Python get_feature_seq Examples

Example #1

File: quality_exp_runs.py Project: vipints/genomeutils

def fetch_training_examples():
    """
    """

    from signal_labels import fetch_signal_seq_examples as fetch_seq
    from data_quality_check import split_train_test_examples

    fetch_seq.get_feature_seq(
        "H_sapiens/ensembl_release_79/STARgenome/hg19_chrOnly.fa",
        "../H_sapiens_stringtie_genes.gff")

    split_train_test_examples.split_data_random_non_overlap()

    split_train_test_examples.get_matching_neg_example(
        "tss_sig_pos_example_1.fa", "tss_sig_neg_example.fa",
        "tss_sig_neg_example_1.fa")
    split_train_test_examples.get_matching_neg_example(
        "tss_sig_pos_example_2.fa", "tss_sig_neg_example.fa",
        "tss_sig_neg_example_2.fa")
    split_train_test_examples.get_matching_neg_example(
        "tss_sig_pos_example_3.fa", "tss_sig_neg_example.fa",
        "tss_sig_neg_example_3.fa")

Example #2

File: quality_exp_runs.py Project: vipints/genomeutils

def fetch_training_examples():
    """
    """

    from signal_labels import fetch_signal_seq_examples as fetch_seq
    from data_quality_check import split_train_test_examples

    fetch_seq.get_feature_seq(
        "H_sapiens/ensembl_release_79/STARgenome/hg19_chrOnly.fa", "../H_sapiens_stringtie_genes.gff"
    )

    split_train_test_examples.split_data_random_non_overlap()

    split_train_test_examples.get_matching_neg_example(
        "tss_sig_pos_example_1.fa", "tss_sig_neg_example.fa", "tss_sig_neg_example_1.fa"
    )
    split_train_test_examples.get_matching_neg_example(
        "tss_sig_pos_example_2.fa", "tss_sig_neg_example.fa", "tss_sig_neg_example_2.fa"
    )
    split_train_test_examples.get_matching_neg_example(
        "tss_sig_pos_example_3.fa", "tss_sig_neg_example.fa", "tss_sig_neg_example_3.fa"
    )

Example #3

File: fetch_training_points.py Project: kuod/genomeutils

from signal_labels import fetch_signal_seq_examples as fetch_seq 
from data_quality_check import split_train_test_examples

fetch_seq.get_feature_seq("H_sapiens/ensembl_release_79/STARgenome/hg19_chrOnly.fa", "../H_sapiens_stringtie_genes.gff")
split_train_test_examples.split_data_random_non_overlap() 

split_train_test_examples.get_matching_neg_example("tss_sig_pos_example_1.fa", "tss_sig_neg_example.fa", "tss_sig_neg_example_1.fa") 
split_train_test_examples.get_matching_neg_example("tss_sig_pos_example_2.fa", "tss_sig_neg_example.fa", "tss_sig_neg_example_2.fa") 
split_train_test_examples.get_matching_neg_example("tss_sig_pos_example_3.fa", "tss_sig_neg_example.fa", "tss_sig_neg_example_3.fa")