Mercurial > repos > iuc > virhunter

annotate predict.py @ 2:ea2cccb9f73e draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter commit c3685ed6a70b47012b62b95a2a3db062bd3b7475
author iuc
date Thu, 05 Jan 2023 14:27:54 +0000
parents 9b12bc1b1e2c
children 302332b914ef
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457fd8fd681a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter commit 628688c1302dbf972e48806d2a5bafe27847bdcc
iuc
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1 #!/usr/bin/env python
457fd8fd681a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter commit 628688c1302dbf972e48806d2a5bafe27847bdcc
iuc
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2 # -*- coding: utf-8 -*-
457fd8fd681a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter commit 628688c1302dbf972e48806d2a5bafe27847bdcc
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3 # Credits: Grigorii Sukhorukov, Macha Nikolski
457fd8fd681a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter commit 628688c1302dbf972e48806d2a5bafe27847bdcc
iuc
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4 import argparse
457fd8fd681a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter commit 628688c1302dbf972e48806d2a5bafe27847bdcc
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5 import os
457fd8fd681a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter commit 628688c1302dbf972e48806d2a5bafe27847bdcc
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6 from pathlib import Path
457fd8fd681a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter commit 628688c1302dbf972e48806d2a5bafe27847bdcc
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7
457fd8fd681a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter commit 628688c1302dbf972e48806d2a5bafe27847bdcc
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8 import numpy as np
457fd8fd681a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter commit 628688c1302dbf972e48806d2a5bafe27847bdcc
iuc
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9 import pandas as pd
457fd8fd681a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter commit 628688c1302dbf972e48806d2a5bafe27847bdcc
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10 from Bio import SeqIO
457fd8fd681a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter commit 628688c1302dbf972e48806d2a5bafe27847bdcc
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11 from joblib import load
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9b12bc1b1e2c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter commit cea5a324cffd684e4cb08438fe5a305cfaf0f73a
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12 from models import model_10, model_5, model_7
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457fd8fd681a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter commit 628688c1302dbf972e48806d2a5bafe27847bdcc
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13 from utils import preprocess as pp
457fd8fd681a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter commit 628688c1302dbf972e48806d2a5bafe27847bdcc
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457fd8fd681a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter commit 628688c1302dbf972e48806d2a5bafe27847bdcc
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15 os.environ["CUDA_VISIBLE_DEVICES"] = ""
457fd8fd681a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter commit 628688c1302dbf972e48806d2a5bafe27847bdcc
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16 os.environ["TF_XLA_FLAGS"] = "--tf_xla_cpu_global_jit"
457fd8fd681a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter commit 628688c1302dbf972e48806d2a5bafe27847bdcc
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17 # loglevel : 0 all printed, 1 I not printed, 2 I and W not printed, 3 nothing printed
457fd8fd681a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter commit 628688c1302dbf972e48806d2a5bafe27847bdcc
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18 os.environ['TF_CPP_MIN_LOG_LEVEL'] = '3'
457fd8fd681a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter commit 628688c1302dbf972e48806d2a5bafe27847bdcc
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19
457fd8fd681a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter commit 628688c1302dbf972e48806d2a5bafe27847bdcc
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20
1
9b12bc1b1e2c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter commit cea5a324cffd684e4cb08438fe5a305cfaf0f73a
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21 def predict_nn(ds_path, nn_weights_path, length, use_10, batch_size=256):
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457fd8fd681a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter commit 628688c1302dbf972e48806d2a5bafe27847bdcc
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22 """
457fd8fd681a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter commit 628688c1302dbf972e48806d2a5bafe27847bdcc
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23 Breaks down contigs into fragments
457fd8fd681a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter commit 628688c1302dbf972e48806d2a5bafe27847bdcc
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24 and uses pretrained neural networks to give predictions for fragments
457fd8fd681a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter commit 628688c1302dbf972e48806d2a5bafe27847bdcc
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25 """
457fd8fd681a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter commit 628688c1302dbf972e48806d2a5bafe27847bdcc
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26 try:
457fd8fd681a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter commit 628688c1302dbf972e48806d2a5bafe27847bdcc
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27 seqs_ = list(SeqIO.parse(ds_path, "fasta"))
457fd8fd681a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter commit 628688c1302dbf972e48806d2a5bafe27847bdcc
