def my_genome_annotation_file(my_data_pypath):
_LOGGER.info('Downloading the genome annotation file...')
url = 'https://www.dropbox.com/s/7oexg6k6aqukzi3/genome_annotations_human_ensembl88_test.gtf.gz?dl=1'
path = str(
my_data_pypath.join('genome_annotations_human_ensembl88_test.gtf.gz'))
misc.http_download(url, path)
return path
def my_gene_file(my_data_pypath):
"""Protein-coding gene file."""
_LOGGER.info('Downloading the gene file...')
url = 'https://www.dropbox.com/s/o3tfaubrcoe92cr/protein_coding_genes_human_ensembl88.tsv?dl=1'
path = str(my_data_pypath.join('protein_coding_genes_human_ensembl88.tsv'))
misc.http_download(url, path)
return path
def my_mrna_read_file(my_data_pypath):
"""mRNA reads"""
_LOGGER.info('Downloading the mRNA read file...')
url = 'https://www.dropbox.com/s/nxu3o28mj7kpm4l/SRR3879606_10k_2.fastq.gz?dl=1'
path = str(my_data_pypath.join('mRNA_reads.fastq.gz'))
misc.http_download(url, path)
return path
def my_barcode_read_file(my_data_pypath):
"""barcode reads"""
_LOGGER.info('Downloading the mRNA read file...')
url = 'https://www.dropbox.com/s/has2sys148jwlwf/SRR3879606_10k_1.fastq.gz?dl=1'
path = str(my_data_pypath.join('barocde_reads.fastq.gz'))
misc.http_download(url, path)
return path
def my_alignment_file(my_data_pypath):
"""Alignment file."""
_LOGGER.info('Downloading the alignment file (+ index file)...')
url = 'https://www.dropbox.com/s/1bkwa3puy504eys/SRR3879606_10k.bam.bai?dl=1'
path = str(my_data_pypath.join('alignment.bam.bai'))
misc.http_download(url, path)
url = 'https://www.dropbox.com/s/jx0049j7w6pbei3/SRR3879606_10k.bam?dl=1'
path = str(my_data_pypath.join('alignment.bam'))
misc.http_download(url, path)
return path
def test_http_download(my_temp_dir):
"""Tests `http_download` function."""
download_file = text(my_temp_dir.join('google.htm'))
misc.http_download('https://www.google.com', download_file)
assert os.stat(download_file).st_size > 0
def test_http_download(my_temp_dir):
"""Tests `http_download` function."""
download_file = text(my_temp_dir.join('google.htm'))
misc.http_download('https://www.google.com', download_file)
assert os.stat(download_file).st_size > 0
def my_gene_expression_filtered_file(my_data_pypath):
_LOGGER.info('Downloading the filtered gene expression file...')
url = 'https://www.dropbox.com/s/1kixrh0cvgf5jqo/SRR3879606_gene_expression_filtered.tsv?dl=1'
path = str(my_data_pypath.join('gene_expression_filtered.tsv'))
misc.http_download(url, path)
return path
def my_barcode_counts_mapped_file(my_data_pypath):
_LOGGER.info('Downloading the mapped barcode counts file...')
url = 'https://www.dropbox.com/s/mq0v2dyskomjoon/SRR3879606_10k_barcode_counts_mapped.tsv?dl=1'
path = str(my_data_pypath.join('barcode_counts_mapped.tsv'))
misc.http_download(url, path)
return path
def my_chromosome_length_file(my_data_pypath):
"""Chromosome length file."""
url = 'https://www.dropbox.com/s/mw8o9ur48pr1squ/chromosome_lengths_human_GRCh38.tsv?dl=1'
path = str(my_data_pypath.join('chromosome_lengths_human_GRCh38.tsv'))
misc.http_download(url, path)
return path