Mercurial > repos > dchristiany > data_manager_proteore
changeset 29:871a7347ca24 draft
planemo upload commit c89c5deac442c0c2aa52b24f2c5af4b290773fc0-dirty
| author | dchristiany |
|---|---|
| date | Mon, 28 Jan 2019 05:16:55 -0500 |
| parents | d235909789ca |
| children | b8271b9a1049 |
| files | data_manager/resource_building.py data_manager/resource_building.xml |
| diffstat | 2 files changed, 28 insertions(+), 8 deletions(-) [+] |
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--- a/data_manager/resource_building.py Fri Jan 25 09:38:35 2019 -0500 +++ b/data_manager/resource_building.py Mon Jan 28 05:16:55 2019 -0500 @@ -60,17 +60,16 @@ # 2. Peptide Atlas ####################################################################################################### def peptide_atlas_sources(data_manager_dict, tissue, target_directory): - # Define PA Human build released number (here early 2018) - atlas_build_id = "472" # Define organism_id (here Human) - to be upraded when other organism added to the project organism_id = "2" # Extract sample_category_id and output filename - sample_category_id = tissue.split("-")[0] - output_file = tissue.split("-")[1] +"_"+ time.strftime("%d-%m-%Y") + ".tsv" - query = "https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/GetPeptides?atlas_build_id=" + \ - atlas_build_id + "&display_options=ShowMappings&organism_id= " + \ - organism_id + "&sample_category_id=" + sample_category_id + \ - "&QUERY_NAME=AT_GetPeptides&output_mode=tsv&apply_action=QUERY" + tissue=tissue.split(".") + sample_category_id = tissue[0] + name = tissue[1] + output_file = name+"_"+time.strftime("%d-%m-%Y") + ".tsv" + query="https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/GetProteins?&atlas_build_id="+sample_category_id+ \ + "&display_options=ShowAbundances&organism_id="+organism_id+"&redundancy_constraint=4&presence_level_constraint=1%2C2"+ \ + "&gene_annotation_level_constraint=leaf&QUERY_NAME=AT_GetProteins&action=QUERY&output_mode=tsv&apply_action=QUERY" download = requests.get(query) decoded_content = download.content.decode('utf-8') cr = csv.reader(decoded_content.splitlines(), delimiter='\t')
--- a/data_manager/resource_building.xml Fri Jan 25 09:38:35 2019 -0500 +++ b/data_manager/resource_building.xml Mon Jan 28 05:16:55 2019 -0500 @@ -41,6 +41,27 @@ </when> <when value="peptide_atlas"> <param name="tissues" type="select" multiple="false" label="Please select the tissue"> + <option value="432.Human_Adrenal_gland">Human Adrenal gland proteome</option> + <option value="441.Human_Brain">Human Brain proteome</option> + <option value="427.Human_Breast">Human Breast proteome</option> + <option value="434.Human_CSF">Human CSF (Cerebro Spinal Fluid) proteome</option> + <option value="374.Human_Colon_cancer">Human Colon cancer proteome</option> + <option value="429.Human_Digestive_system">Human Digestive system proteome</option> + <option value="430.Human_Female_reproductive_system">Human Female reproductive system proteome></option> + <option value="418.Human_Heart">Human Heart proteome</option> + <option value="424.Human_Kidney">Human Kidney proteome</option> + <option value="425.Human_Liver">Human Liver proteome</option> + <option value="419.Human_Lung">Human Lung proteome</option> + <option value="431.Human_Male_reproductive_system">Human Male reproductive system proteome</option> + <option value="420.Human_Pancreas">Human Pancreas proteome</option> + <option value="465.Human_Plasma_non_glyco">Human Plasma non glyco proteome</option> + <option value="421.Human_Spleen">Human Spleen proteome</option> + <option value="463.Human_Testis">Human Testis proteome</option> + <option value="422.Human_Urinary_bladder">Human Bladder proteome</option> + <option value="423.Human_Urine">Human Urine proteome</option> + + + <option value="1-Human_Liver">Human liver</option> <option value="2-Human_Brain">Human brain</option> <option value="4-Human_Heart">Human heart</option>