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28 except FileNotFoundError:
457fd8fd681a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter commit 628688c1302dbf972e48806d2a5bafe27847bdcc
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29 raise Exception("test dataset was not found. Change ds variable")
457fd8fd681a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter commit 628688c1302dbf972e48806d2a5bafe27847bdcc
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30 out_table = {
457fd8fd681a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter commit 628688c1302dbf972e48806d2a5bafe27847bdcc
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31 "id": [],
457fd8fd681a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter commit 628688c1302dbf972e48806d2a5bafe27847bdcc
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32 "length": [],
457fd8fd681a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter commit 628688c1302dbf972e48806d2a5bafe27847bdcc
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33 "fragment": [],
457fd8fd681a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter commit 628688c1302dbf972e48806d2a5bafe27847bdcc
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34 "pred_plant_5": [],
457fd8fd681a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter commit 628688c1302dbf972e48806d2a5bafe27847bdcc
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35 "pred_vir_5": [],
457fd8fd681a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter commit 628688c1302dbf972e48806d2a5bafe27847bdcc
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36 "pred_bact_5": [],
457fd8fd681a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter commit 628688c1302dbf972e48806d2a5bafe27847bdcc
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37 "pred_plant_7": [],
457fd8fd681a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter commit 628688c1302dbf972e48806d2a5bafe27847bdcc
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38 "pred_vir_7": [],
457fd8fd681a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter commit 628688c1302dbf972e48806d2a5bafe27847bdcc
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39 "pred_bact_7": [],
457fd8fd681a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter commit 628688c1302dbf972e48806d2a5bafe27847bdcc
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40 }
1
9b12bc1b1e2c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter commit cea5a324cffd684e4cb08438fe5a305cfaf0f73a
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41 if use_10:
9b12bc1b1e2c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter commit cea5a324cffd684e4cb08438fe5a305cfaf0f73a
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42 out_table_ = {
9b12bc1b1e2c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter commit cea5a324cffd684e4cb08438fe5a305cfaf0f73a
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43 "pred_plant_10": [],
9b12bc1b1e2c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter commit cea5a324cffd684e4cb08438fe5a305cfaf0f73a
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44 "pred_vir_10": [],
9b12bc1b1e2c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter commit cea5a324cffd684e4cb08438fe5a305cfaf0f73a
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45 "pred_bact_10": [],
9b12bc1b1e2c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter commit cea5a324cffd684e4cb08438fe5a305cfaf0f73a
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46 }
9b12bc1b1e2c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter commit cea5a324cffd684e4cb08438fe5a305cfaf0f73a
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47 out_table.update(out_table_)
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457fd8fd681a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter commit 628688c1302dbf972e48806d2a5bafe27847bdcc
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48 if not seqs_:
457fd8fd681a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter commit 628688c1302dbf972e48806d2a5bafe27847bdcc
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49 raise ValueError("All sequences were smaller than length of the model")
457fd8fd681a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter commit 628688c1302dbf972e48806d2a5bafe27847bdcc
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50 test_fragments = []
457fd8fd681a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter commit 628688c1302dbf972e48806d2a5bafe27847bdcc
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51 test_fragments_rc = []
457fd8fd681a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter commit 628688c1302dbf972e48806d2a5bafe27847bdcc
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52 for seq in seqs_:
457fd8fd681a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter commit 628688c1302dbf972e48806d2a5bafe27847bdcc
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53 fragments_, fragments_rc, _ = pp.fragmenting([seq], length, max_gap=0.8,
457fd8fd681a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter commit 628688c1302dbf972e48806d2a5bafe27847bdcc
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54 sl_wind_step=int(length / 2))
457fd8fd681a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter commit 628688c1302dbf972e48806d2a5bafe27847bdcc
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55 test_fragments.extend(fragments_)
457fd8fd681a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter commit 628688c1302dbf972e48806d2a5bafe27847bdcc
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56 test_fragments_rc.extend(fragments_rc)
457fd8fd681a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter commit 628688c1302dbf972e48806d2a5bafe27847bdcc
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57 for j in range(len(fragments_)):
457fd8fd681a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter commit 628688c1302dbf972e48806d2a5bafe27847bdcc
