Mercurial > repos > dchristiany > data_manager_proteore

comparison data_manager/resource_building.py @ 35:b312ea6438a2 draft

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planemo upload commit c89c5deac442c0c2aa52b24f2c5af4b290773fc0-dirty
author dchristiany
date Mon, 28 Jan 2019 09:28:06 -0500
parents 0c0586ac3e29
children a4811c440b45
comparison
equal deleted inserted replaced
34:0c0586ac3e29 35:b312ea6438a2
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="+ \
72 sample_category_id+"&display_options=ShowAbundances&organism_id="+organism_id+ \ 72 sample_category_id+"&display_options=ShowAbundances&organism_id="+organism_id+ \
73 "&redundancy_constraint=4&presence_level_constraint=1%2C2&gene_annotation_level_constraint=leaf\ 73 "&redundancy_constraint=4&presence_level_constraint=1%2C2&gene_annotation_level_constraint=leaf\
74 &QUERY_NAME=AT_GetProteins&action=QUERY&output_mode=tsv&apply_action=QUERY" 74 &QUERY_NAME=AT_GetProteins&action=QUERY&output_mode=tsv&apply_action=QUERY"
75
76 print (query)
77 75
78 with requests.Session() as s: 76 with requests.Session() as s:
79 download = s.get(query) 77 download = s.get(query)
80 decoded_content = download.content.decode('utf-8') 78 decoded_content = download.content.decode('utf-8')
81 cr = csv.reader(decoded_content.splitlines(), delimiter='\t') 79 cr = csv.reader(decoded_content.splitlines(), delimiter='\t')