impc_tools: impc_tool.py annotate

author	andrea.furlani
date	Thu, 09 Jun 2022 10:51:23 +0000
parents
children

rev	line source
0 4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	1 import sys
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	2 import requests
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	3 import pandas as pd
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	4 import urllib.request as url
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	5
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	6 impc_api_url = "https://www.gentar.org/impc-dev-api/"
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	7 impc_api_search_url = f"{impc_api_url}/genes"
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	8 impc_api_gene_bundle_url = f"{impc_api_url}/geneBundles"
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	9
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	10
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	11 def stop_err(msg):
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	12 sys.exit(msg)
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	13
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	14
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	15 def main():
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	16 inp = str(sys.argv[1])
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	17 query = str(sys.argv[3])
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	18
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	19 try:
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	20 if query == '7':
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	21 full_gene_table()
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	22 sys.exit(0)
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	23
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	24 if str(sys.argv[5])=="txt":
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	25 s = str(sys.argv[6])
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	26 if s == "t":
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	27 sep = "\t"
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	28 elif s == "s":
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	29 sep = " "
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	30 elif s in ",;.":
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	31 sep = s
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	32 else:
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	33 sys.exit("Separator not valid, please change it.")
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	34 inp = pd.read_csv(inp, header=None, delimiter=sep)
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	35 if len(inp.columns)==1:
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	36 inp = str(inp[0].values[0]).replace("'","")
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	37 else:
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	38 inp = inp.to_string(header=False, index=False).replace(" ",",")
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	39
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	40 if query == '8':
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	41 genes_in_pipeline(inp)
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	42 sys.exit(0)
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	43 elif query == '10': # it's here but not totally implemented
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	44 par_pip_ma(inp)
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	45 sys.exit(0)
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	46 elif query == '11': # it's here but not totally implemented
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	47 par_gen(inp)
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	48 sys.exit(0)
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	49 else:
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	50 tmp = inp.split(",")
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	51 final_list = []
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	52 sym_list = []
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	53 for i in tmp:
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	54 if 'MGI:' in i or 'MP:' in i:
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	55 final_list.append(i)
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	56 else:
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	57 sym_list.append(i)
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	58 del(i)
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	59 if len(sym_list) != 0:
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	60 sym_list = ",".join(sym_list)
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	61 biodbnet = f'https://biodbnet.abcc.ncifcrf.gov/webServices/rest.php/biodbnetRestApi.xml?method=db2db&format=row&input=genesymbol&inputValues={sym_list}&outputs=mgiid&taxonId=10090'
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	62 u = url.urlopen(biodbnet)
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	63 db = pd.read_xml(u, elems_only=True)
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	64 if len(db) == 0 and len(final_list) == 0:
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	65 stop_err("It was not possible to map the input.")
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	66 else:
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	67 for i in range(0,len(db)):
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	68 final_list.append(db['MGIID'][i][4:])
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	69
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	70 inp= ",".join(final_list)
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	71
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	72
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	73 if query == '1':
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	74 get_pheno(inp)
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	75 sys.exit(0)
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	76 elif query == '2':
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	77 get_genes(inp)
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	78 sys.exit(0)
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	79 elif query == '3':
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	80 gene_set(inp)
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	81 sys.exit(0)
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	82 elif query == '4':
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	83 extr_img(inp)
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	84 sys.exit(0)
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	85 elif query == '5':
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	86 parameters(inp)
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	87 sys.exit(0)
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	88 elif query == '6':
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	89 sign_par(inp)
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	90 sys.exit(0)
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	91 elif query == '9':
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	92 sign_mp(inp)
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	93 sys.exit(0)
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	94 else:
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	95 stop_err("Error, non-implemented query selected: " + query)
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	96 except Exception as ex:
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	97 stop_err('Error running get_pheno.py:\n' + str(ex))
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	98
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	99
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	100 # 1-Given a gene id, retrieve all the phenotypes related to it (id and name)
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	101 def get_pheno(inp):
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	102 head = sys.argv[4]
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	103 mgi_accession_id = inp
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	104
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	105 gene_url = f"{impc_api_search_url}/{mgi_accession_id}"
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	106 gene_data = requests.get(gene_url).json()
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	107
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	108 p_list = []
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	109 id_list = []