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58 out_table["id"].append(seq.id)
457fd8fd681a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter commit 628688c1302dbf972e48806d2a5bafe27847bdcc
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59 out_table["length"].append(len(seq.seq))
457fd8fd681a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter commit 628688c1302dbf972e48806d2a5bafe27847bdcc
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60 out_table["fragment"].append(j)
457fd8fd681a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter commit 628688c1302dbf972e48806d2a5bafe27847bdcc
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61 test_encoded = pp.one_hot_encode(test_fragments)
457fd8fd681a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter commit 628688c1302dbf972e48806d2a5bafe27847bdcc
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62 test_encoded_rc = pp.one_hot_encode(test_fragments_rc)
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63 if use_10:
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64 zipped_models = zip([model_5.model(length), model_7.model(length), model_10.model(length)], [5, 7, 10])
9b12bc1b1e2c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter commit cea5a324cffd684e4cb08438fe5a305cfaf0f73a
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65 else:
9b12bc1b1e2c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter commit cea5a324cffd684e4cb08438fe5a305cfaf0f73a
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66 zipped_models = zip([model_5.model(length), model_7.model(length)], [5, 7])
9b12bc1b1e2c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter commit cea5a324cffd684e4cb08438fe5a305cfaf0f73a
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67 for model, s in zipped_models:
0
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68 model.load_weights(Path(nn_weights_path, f"model_{s}_{length}.h5"))
457fd8fd681a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter commit 628688c1302dbf972e48806d2a5bafe27847bdcc
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69 prediction = model.predict([test_encoded, test_encoded_rc], batch_size)
457fd8fd681a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter commit 628688c1302dbf972e48806d2a5bafe27847bdcc
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70 out_table[f"pred_plant_{s}"].extend(list(prediction[..., 0]))
457fd8fd681a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter commit 628688c1302dbf972e48806d2a5bafe27847bdcc
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71 out_table[f"pred_vir_{s}"].extend(list(prediction[..., 1]))
457fd8fd681a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter commit 628688c1302dbf972e48806d2a5bafe27847bdcc
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72 out_table[f"pred_bact_{s}"].extend(list(prediction[..., 2]))
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73
0
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74 return pd.DataFrame(out_table)
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75
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76
1
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77 def predict_rf(df, rf_weights_path, length, use_10):
0
457fd8fd681a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter commit 628688c1302dbf972e48806d2a5bafe27847bdcc
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78 """
457fd8fd681a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter commit 628688c1302dbf972e48806d2a5bafe27847bdcc
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79 Using predictions by predict_nn and weights of a trained RF classifier gives a single prediction for a fragment
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80 """
457fd8fd681a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter commit 628688c1302dbf972e48806d2a5bafe27847bdcc
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81
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82 clf = load(Path(rf_weights_path, f"RF_{length}.joblib"))
1
9b12bc1b1e2c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter commit cea5a324cffd684e4cb08438fe5a305cfaf0f73a
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83 if use_10:
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84 X = df[
9b12bc1b1e2c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter commit cea5a324cffd684e4cb08438fe5a305cfaf0f73a
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85 ["pred_plant_5", "pred_vir_5", "pred_plant_7", "pred_vir_7", "pred_plant_10", "pred_vir_10", ]]
9b12bc1b1e2c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter commit cea5a324cffd684e4cb08438fe5a305cfaf0f73a
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86 else:
9b12bc1b1e2c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter commit cea5a324cffd684e4cb08438fe5a305cfaf0f73a
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87 X = df[
9b12bc1b1e2c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter commit cea5a324cffd684e4cb08438fe5a305cfaf0f73a
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88 ["pred_plant_5", "pred_vir_5", "pred_plant_7", "pred_vir_7", ]]
0
457fd8fd681a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter commit 628688c1302dbf972e48806d2a5bafe27847bdcc
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89 y_pred = clf.predict(X)
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90 mapping = {0: "plant", 1: "virus", 2: "bacteria"}
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91 df["RF_decision"] = np.vectorize(mapping.get)(y_pred)
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92 prob_classes = clf.predict_proba(X)
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93 df["RF_pred_plant"] = prob_classes[..., 0]
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94 df["RF_pred_vir"] = prob_classes[..., 1]
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95 df["RF_pred_bact"] = prob_classes[..., 2]
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96 return df
