Mercurial > repos > scottx611x > data_manager_fetch_gene_annotation
comparison data_manager_gene_annotation/data_manager/data_manager.py @ 16:9002c2f64e2a draft
Uploaded
| author | scottx611x |
|---|---|
| date | Wed, 22 Jun 2016 16:35:28 -0400 |
| parents | 6261b513ae1b |
| children | 6a67977a23da |
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| 15:6261b513ae1b | 16:9002c2f64e2a |
|---|---|
| 28 | 28 |
| 29 args = parser.parse_args() | 29 args = parser.parse_args() |
| 30 | 30 |
| 31 | 31 |
| 32 def url_download(url, name, workdir): | 32 def url_download(url, name, workdir): |
| 33 # Create path if it doesn't exist | |
| 34 if not os.path.exists(workdir): | |
| 35 os.makedirs(workdir) | |
| 36 | 33 |
| 37 response = requests.get(url=url, stream=True) | 34 response = requests.get(url=url, stream=True) |
| 38 | 35 |
| 39 # Create path that we will write the file to | 36 # Create path that we will write the file to |
| 40 file_path = os.path.join(workdir, 'download_{}.dat'.format(name)) | 37 file_path = 'download_{}.dat'.format(name) |
| 41 | 38 |
| 42 block_size = 10 * 1024 * 1024 # 10MB chunked download | 39 block_size = 10 * 1024 * 1024 # 10MB chunked download |
| 43 with open(file_path, 'w+') as f: | 40 with open(file_path, 'w+') as f: |
| 44 try: | 41 try: |
| 45 for buf in response.iter_content(block_size): | 42 for buf in response.iter_content(block_size): |
| 54 | 51 |
| 55 def main(args): | 52 def main(args): |
| 56 workdir = os.path.join(os.getcwd(), 'gene_annotation') | 53 workdir = os.path.join(os.getcwd(), 'gene_annotation') |
| 57 | 54 |
| 58 # Attempt to download gene annotation file from given url | 55 # Attempt to download gene annotation file from given url |
| 59 gene_annotation_file_path = url_download(args.url, args.name, workdir) | 56 gene_annotation_file_path = url_download("http://www.scott-ouellette.com/gene_annotations/chr1-hg19_genes.gtf", args.name, workdir) |
| 60 | 57 |
| 61 # Update Data Manager Json and write out | 58 # Update Data Manager Json and write out |
| 62 data_manager_entry = { | 59 data_manager_entry = { |
| 63 'data_tables': { | 60 'data_tables': { |
| 64 'gene_annotation': { | 61 'gene_annotation': { |
| 65 'date': str(datetime.datetime.now()), | 62 'date': str(datetime.datetime.now()), |
| 66 'dbkey': str(args.name), | 63 'dbkey': str(args.name), |
| 67 'name': str(args.name), | 64 'name': str(args.name), |
| 68 'path': gene_annotation_file_path, | |
| 69 } | 65 } |
| 70 } | 66 } |
| 71 } | 67 } |
| 72 | 68 |
| 73 with open(os.path.join(workdir, args.output), "w+") as f: | 69 with open(os.path.join(workdir, args.output), "w+") as f: |