff changeset
39 def load(self):
8918de535391 planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 2fc7f3c08f30e2d81dc4ad19759dfe7ba9b0a3a1
rnateam
parents:
diff changeset
40 """Load dataset in memory."""
8918de535391 planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 2fc7f3c08f30e2d81dc4ad19759dfe7ba9b0a3a1
rnateam
parents:
diff changeset
41 raise NotImplementedError()
8918de535391 planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 2fc7f3c08f30e2d81dc4ad19759dfe7ba9b0a3a1
rnateam
parents:
diff changeset
42
8918de535391 planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 2fc7f3c08f30e2d81dc4ad19759dfe7ba9b0a3a1
rnateam
parents:
diff changeset
43
8918de535391 planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 2fc7f3c08f30e2d81dc4ad19759dfe7ba9b0a3a1
rnateam
parents:
diff changeset
44 class PredictDataset(Dataset):
8918de535391 planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 2fc7f3c08f30e2d81dc4ad19759dfe7ba9b0a3a1
rnateam
parents:
diff changeset
45 """Test dataset."""
8918de535391 planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 2fc7f3c08f30e2d81dc4ad19759dfe7ba9b0a3a1
rnateam
parents:
diff changeset
46
8918de535391 planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 2fc7f3c08f30e2d81dc4ad19759dfe7ba9b0a3a1
rnateam
parents:
diff changeset
47 def __init__(self, fp, fr):
8918de535391 planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 2fc7f3c08f30e2d81dc4ad19759dfe7ba9b0a3a1
rnateam
parents:
diff changeset
48 """
8918de535391 planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 2fc7f3c08f30e2d81dc4ad19759dfe7ba9b0a3a1
rnateam
parents:
diff changeset
49 Constructor.
8918de535391 planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 2fc7f3c08f30e2d81dc4ad19759dfe7ba9b0a3a1
rnateam
parents:
diff changeset
50
8918de535391 planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 2fc7f3c08f30e2d81dc4ad19759dfe7ba9b0a3a1
rnateam
parents:
diff changeset
51 Parameters
8918de535391 planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 2fc7f3c08f30e2d81dc4ad19759dfe7ba9b0a3a1
rnateam
parents:
diff changeset
52 ----------
8918de535391 planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 2fc7f3c08f30e2d81dc4ad19759dfe7ba9b0a3a1
rnateam
parents:
diff changeset
53 fp : str
8918de535391 planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 2fc7f3c08f30e2d81dc4ad19759dfe7ba9b0a3a1
rnateam
parents:
diff changeset
54 The name of the HDF5 file containing features for the proteins.
8918de535391 planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 2fc7f3c08f30e2d81dc4ad19759dfe7ba9b0a3a1
rnateam
parents:
diff changeset
55
8918de535391 planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 2fc7f3c08f30e2d81dc4ad19759dfe7ba9b0a3a1
rnateam
parents:
diff changeset
56 fr : str
8918de535391 planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 2fc7f3c08f30e2d81dc4ad19759dfe7ba9b0a3a1
rnateam
parents:
diff changeset
57 The name of the HDF5 file containing features for the RNAs.
8918de535391 planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 2fc7f3c08f30e2d81dc4ad19759dfe7ba9b0a3a1
rnateam
parents:
diff changeset
58 """
8918de535391 planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 2fc7f3c08f30e2d81dc4ad19759dfe7ba9b0a3a1
rnateam
parents:
diff changeset
59 super(PredictDataset, self).__init__(fp, fr)
8918de535391 planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 2fc7f3c08f30e2d81dc4ad19759dfe7ba9b0a3a1
rnateam
parents:
diff changeset
60
8918de535391 planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 2fc7f3c08f30e2d81dc4ad19759dfe7ba9b0a3a1
rnateam
parents:
diff changeset
61 def load(self):
8918de535391 planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 2fc7f3c08f30e2d81dc4ad19759dfe7ba9b0a3a1
rnateam
parents:
diff changeset
62 """
8918de535391 planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 2fc7f3c08f30e2d81dc4ad19759dfe7ba9b0a3a1
rnateam
parents:
diff changeset
63 Load dataset in memory.
8918de535391 planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 2fc7f3c08f30e2d81dc4ad19759dfe7ba9b0a3a1
rnateam
parents:
diff changeset
64
8918de535391 planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 2fc7f3c08f30e2d81dc4ad19759dfe7ba9b0a3a1
rnateam
parents:
diff changeset
65 Return
8918de535391 planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 2fc7f3c08f30e2d81dc4ad19759dfe7ba9b0a3a1
rnateam
parents:
diff changeset
66 ------
8918de535391 planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 2fc7f3c08f30e2d81dc4ad19759dfe7ba9b0a3a1
rnateam
parents:
diff changeset
67 Examples to predict. For each example:
8918de535391 planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 2fc7f3c08f30e2d81dc4ad19759dfe7ba9b0a3a1
rnateam
parents:
diff changeset
68 - p contains the protein features,
8918de535391 planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 2fc7f3c08f30e2d81dc4ad19759dfe7ba9b0a3a1
rnateam
parents:
diff changeset
69 - r contains the RNA features,
8918de535391 planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 2fc7f3c08f30e2d81dc4ad19759dfe7ba9b0a3a1
rnateam
parents:
diff changeset
70 - p_names contains the name of the 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
71 - r_names contains the name of the 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
72
8918de535391 planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 2fc7f3c08f30e2d81dc4ad19759dfe7ba9b0a3a1
rnateam
parents:
diff changeset
73 """
8918de535391 planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 2fc7f3c08f30e2d81dc4ad19759dfe7ba9b0a3a1
rnateam
parents:
diff changeset
74 protein_input_dim = self.Fp.shape[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
75 rna_input_dim = self.Fr.shape[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
76 num_examples = self.Fp.shape[1] * self.Fr.shape[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
77 p = np.zeros((num_examples, protein_input_dim)).astype(config.floatX)
8918de535391 planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 2fc7f3c08f30e2d81dc4ad19759dfe7ba9b0a3a1
rnateam
parents:
diff changeset
78 p_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
79 r = np.zeros((num_examples, rna_input_dim)).astype(config.floatX)
8918de535391 planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 2fc7f3c08f30e2d81dc4ad19759dfe7ba9b0a3a1
rnateam
parents:
diff changeset
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))