sklearn_stacking_ensemble_models: model

annotate model_prediction.py @ 7:00819b7f2f55 draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c"

author	bgruening
date	Wed, 22 Jan 2020 12:33:01 +0000
parents	963e449636d3
children	b8c92e94ac1d

rev	line source
2 e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	1 import argparse
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	2 import json
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	3 import numpy as np
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	4 import pandas as pd
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	5 import warnings
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	6
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	7 from scipy.io import mmread
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	8 from sklearn.pipeline import Pipeline
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	9
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	10 from galaxy_ml.utils import (load_model, read_columns,
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	11 get_module, try_get_attr)
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	12
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	13
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	14 N_JOBS = int(__import__('os').environ.get('GALAXY_SLOTS', 1))
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	15
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	16
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	17 def main(inputs, infile_estimator, outfile_predict,
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	18 infile_weights=None, infile1=None,
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	19 fasta_path=None, ref_seq=None,
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	20 vcf_path=None):
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	21 """
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	22 Parameter
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	23 ---------
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	24 inputs : str
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	25 File path to galaxy tool parameter
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	26
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	27 infile_estimator : strgit
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	28 File path to trained estimator input
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	29
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	30 outfile_predict : str
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	31 File path to save the prediction results, tabular
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	32
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	33 infile_weights : str
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	34 File path to weights input
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	35
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	36 infile1 : str
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	37 File path to dataset containing features
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	38
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	39 fasta_path : str
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	40 File path to dataset containing fasta file
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	41
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	42 ref_seq : str
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	43 File path to dataset containing the reference genome sequence.
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	44
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	45 vcf_path : str
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	46 File path to dataset containing variants info.
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	47 """
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	48 warnings.filterwarnings('ignore')
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	49
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	50 with open(inputs, 'r') as param_handler:
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	51 params = json.load(param_handler)
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	52
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	53 # load model
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	54 with open(infile_estimator, 'rb') as est_handler:
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	55 estimator = load_model(est_handler)
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	56
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	57 main_est = estimator
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	58 if isinstance(estimator, Pipeline):
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	59 main_est = estimator.steps[-1][-1]
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	60 if hasattr(main_est, 'config') and hasattr(main_est, 'load_weights'):
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	61 if not infile_weights or infile_weights == 'None':
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	62 raise ValueError("The selected model skeleton asks for weights, "
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	63 "but dataset for weights wan not selected!")
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	64 main_est.load_weights(infile_weights)
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	65
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	66 # handle data input
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	67 input_type = params['input_options']['selected_input']
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	68 # tabular input
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	69 if input_type == 'tabular':
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	70 header = 'infer' if params['input_options']['header1'] else None
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	71 column_option = (params['input_options']
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	72 ['column_selector_options_1']
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	73 ['selected_column_selector_option'])
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	74 if column_option in ['by_index_number', 'all_but_by_index_number',
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	75 'by_header_name', 'all_but_by_header_name']:
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	76 c = params['input_options']['column_selector_options_1']['col1']
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	77 else:
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	78 c = None
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	79
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	80 df = pd.read_csv(infile1, sep='\t', header=header, parse_dates=True)
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	81
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	82 X = read_columns(df, c=c, c_option=column_option).astype(float)
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	83
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	84 if params['method'] == 'predict':
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	85 preds = estimator.predict(X)
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	86 else:
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	87 preds = estimator.predict_proba(X)
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	88
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	89 # sparse input
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	90 elif input_type == 'sparse':
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	91 X = mmread(open(infile1, 'r'))
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	92 if params['method'] == 'predict':
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	93 preds = estimator.predict(X)
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	94 else:
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	95 preds = estimator.predict_proba(X)
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	96
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	97 # fasta input
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	98 elif input_type == 'seq_fasta':
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	99 if not hasattr(estimator, 'data_batch_generator'):
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	100 raise ValueError(
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	101 "To do prediction on sequences in fasta input, "
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	102 "the estimator must be a `KerasGBatchClassifier`"
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	103 "equipped with data_batch_generator!")
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	104 pyfaidx = get_module('pyfaidx')
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	105 sequences = pyfaidx.Fasta(fasta_path)
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	106 n_seqs = len(sequences.keys())
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	107 X = np.arange(n_seqs)[:, np.newaxis]
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	108 seq_length = estimator.data_batch_generator.seq_length
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	109 batch_size = getattr(estimator, 'batch_size', 32)
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	110 steps = (n_seqs + batch_size - 1) // batch_size
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	111
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	112 seq_type = params['input_options']['seq_type']
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	113 klass = try_get_attr(
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	114 'galaxy_ml.preprocessors', seq_type)
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	115
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	116 pred_data_generator = klass(
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	117 fasta_path, seq_length=seq_length)
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	118
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	119 if params['method'] == 'predict':
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	120 preds = estimator.predict(
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	121 X, data_generator=pred_data_generator, steps=steps)
