view @ 29:95d0f81e46e8 draft

"planemo upload for repository commit eb703290e2589561ea215c84aa9f71bcfe1712c6"
author bgruening
date Fri, 01 Nov 2019 17:14:31 -0400
parents 8e49f26b14d3
children 64b771b1471a
line wrap: on
line source

import argparse
import json
import numpy as np
import pandas as pd
import tabix
import warnings

from 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,
    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.

    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!")

    # 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']
        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']
            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)
            preds = estimator.predict_proba(X)

    # sparse input
    elif input_type == 'sparse':
        X = mmread(open(infile1, 'r'))
        if params['method'] == 'predict':
            preds = estimator.predict(X)
            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)
            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',

        options = params['input_options']
        if options['blacklist_regions'] == 'none':
            options['blacklist_regions'] = None

        pred_data_generator = klass(
            ref_genome_path=ref_seq, vcf_path=vcf_path, **options)

        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]
                    rows = blacklist_tabix.query(chrom, start, end)
                    found = 0
                    for row in rows:
                        found = 1
                    if found:
                except tabix.TabixError:

                clean_variants.append((chrom, pos, name, ref, alt, strand))
            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'])
        header_done = False

        steps_done = 0

        # TODO: multiple threading
            while steps_done < len(gen_flow):
                index_array = next(gen_flow.index_generator)
                batch_X = gen_flow._get_batches_of_transformed_samples(

                if params['method'] == 'predict':
                    batch_preds = estimator.predict(
                        # The presence of `pred_data_generator` below is to
                        # override model carrying data_generator if there
                        # is any.
                    batch_preds = estimator.predict_proba(
                        # The presence of `pred_data_generator` below is to
                        # override model carrying data_generator if there
                        # is any.

                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

            # TODO: make api `pred_data_generator.close()`
        return 0
    # end input

    # output
    if len(preds.shape) == 1:
        rval = pd.DataFrame(preds, columns=['Predicted'])
        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,