Mercurial > repos > dchristiany > data_manager_proteore
comparison data_manager/resource_building.py @ 35:b312ea6438a2 draft
planemo upload commit c89c5deac442c0c2aa52b24f2c5af4b290773fc0-dirty
author | dchristiany |
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date | Mon, 28 Jan 2019 09:28:06 -0500 |
parents | 0c0586ac3e29 |
children | a4811c440b45 |
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34:0c0586ac3e29 | 35:b312ea6438a2 |
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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') |