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97
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98
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99 def predict_contigs(df):
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100 """
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101 Based on predictions of predict_rf for fragments gives a final prediction for the whole contig
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102 """
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103 df = (
1
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104 df.groupby(["id", "length", 'RF_decision'], sort=False).size().unstack(fill_value=0)
0
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105 )
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106 df = df.reset_index()
2
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107 df = df.reindex(['length', 'id', 'virus', 'plant', 'bacteria'], axis=1).fillna(value=0)
0
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108 conditions = [
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109 (df['virus'] > df['plant']) & (df['virus'] > df['bacteria']),
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110 (df['plant'] > df['virus']) & (df['plant'] > df['bacteria']),
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111 (df['bacteria'] >= df['plant']) & (df['bacteria'] >= df['virus']),
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112 ]
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113 choices = ['virus', 'plant', 'bacteria']
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114 df['decision'] = np.select(conditions, choices, default='bacteria')
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115 df = df.loc[:, ['length', 'id', 'virus', 'plant', 'bacteria', 'decision']]
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116 df = df.rename(columns={'virus': '# viral fragments', 'bacteria': '# bacterial fragments', 'plant': '# plant fragments'})
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117 df['# viral / # total'] = (df['# viral fragments'] / (df['# viral fragments'] + df['# bacterial fragments'] + df['# plant fragments'])).round(3)
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118 df['# viral / # total * length'] = df['# viral / # total'] * df['length']
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119 df = df.sort_values(by='# viral / # total * length', ascending=False)
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120 return df
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121
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122
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123 def predict(test_ds, weights, out_path, return_viral, limit):
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124 """Predicts viral contigs from the fasta file
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125
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126 test_ds: path to the input file with contigs in fasta format (str or list of str)
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127 weights: path to the folder containing weights for NN and RF modules trained on 500 and 1000 fragment lengths (str)
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128 out_path: path to the folder to store predictions (str)
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129 return_viral: whether to return contigs annotated as viral in separate fasta file (True/False)
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130 limit: Do predictions only for contigs > l. We suggest l=750. (int)
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131 """
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132 test_ds = test_ds
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133 if isinstance(test_ds, list):
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134 pass
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135 elif isinstance(test_ds, str):
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136 test_ds = [test_ds]
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137 else:
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138 raise ValueError('test_ds was incorrectly assigned in the config file')
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139
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140 assert Path(test_ds[0]).exists(), f'{test_ds[0]} does not exist'
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141 assert Path(weights).exists(), f'{weights} does not exist'
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142 assert isinstance(limit, int), 'limit should be an integer'
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143 Path(out_path).mkdir(parents=True, exist_ok=True)
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144 use_10 = Path(weights, 'model_10_500.h5').exists()
0
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145 for ts in test_ds:
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146 dfs_fr = []
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147 dfs_cont = []
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148 for l_ in 500, 1000:
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149 # print(f'starting prediction for {Path(ts).name} for fragment length {l_}')
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150 df = predict_nn(
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151 ds_path=ts,
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152 nn_weights_path=weights,
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153 length=l_,
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154 use_10=use_10
0
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155 )
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156 print(df)
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157 df = predict_rf(
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158 df=df,
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159 rf_weights_path=weights,
