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