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	122 else:
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	123 preds = estimator.predict_proba(
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	124 X, data_generator=pred_data_generator, steps=steps)
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	125
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	126 # vcf input
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	127 elif input_type == 'variant_effect':
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	128 klass = try_get_attr('galaxy_ml.preprocessors',
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	129 'GenomicVariantBatchGenerator')
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	130
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	131 options = params['input_options']
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	132 options.pop('selected_input')
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	133 if options['blacklist_regions'] == 'none':
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	134 options['blacklist_regions'] = None
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	135
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	136 pred_data_generator = klass(
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	137 ref_genome_path=ref_seq, vcf_path=vcf_path, **options)
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	138
7 00819b7f2f55 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 756f8be9c3cd437e131e6410cd625c24fe078e8c" bgruening parents: 3 diff changeset	139 pred_data_generator.set_processing_attrs()
2 e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	140
3 963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: 2 diff changeset	141 variants = pred_data_generator.variants
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: 2 diff changeset	142
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: 2 diff changeset	143 # predict 1600 sample at once then write to file
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: 2 diff changeset	144 gen_flow = pred_data_generator.flow(batch_size=1600)
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: 2 diff changeset	145
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: 2 diff changeset	146 file_writer = open(outfile_predict, 'w')
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: 2 diff changeset	147 header_row = '\t'.join(['chrom', 'pos', 'name', 'ref',
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: 2 diff changeset	148 'alt', 'strand'])
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: 2 diff changeset	149 file_writer.write(header_row)
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: 2 diff changeset	150 header_done = False
2 e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	151
3 963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: 2 diff changeset	152 steps_done = 0
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: 2 diff changeset	153
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: 2 diff changeset	154 # TODO: multiple threading
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: 2 diff changeset	155 try:
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: 2 diff changeset	156 while steps_done < len(gen_flow):
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: 2 diff changeset	157 index_array = next(gen_flow.index_generator)
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: 2 diff changeset	158 batch_X = gen_flow._get_batches_of_transformed_samples(
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: 2 diff changeset	159 index_array)
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: 2 diff changeset	160
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: 2 diff changeset	161 if params['method'] == 'predict':
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: 2 diff changeset	162 batch_preds = estimator.predict(
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: 2 diff changeset	163 batch_X,
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: 2 diff changeset	164 # The presence of `pred_data_generator` below is to
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: 2 diff changeset	165 # override model carrying data_generator if there
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: 2 diff changeset	166 # is any.
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: 2 diff changeset	167 data_generator=pred_data_generator)
2 e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	168 else:
3 963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: 2 diff changeset	169 batch_preds = estimator.predict_proba(
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: 2 diff changeset	170 batch_X,
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: 2 diff changeset	171 # The presence of `pred_data_generator` below is to
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: 2 diff changeset	172 # override model carrying data_generator if there
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: 2 diff changeset	173 # is any.
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: 2 diff changeset	174 data_generator=pred_data_generator)
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: 2 diff changeset	175
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: 2 diff changeset	176 if batch_preds.ndim == 1:
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: 2 diff changeset	177 batch_preds = batch_preds[:, np.newaxis]
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: 2 diff changeset	178
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: 2 diff changeset	179 batch_meta = variants[index_array]
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: 2 diff changeset	180 batch_out = np.column_stack([batch_meta, batch_preds])
2 e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	181
3 963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: 2 diff changeset	182 if not header_done:
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: 2 diff changeset	183 heads = np.arange(batch_preds.shape[-1]).astype(str)
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: 2 diff changeset	184 heads_str = '\t'.join(heads)
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: 2 diff changeset	185 file_writer.write("\t%s\n" % heads_str)
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: 2 diff changeset	186 header_done = True
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: 2 diff changeset	187
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: 2 diff changeset	188 for row in batch_out:
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: 2 diff changeset	189 row_str = '\t'.join(row)
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: 2 diff changeset	190 file_writer.write("%s\n" % row_str)
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: 2 diff changeset	191
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: 2 diff changeset	192 steps_done += 1
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: 2 diff changeset	193
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: 2 diff changeset	194 finally:
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: 2 diff changeset	195 file_writer.close()
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: 2 diff changeset	196 # TODO: make api `pred_data_generator.close()`
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: 2 diff changeset	197 pred_data_generator.close()
963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: 2 diff changeset	198 return 0
2 e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	199 # end input
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	200
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	201 # output
3 963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: 2 diff changeset	202 if len(preds.shape) == 1:
2 e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	203 rval = pd.DataFrame(preds, columns=['Predicted'])
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	204 else:
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	205 rval = pd.DataFrame(preds)
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	206
3 963e449636d3 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16" bgruening parents: 2 diff changeset	207 rval.to_csv(outfile_predict, sep='\t', header=True, index=False)
2 e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	208
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	209
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	210 if __name__ == '__main__':
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	211 aparser = argparse.ArgumentParser()
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	212 aparser.add_argument("-i", "--inputs", dest="inputs", required=True)
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	213 aparser.add_argument("-e", "--infile_estimator", dest="infile_estimator")
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	214 aparser.add_argument("-w", "--infile_weights", dest="infile_weights")
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	215 aparser.add_argument("-X", "--infile1", dest="infile1")
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	216 aparser.add_argument("-O", "--outfile_predict", dest="outfile_predict")
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	217 aparser.add_argument("-f", "--fasta_path", dest="fasta_path")
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	218 aparser.add_argument("-r", "--ref_seq", dest="ref_seq")
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	219 aparser.add_argument("-v", "--vcf_path", dest="vcf_path")
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	220 args = aparser.parse_args()
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	221
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	222 main(args.inputs, args.infile_estimator, args.outfile_predict,
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	223 infile_weights=args.infile_weights, infile1=args.infile1,
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	224 fasta_path=args.fasta_path, ref_seq=args.ref_seq,
e18d9b17c322 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c035d399196b3bef9982db4f8e47331411dbb20e bgruening parents: diff changeset	225 vcf_path=args.vcf_path)

Mercurial > repos > bgruening > sklearn_stacking_ensemble_models

annotate model_prediction.py @ 7:00819b7f2f55 draft