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160 length=l_,
1
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161 use_10=use_10
0
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162 )
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163 df = df.round(3)
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164 dfs_fr.append(df)
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165 df = predict_contigs(df)
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166 dfs_cont.append(df)
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167 # print('prediction finished')
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168 df_500 = dfs_fr[0][(dfs_fr[0]['length'] >= limit) & (dfs_fr[0]['length'] < 1500)]
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169 df_1000 = dfs_fr[1][(dfs_fr[1]['length'] >= 1500)]
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170 df = pd.concat([df_1000, df_500], ignore_index=True)
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171 pred_fr = Path(out_path, 'predicted_fragments.csv')
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172 df.to_csv(pred_fr)
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173
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174 df_500 = dfs_cont[0][(dfs_cont[0]['length'] >= limit) & (dfs_cont[0]['length'] < 1500)]
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175 df_1000 = dfs_cont[1][(dfs_cont[1]['length'] >= 1500)]
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176 df = pd.concat([df_1000, df_500], ignore_index=True)
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177 pred_contigs = Path(out_path, 'predicted.csv')
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178 df.to_csv(pred_contigs)
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179
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180 if return_viral:
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181 viral_ids = list(df[df["decision"] == "virus"]["id"])
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182 seqs_ = list(SeqIO.parse(ts, "fasta"))
457fd8fd681a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter commit 628688c1302dbf972e48806d2a5bafe27847bdcc
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183 viral_seqs = [s_ for s_ in seqs_ if s_.id in viral_ids]
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184 SeqIO.write(viral_seqs, Path(out_path, 'viral.fasta'), 'fasta')
457fd8fd681a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter commit 628688c1302dbf972e48806d2a5bafe27847bdcc
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185
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186
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187 if __name__ == '__main__':
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188 parser = argparse.ArgumentParser()
457fd8fd681a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter commit 628688c1302dbf972e48806d2a5bafe27847bdcc
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189 parser.add_argument("--test_ds", help="path to the input file with contigs in fasta format (str or list of str)")
457fd8fd681a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter commit 628688c1302dbf972e48806d2a5bafe27847bdcc
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190 parser.add_argument("--weights", help="path to the folder containing weights for NN and RF modules trained on 500 and 1000 fragment lengths (str)")
457fd8fd681a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter commit 628688c1302dbf972e48806d2a5bafe27847bdcc
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191 parser.add_argument("--out_path", help="path to the folder to store predictions (str)")
457fd8fd681a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter commit 628688c1302dbf972e48806d2a5bafe27847bdcc
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192 parser.add_argument("--return_viral", help="whether to return contigs annotated as viral in separate fasta file (True/False)")
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193 parser.add_argument("--limit", help="Do predictions only for contigs > l. We suggest l=750. (int)", type=int, default=750)
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194
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195 args = parser.parse_args()
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196 if args.test_ds:
457fd8fd681a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter commit 628688c1302dbf972e48806d2a5bafe27847bdcc
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197 test_ds = args.test_ds
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198 if args.weights:
457fd8fd681a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter commit 628688c1302dbf972e48806d2a5bafe27847bdcc
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199 weights = args.weights
457fd8fd681a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter commit 628688c1302dbf972e48806d2a5bafe27847bdcc
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200 if args.out_path:
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201 out_path = args.out_path
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202 if args.return_viral:
457fd8fd681a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter commit 628688c1302dbf972e48806d2a5bafe27847bdcc
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203 return_viral = args.return_viral
457fd8fd681a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter commit 628688c1302dbf972e48806d2a5bafe27847bdcc
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204 if args.limit:
457fd8fd681a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter commit 628688c1302dbf972e48806d2a5bafe27847bdcc
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205 limit = args.limit
457fd8fd681a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter commit 628688c1302dbf972e48806d2a5bafe27847bdcc
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206 predict(test_ds, weights, out_path, return_viral, limit)