--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/model_prediction.py	Fri Nov 01 17:26:59 2019 -0400
@@ -0,0 +1,262 @@
+import argparse
+import json
+import numpy as np
+import pandas as pd
+import tabix
+import warnings
+
+from scipy.io import mmread
+from sklearn.pipeline import Pipeline
+
+from galaxy_ml.externals.selene_sdk.sequences import Genome
+from galaxy_ml.utils import (load_model, read_columns,
+                             get_module, try_get_attr)
+
+
+N_JOBS = int(__import__('os').environ.get('GALAXY_SLOTS', 1))
+
+
+def main(inputs, infile_estimator, outfile_predict,
+         infile_weights=None, infile1=None,
+         fasta_path=None, ref_seq=None,
+         vcf_path=None):
+    """
+    Parameter
+    ---------
+    inputs : str
+        File path to galaxy tool parameter
+
+    infile_estimator : strgit
+        File path to trained estimator input
+
+    outfile_predict : str
+        File path to save the prediction results, tabular
+
+    infile_weights : str
+        File path to weights input
+
+    infile1 : str
+        File path to dataset containing features
+
+    fasta_path : str
+        File path to dataset containing fasta file
+
+    ref_seq : str
+        File path to dataset containing the reference genome sequence.
+
+    vcf_path : str
+        File path to dataset containing variants info.
+    """
+    warnings.filterwarnings('ignore')
+
+    with open(inputs, 'r') as param_handler:
+        params = json.load(param_handler)
+
+    # load model
+    with open(infile_estimator, 'rb') as est_handler:
+        estimator = load_model(est_handler)
+
+    main_est = estimator
+    if isinstance(estimator, Pipeline):
+        main_est = estimator.steps[-1][-1]
+    if hasattr(main_est, 'config') and hasattr(main_est, 'load_weights'):
+        if not infile_weights or infile_weights == 'None':
+            raise ValueError("The selected model skeleton asks for weights, "
+                             "but dataset for weights wan not selected!")
+        main_est.load_weights(infile_weights)
+
+    # handle data input
+    input_type = params['input_options']['selected_input']
+    # tabular input
+    if input_type == 'tabular':
+        header = 'infer' if params['input_options']['header1'] else None
+        column_option = (params['input_options']
+                               ['column_selector_options_1']
+                               ['selected_column_selector_option'])
+        if column_option in ['by_index_number', 'all_but_by_index_number',
+                             'by_header_name', 'all_but_by_header_name']:
+            c = params['input_options']['column_selector_options_1']['col1']
+        else:
+            c = None
+
+        df = pd.read_csv(infile1, sep='\t', header=header, parse_dates=True)
+
+        X = read_columns(df, c=c, c_option=column_option).astype(float)
+
+        if params['method'] == 'predict':
+            preds = estimator.predict(X)
+        else:
+            preds = estimator.predict_proba(X)
+
+    # sparse input
+    elif input_type == 'sparse':
+        X = mmread(open(infile1, 'r'))
+        if params['method'] == 'predict':
+            preds = estimator.predict(X)
+        else:
+            preds = estimator.predict_proba(X)
+
+    # fasta input
+    elif input_type == 'seq_fasta':
+        if not hasattr(estimator, 'data_batch_generator'):
+            raise ValueError(
+                "To do prediction on sequences in fasta input, "
+                "the estimator must be a `KerasGBatchClassifier`"
+                "equipped with data_batch_generator!")