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	110
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	111 if gene_data['significantMpTerms'] == None:
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	112 stop_err("No significant MP terms found for this gene")
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	113 else:
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	114 for x in gene_data['significantMpTerms']:
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	115 p_list.append(x['mpTermId'])
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	116 id_list.append(x['mpTermName'])
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	117
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	118 df = pd.DataFrame()
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	119 df['MP term name'] = p_list
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	120 df['MP term id'] = id_list
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	121
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	122 if head == 'True':
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	123 df.to_csv(sys.argv[2], header=True, index=False, sep="\t", index_label=False)
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	124 else:
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	125 df.to_csv(sys.argv[2], header=False, index=False, sep="\t", index_label=False)
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	126
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	127
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	128 # 3-Extract all genes having a particular phenotype or a set of phenotypes (e.g. relevant to a disease)
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	129 def get_genes(inp):
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	130 head = sys.argv[4]
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	131 target_mp_terms = inp
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	132
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	133 ## All the data is paginated using the page and size parameters, by default the endpoint returns the first 20 hits
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	134 gene_by_phenotypes_query = f"{impc_api_search_url}/search/findAllBySignificantMpTermIdsContains?mpTermIds={target_mp_terms}&page=0&size=20"
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	135 genes_with_clinical_chemistry_phenotypes = requests.get(gene_by_phenotypes_query).json()
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	136 print(f"Genes with {target_mp_terms}: {genes_with_clinical_chemistry_phenotypes['page']['totalElements']}")
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	137 list_of_genes = pd.DataFrame(columns=['Gene accession id', 'Gene name', 'Gene bundle url'])
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	138 acc = []
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	139 name = []
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	140 url = []
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	141
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	142 for gene in genes_with_clinical_chemistry_phenotypes['_embedded']['genes']:
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	143 acc.append(gene['mgiAccessionId'])
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	144 name.append(gene['markerName'])
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	145 url.append(gene['_links']['geneBundle']['href'])
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	146
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	147 list_of_genes['Gene accession id'] = acc
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	148 list_of_genes['Gene name'] = name
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	149 list_of_genes['Gene bundle url'] = url
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	150
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	151 if head == 'True':
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	152 list_of_genes.to_csv(sys.argv[2], header=True, index=False, sep="\t", index_label=False)
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	153 else:
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	154 list_of_genes.to_csv(sys.argv[2], header=False, index=False, sep="\t", index_label=False)
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	155
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	156 # 4. Extract all phenotypes which are present in a particular gene set (e.g. genes together in a pathway)
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	157
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	158 def gene_set(inp):
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	159 head = sys.argv[4]
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	160 target_genes = inp
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	161
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	162 genes_in_gene_list_query = f"{impc_api_search_url}/search/findAllByMgiAccessionIdIn?mgiAccessionIds={target_genes}"
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	163
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	164 genes_in_gene_list = requests.get(genes_in_gene_list_query).json()
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	165 list_of_mp_terms_vs_gene_index = {}
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	166
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	167 for gene in genes_in_gene_list['_embedded']['genes']:
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	168 mp_terms = gene['significantMpTerms']
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	169 gene_acc_id = gene["mgiAccessionId"]
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	170 if mp_terms is None:
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	171 continue
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	172 for mp_term_name in mp_terms:
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	173 if mp_term_name['mpTermId'] not in list_of_mp_terms_vs_gene_index:
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	174 list_of_mp_terms_vs_gene_index[mp_term_name['mpTermId']] = {"mp_term": mp_term_name['mpTermId'], "genes": []}
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	175 list_of_mp_terms_vs_gene_index[mp_term_name['mpTermId']]["genes"].append(gene_acc_id)
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	176 genes_by_mp_term = list(list_of_mp_terms_vs_gene_index.values())
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	177
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	178 df = pd.DataFrame()
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	179 terms = []
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	180 genes = []
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	181 for i in genes_by_mp_term:
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	182 terms.append(i['mp_term'])
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	183 genes.append(i['genes'])
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	184
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	185 df['mp_term'] = terms
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	186 df['genes'] = genes
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	187
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	188 if head == 'True':
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	189 df.to_csv(sys.argv[2], header=True, index=False, sep="\t", index_label=False)
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	190 else:
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	191 df.to_csv(sys.argv[2], header=False, index=False, sep="\t", index_label=False)
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	192
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	193 # 7. Extract images with a particular phenotype or a set of phenotypes
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	194
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	195
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	196 def extr_img(inp):
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	197 head = sys.argv[4]
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	198 target_mp_terms = inp # ['MP:0002110', 'MP:0000559']
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	199
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	200 ## All the data is paginated using the page and size parameters, by default the endpoint returns the first 20 hits
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	201 gene_by_phenotypes_query = f"{impc_api_search_url}/search/findAllBySignificantMpTermIdsContains?mpTermIds={target_mp_terms}&page=0&size=20"
