From e48f215227a0b3e9459d47d71f0b66dd36eb6af0 Mon Sep 17 00:00:00 2001 From: Tanushree Tunstall Date: Thu, 12 Aug 2021 10:06:43 +0100 Subject: [PATCH] ran b9 and b10 for gid after Dynamut team reran due to server issues --- dynamut/get_results_dynamut.py | 2 +- dynamut/run_get_results_dynamut.py | 19 ++++++++++--------- 2 files changed, 11 insertions(+), 10 deletions(-) diff --git a/dynamut/get_results_dynamut.py b/dynamut/get_results_dynamut.py index d79c4f1..4c293b0 100755 --- a/dynamut/get_results_dynamut.py +++ b/dynamut/get_results_dynamut.py @@ -86,7 +86,7 @@ def get_results(url_file, host_url, output_dir, outfile_suffix): # Download .tar.gz file prediction_number = re.search(r'([0-9]+$)', line).group(0) tgz_url = f"{host_url}/dynamut/results_file/results_" + prediction_number + '.tar.gz' - tgz_filename = dynamut_results_dir + '/' + outfile_suffix + '_results_' + prediction_number + '.tar.gz' + tgz_filename = dynamut_results_dir + outfile_suffix + '_results_' + prediction_number + '.tar.gz' response_tgz = requests.get(tgz_url, stream = True) if response_tgz.status_code == 200: print('\nDownloading tar.gz file:', tgz_url diff --git a/dynamut/run_get_results_dynamut.py b/dynamut/run_get_results_dynamut.py index 872b03e..423204a 100755 --- a/dynamut/run_get_results_dynamut.py +++ b/dynamut/run_get_results_dynamut.py @@ -22,28 +22,29 @@ drug = 'streptomycin' datadir = homedir + '/git/Data/' indir = datadir + drug + '/input/' outdir = datadir + drug + '/output/' -outdir_dynamut_temp = datadir + drug + '/output/dynamut_results/dynamut_temp/' +outdir_dynamut_temp = outdir + 'dynamut_results/dynamut_temp/' #============================================================================== # batch 8: 08.txt, # RETRIEVED 23 Feb 08:54 #my_url_file = outdir + '/dynamut_temp/dynamut_result_url_gid_b8.txt' #my_suffix = 'gid_b7' -#b09 and b10 failed! +#b09 and b10 failed, ran by Carlos, and returned results on 12 Aug -# batch 9: 09.txt, -my_url_file = outdir_dynamut_temp + 'dynamut_result_url_gid_b10_ab.txt' -my_suffix = 'gid_b10_ab' +# batch 9 and 10: RETRIEVED 12 Aug 09:25 +my_url_file = outdir_dynamut_temp + 'dynamut_result_url_gid_b10.txt' +my_suffix = 'gid_b10' #============================================================================== #========================== # CALL: get_results() # Data: gid+streptomycin #========================== -print(my_url_file, 'suffix:', my_suffix) +# output file saves in dynamut_results/ (created if it doesn't exist) inside outdir +print('Fetching results from url file :', my_url_file, '\nsuffix:', my_suffix) get_results(url_file = my_url_file - , host_url = my_host - , output_dir = outdir - , outfile_suffix = my_suffix) + , host_url = my_host + , output_dir = outdir + , outfile_suffix = my_suffix) ########################################################################