+        pyfaidx = get_module('pyfaidx')
+        sequences = pyfaidx.Fasta(fasta_path)
+        n_seqs = len(sequences.keys())
+        X = np.arange(n_seqs)[:, np.newaxis]
+        seq_length = estimator.data_batch_generator.seq_length
+        batch_size = getattr(estimator, 'batch_size', 32)
+        steps = (n_seqs + batch_size - 1) // batch_size
+
+        seq_type = params['input_options']['seq_type']
+        klass = try_get_attr(
+            'galaxy_ml.preprocessors', seq_type)
+
+        pred_data_generator = klass(
+            fasta_path, seq_length=seq_length)
+
+        if params['method'] == 'predict':
+            preds = estimator.predict(
+                X, data_generator=pred_data_generator, steps=steps)
+        else:
+            preds = estimator.predict_proba(
+                X, data_generator=pred_data_generator, steps=steps)
+
+    # vcf input
+    elif input_type == 'variant_effect':
+        klass = try_get_attr('galaxy_ml.preprocessors',
+                             'GenomicVariantBatchGenerator')
+
+        options = params['input_options']
+        options.pop('selected_input')
+        if options['blacklist_regions'] == 'none':
+            options['blacklist_regions'] = None
+
+        pred_data_generator = klass(
+            ref_genome_path=ref_seq, vcf_path=vcf_path, **options)
+
+        pred_data_generator.fit()
+
+        variants = pred_data_generator.variants
+        # TODO : remove the following block after galaxy-ml v0.7.13
+        blacklist_tabix = getattr(pred_data_generator.reference_genome_,
+                                  '_blacklist_tabix', None)
+        clean_variants = []
+        if blacklist_tabix:
+            start_radius = pred_data_generator.start_radius_
+            end_radius = pred_data_generator.end_radius_
+
+            for chrom, pos, name, ref, alt, strand in variants:
+                center = pos + len(ref) // 2
+                start = center - start_radius
+                end = center + end_radius
+
+                if isinstance(pred_data_generator.reference_genome_, Genome):
+                    if "chr" not in chrom:
+                        chrom = "chr" + chrom
+                    if "MT" in chrom:
+                        chrom = chrom[:-1]
+                try:
+                    rows = blacklist_tabix.query(chrom, start, end)
+                    found = 0
+                    for row in rows:
+                        found = 1
+                        break
+                    if found:
+                        continue
+                except tabix.TabixError:
+                    pass
+
+                clean_variants.append((chrom, pos, name, ref, alt, strand))
+        else:
+            clean_variants = variants
+
+        setattr(pred_data_generator, 'variants', clean_variants)
+
+        variants = np.array(clean_variants)
+        # predict 1600 sample at once then write to file
+        gen_flow = pred_data_generator.flow(batch_size=1600)
+
+        file_writer = open(outfile_predict, 'w')
+        header_row = '\t'.join(['chrom', 'pos', 'name', 'ref',
+                                'alt', 'strand'])
+        file_writer.write(header_row)
+        header_done = False
+
+        steps_done = 0
+
+        # TODO: multiple threading
+        try:
+            while steps_done < len(gen_flow):
+                index_array = next(gen_flow.index_generator)
+                batch_X = gen_flow._get_batches_of_transformed_samples(
+                    index_array)
+
+                if params['method'] == 'predict':
+                    batch_preds = estimator.predict(
+                        batch_X,
+                        # The presence of `pred_data_generator` below is to
+                        # override model carrying data_generator if there
+                        # is any.
+                        data_generator=pred_data_generator)
+                else:
+                    batch_preds = estimator.predict_proba(
+                        batch_X,
+                        # The presence of `pred_data_generator` below is to
+                        # override model carrying data_generator if there
+                        # is any.
+                        data_generator=pred_data_generator)
+
+                if batch_preds.ndim == 1:
+                    batch_preds = batch_preds[:, np.newaxis]
+
+                batch_meta = variants[index_array]
+                batch_out = np.column_stack([batch_meta, batch_preds])
+
+                if not header_done:
+                    heads = np.arange(batch_preds.shape[-1]).astype(str)
+                    heads_str = '\t'.join(heads)
+                    file_writer.write("\t%s\n" % heads_str)
+                    header_done = True
+
+                for row in batch_out:
+                    row_str = '\t'.join(row)
+                    file_writer.write("%s\n" % row_str)
+
+                steps_done += 1
+
+        finally:
+            file_writer.close()
+            # TODO: make api `pred_data_generator.close()`
+            pred_data_generator.close()
+        return 0
+    # end input
+
+    # output
+    if len(preds.shape) == 1:
+        rval = pd.DataFrame(preds, columns=['Predicted'])
+    else:
+        rval = pd.DataFrame(preds)
+
+    rval.to_csv(outfile_predict, sep='\t', header=True, index=False)
+
+
+if __name__ == '__main__':
+    aparser = argparse.ArgumentParser()
+    aparser.add_argument("-i", "--inputs", dest="inputs", required=True)
+    aparser.add_argument("-e", "--infile_estimator", dest="infile_estimator")
+    aparser.add_argument("-w", "--infile_weights", dest="infile_weights")
+    aparser.add_argument("-X", "--infile1", dest="infile1")
+    aparser.add_argument("-O", "--outfile_predict", dest="outfile_predict")
+    aparser.add_argument("-f", "--fasta_path", dest="fasta_path")
+    aparser.add_argument("-r", "--ref_seq", dest="ref_seq")
+    aparser.add_argument("-v", "--vcf_path", dest="vcf_path")
+    args = aparser.parse_args()
+
+    main(args.inputs, args.infile_estimator, args.outfile_predict,
+         infile_weights=args.infile_weights, infile1=args.infile1,
+         fasta_path=args.fasta_path, ref_seq=args.ref_seq,
+         vcf_path=args.vcf_path)