Mercurial > repos > dchristiany > data_manager_proteore

comparison data_manager/resource_building.py @ 32:76924e57a230 draft

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planemo upload commit c89c5deac442c0c2aa52b24f2c5af4b290773fc0-dirty
author dchristiany
date Mon, 28 Jan 2019 08:34:02 -0500
parents b8271b9a1049
children cdeffb3670c3
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31:e248f8f532a7 32:76924e57a230
61 ####################################################################################################### 61 #######################################################################################################
62 def peptide_atlas_sources(data_manager_dict, tissue, target_directory): 62 def peptide_atlas_sources(data_manager_dict, tissue, target_directory):
63 # Define organism_id (here Human) - to be upraded when other organism added to the project 63 # Define organism_id (here Human) - to be upraded when other organism added to the project
64 organism_id = "2" 64 organism_id = "2"
65 # Extract sample_category_id and output filename 65 # Extract sample_category_id and output filename
66 tissue=tissue.split(".") 66 tissue=tissue.split("-")
67 sample_category_id = tissue[0] 67 sample_category_id = tissue[0]
68 name = tissue[1] 68 name = tissue[1]
69 output_file = name+"_"+time.strftime("%d-%m-%Y") + ".tsv" 69 output_file = name+"_"+time.strftime("%d-%m-%Y") + ".tsv"
70 70
71 query="https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/GetProteins?&atlas_build_id="+ \ 71 query="https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/GetProteins?&atlas_build_id="+ \