tanu/LSHTM_analysis
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minor cody tidy up

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Tanushree Tunstall 2021-02-12 16:50:34 +00:00
parent 9c221e6786
commit b2397ea99d
2 changed files with 9 additions and 9 deletions
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10
dynamut/examples.py
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@ -8,16 +8,16 @@ Created on Fri Feb 12 12:15:26 2021
import os
homedir = os.path.expanduser('~')
os.chdir (homedir + '/git/LSHTM_analysis/dynamut')
from get_results import *
from submit import *
from get_results import *
#%%#####################################################################
#EXAMPLE RUN for different stages
#=====================
# STAGE: submit.py
#=====================
my_host = 'http://biosig.unimelb.edu.au'
my_prediction_url = f"{host}/dynamut/prediction_list"
print(prediction_url)
my_prediction_url = f"{my_host}/dynamut/prediction_list"
print(my_prediction_url)
my_outdir = homedir + '/git/LSHTM_analysis/dynamut'
my_chain = 'A'
@ -40,7 +40,7 @@ submit_dynamut(host_url = my_host
, outfile_suffix = my_suffix)
#%%###################################################################
#=====================
# STAGE:get_results.py
# STAGE: get_results.py
#=====================
my_host = 'http://biosig.unimelb.edu.au'
my_outdir = homedir + '/git/LSHTM_analysis/dynamut'
@ -68,4 +68,4 @@ get_results(my_url_file_single
, host_url = my_host
, output_dir = my_outdir
, outfile_suffix = my_suffix)
#%%###################################################################
#%%###################################################################

8
dynamut/submit.py
View file

@ -41,19 +41,19 @@ def submit_dynamut(host_url
@param chain: single-letter(caps)
@type chr
@param email_address: email address to inform of results
@type chr
@param prediction_url: dynamut url for prediction
@type string
@param output_dir: output dir
@type string
@param outfile_suffix: outfile_suffix
@type string, default is batch no.
@param outfile_suffix: to append to outfile
@type string
@return writes a .txt file containing url for the snps processed with user provided suffix in filename
@return writes a .txt file containing url for the snps processed with user provided suffix in filename
@type string
"""