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	202 genes_with_morphology_mps = requests.get(gene_by_phenotypes_query).json()
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	203 list_of_gene_bundle_urls = [gene["_links"]["geneBundle"]['href'] for gene in
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	204 genes_with_morphology_mps['_embedded']['genes']]
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	205
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	206 gene_bundles = []
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	207 for gene_bundle_url in list_of_gene_bundle_urls:
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	208 gene_bundle = requests.get(gene_bundle_url).json()
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	209 gene_bundles.append(gene_bundle)
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	210
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	211 images_with_morphology_mps = []
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	212
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	213 ## Doing just the first 20 and filtering out fields on the images
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	214 display_fields = ['geneSymbol', 'parameterName', 'biologicalSampleGroup', 'colonyId', 'zygosity', 'sex',
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	215 'downloadUrl', 'externalSampleId', 'thumbnailUrl']
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	216
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	217
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	218 for gene_bundle in gene_bundles[:20]:
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	219 if len(gene_bundle) == 4:
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	220 continue
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	221 if gene_bundle["geneImages"] is not None:
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	222 images = gene_bundle["geneImages"]
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	223 for image in images:
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	224 display_image = {k: v for k, v in image.items() if k in display_fields}
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	225 images_with_morphology_mps.append(display_image)
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	226
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	227 images_table = []
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	228 print(f"Images related to phenotype {target_mp_terms}: {len(images_with_morphology_mps)}")
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	229 ## Displaying just the first 20 images
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	230 for i in images_with_morphology_mps[:20]:
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	231 row = [f"<img src='{i['thumbnailUrl']}' />"] + list(i.values())
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	232 images_table.append(row)
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	233
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	234 df = pd.DataFrame()
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	235 externalSampleId = []
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	236 geneSymbol = []
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	237 biologicalSampleGroup = []
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	238 sex = []
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	239 colonyId = []
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	240 zygosity = []
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	241 parameterName = []
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	242 downloadUrl = []
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	243 thumbnailUrl = []
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	244
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	245 for i in images_table:
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	246 externalSampleId.append(i[1])
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	247 geneSymbol.append(i[2])
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	248 biologicalSampleGroup.append(i[3])
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	249 sex.append(i[4])
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	250 colonyId.append(i[5])
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	251 zygosity.append(i[6])
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	252 parameterName.append(i[7])
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	253 downloadUrl.append(i[8])
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	254 thumbnailUrl.append(i[9])
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	255
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	256 df['externalSampleId'] = externalSampleId
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	257 df['geneSymbol'] = geneSymbol
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	258 df['biologicalSampleGroup'] = biologicalSampleGroup
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	259 df['sex'] = sex
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	260 df['colonyId'] = colonyId
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	261 df['zygosity'] = zygosity
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	262 df['parameterName'] = parameterName
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	263 df['downloadUrl'] = downloadUrl
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	264 df['thumbnailUrl'] = thumbnailUrl
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	265
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	266 if head == 'True':
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	267 df.to_csv(sys.argv[2], header=True, index=False, sep="\t", index_label=False)
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	268 else:
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	269 df.to_csv(sys.argv[2], header=False, index=False, sep="\t", index_label=False)
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	270
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	271 # 11- Which parameters have been measured for a particular knockout EASY
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	272
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	273
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	274 def parameters(inp):
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	275 head = sys.argv[4]
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	276 knockout = inp # "MGI:104636"
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	277 gene_info = requests.get(impc_api_search_url + "/" + knockout).json()
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	278
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	279 if gene_info['phenotypingDataAvailable']:
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	280 geneBundle = requests.get(gene_info['_links']['geneBundle']['href']).json()
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	281 gen_imgs = geneBundle['geneImages']
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	282 par_list = []
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	283 l = {}
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	284 for i in gen_imgs:
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	285 l = {"Parameter Name": i['parameterName']}
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	286 if l not in par_list:
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	287 par_list.append(l)
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	288 df = pd.DataFrame()
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	289 l = []
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	290
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	291 for i in par_list:
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	292 l.append(i['Parameter Name'])
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	293
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	294 df['Parameter'] = l
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	295 if head == 'True':
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	296 df.to_csv(sys.argv[2], header=True, index=False, sep="\t", index_label=False)
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	297 else:
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	298 df.to_csv(sys.argv[2], header=False, index=False, sep="\t", index_label=False)
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	299
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	300 else:
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	301 stop_err("No parameters available for this knockout gene")
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	302
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	303
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	304 # 12- Which parameters identified a significant finding for a particular knockout line (colony) EASY
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	305 def sign_par(inp):
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	306 head = sys.argv[4]
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	307 knockout = inp # "MGI:104636"
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	308
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	309 gene_info = requests.get(f"{impc_api_url}statisticalResults/search/findAllByMarkerAccessionIdIsAndSignificantTrue?mgiAccessionId=" + knockout).json()
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	310 gene_stats = gene_info['_embedded']['statisticalResults']
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	311
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	312 if len(gene_stats) == 0:
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	313 stop_err("No statistically relevant parameters found for this knockout gene")
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	314 else:
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	315 df = pd.DataFrame()
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	316 n = []
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	317 p = []
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	318 for g in gene_stats:
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	319 n.append(g['parameterName'])
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	320 p.append(g['pvalue'])
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	321
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	322 df['Parameter name'] = n
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	323 df['p-value'] = p
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	324 if head == 'True':
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	325 df.to_csv(sys.argv[2], header=True, index=False, sep="\t", index_label=False)
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	326 else:
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	327 df.to_csv(sys.argv[2], header=False, index=False, sep="\t", index_label=False)
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	328
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	329
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	330 # 13- List of genes names and ID measured in a pipeline
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	331 def genes_in_pipeline(inp):
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	332 head = sys.argv[4]
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	333 pip = inp
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	334
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	335 g_in_p_query = f"{impc_api_search_url}/search/findAllByTestedPipelineId?pipelineId={pip}&page=0&size=1000"
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	336 genes_in_pip = requests.get(g_in_p_query).json()
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	337 pages = genes_in_pip['page']['totalPages']
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	338 max_elem = genes_in_pip['page']['totalElements']
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	339
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	340 print(f"Genes with {pip}: {genes_in_pip['page']['totalElements']}")
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	341 d ={ }
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	342 list_d = []
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	343 list_of_genes = pd.DataFrame(columns=['Gene accession id', 'Gene name'])
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	344 acc = []
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	345 name = []
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	346
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	347 if max_elem > 1000:
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	348 g_in_p_query = genes_in_pip['_embedded']['genes']
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	349 for i in range(1,pages):
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	350 gl = requests.get(f'{impc_api_search_url}/search/findAllByTestedPipelineId?pipelineId={pip}&page={i}&size=1000').json()['_embedded']['genes']
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	351 g_in_p_query += gl
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	352 else:
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	353 g_in_p_query = genes_in_pip['_embedded']['genes']
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	354
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	355 for g in g_in_p_query:
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	356 d = {"Gene Accession ID": g['mgiAccessionId'], "Gene Name": g['markerName']}
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	357 list_d.append(d)
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	358
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	359 for i in list_d:
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	360 acc.append(i['Gene Accession ID'])
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	361 name.append(i['Gene Name'])
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	362
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	363 list_of_genes['Gene accession id'] = acc
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	364 list_of_genes['Gene name'] = name
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	365
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	366 if head == 'True':
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	367 list_of_genes.to_csv(sys.argv[2], header=True, index=False, sep="\t", index_label=False)
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	368 else:
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	369 list_of_genes.to_csv(sys.argv[2], header=False, index=False, sep="\t", index_label=False)
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	370
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	371
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	372 # 14- Extract all genes and corresponding phenotypes related to a particular organ system(eg: significatMPTerm)
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	373 def sign_mp(inp):
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	374 head = sys.argv[4]
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	375 mp_term = inp # ['MP:0005391']
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	376
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	377 gene_by_mpterm_query = f"{impc_api_search_url}/search/findAllBySignificantMpTermIdsContains?mpTermIds={mp_term}&size=1000"
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	378 genes_with_mpterm = requests.get(gene_by_mpterm_query).json()
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	379
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	380 pages = genes_with_mpterm['page']['totalPages']
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	381 genes_info = genes_with_mpterm['_embedded']['genes']
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	382
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	383 for pn in range(1,pages):
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	384 pq = f"{impc_api_search_url}/search/findAllBySignificantMpTermIdsContains?mpTermIds={mp_term}&page={pn}&size=1000"
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	385 g = requests.get(pq).json()['_embedded']['genes']
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	386 genes_info += g
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	387
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	388 list_d=[]
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	389 d={}
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	390 for g in genes_info:
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	391 names=[]
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	392 ids=[]
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	393 for s in g['significantMpTerms']:
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	394 names.append(s['mpTermName'])
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	395 ids.append(s['mpTermId'])
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	396 d={'Gene':g['mgiAccessionId'], 'mpTermId': ids, 'mpTermName':names}
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	397 list_d.append(d)
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	398
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	399
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	400 g = []
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	401 ids = []
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	402 names = []
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	403 for i in list_d:
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	404 g.append(i['Gene'])
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	405 ids.append(i['mpTermId'])
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	406 names.append(i['mpTermName'])
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	407
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	408 df = pd.DataFrame()
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	409 df['Gene Id']=g
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	410 df['Significant MP terms Ids']=ids
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	411 df['Significant MP terms Names']=names
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	412
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	413 if head == 'True':
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	414 df.to_csv(sys.argv[2], header=True, index=False, sep="\t", index_label=False)
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	415 else:
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	416 df.to_csv(sys.argv[2], header=False, index=False, sep="\t", index_label=False)
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	417
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	418
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	419 # 16- Full table of genes and all identified phenotypes
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	420
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	421 def full_gene_table():
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	422 head = sys.argv[4]
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	423 gene_list = requests.get(impc_api_search_url + '?page=0&size=1000').json()
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	424 pages = gene_list['page']['totalPages']
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	425 genes_info = gene_list['_embedded']['genes']
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	426
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	427 for pn in range(1,pages):
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	428 gp = requests.get(impc_api_search_url + f'?page={pn}&size=1000').json()['_embedded']['genes']
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	429 genes_info += gp
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	430
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	431 d = {}
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	432 list_d=[]
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	433
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	434 for i in genes_info:
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	435 l = []
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	436 if i['significantMpTerms'] is None:
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	437 d={"Gene": i['mgiAccessionId'], "Identified phenotypes": "None"}
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	438 else:
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	439 d = {"Gene": i['mgiAccessionId'], "Identified phenotypes": [sub['mpTermId'] for sub in i['significantMpTerms']]}
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	440 list_d.append(d)
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	441
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	442 df = pd.DataFrame()
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	443 g = []
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	444 p = []
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	445 for i in list_d:
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	446 g.append(i['Gene'])
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	447 p.append(i['Identified phenotypes'])
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	448
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	449 df['MGI id'] = g
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	450 df['MP term list'] = p
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	451
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	452 for i in range(0, len(df)):
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	453 if df['MP term list'][i] != "None":
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	454 df['MP term list'][i] = str(df['MP term list'][i])[1:-1].replace("'", "")
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	455
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	456 if str(sys.argv[1]) == 'True':
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	457 if head == 'True':
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	458 df.to_csv(sys.argv[2], header=True, index=False, sep="\t", index_label=False)
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	459 else:
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	460 df.to_csv(sys.argv[2], header=False, index=False, sep="\t", index_label=False)
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	461 else:
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	462 df = df[df['MP term list'] != "None"]
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	463 df.reset_index(drop=True, inplace=True)
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	464 if head == 'True':
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	465 df.to_csv(sys.argv[2], header=True, index=False, sep="\t", index_label=False)
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	466 else:
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	467 df.to_csv(sys.argv[2], header=False, index=False, sep="\t", index_label=False)
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	468
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	469 # Old method, chech which is faster
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	470 # max_elem = gene_list['page']['totalElements']
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	471 # d = {}
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	472 # list_d = []
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	473 # for i in range(0, pages):
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	474 # gl = requests.get(impc_api_search_url + '?page=' + str(i) + '&size=' + str(max_elem)).json()
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	475 # for g in gl['_embedded']['genes']:
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	476 # if g['significantMpTerms'] is None:
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	477 # d = {"Gene": g['mgiAccessionId'], "Identified phenotypes": "None"}
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	478 # else:
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	479 # d = {"Gene": g['mgiAccessionId'], "Identified phenotypes": [ sub['mpTermId'] for sub in g['significantMpTerms'] ]}
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	480 # list_d.append(d)
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	481
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	482
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	483
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	484
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	485 # 18- Extract measurements and analysis for a parameter or pipeline
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	486
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	487 def par_pip_ma(inp):
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	488 head = sys.argv[4]
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	489 id = inp
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	490
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	491 if id[0:4] == "IMPC":
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	492 par = True
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	493 ma_query = f"{impc_api_search_url}/search/findAllByTestedParameterId?parameterId={id}&page=0&size=1000"
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	494 else:
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	495 ma_query = f"{impc_api_search_url}/search/findAllByTestedPipelineId?pipelineId={id}&page=0&size=1000"
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	496 par = False
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	497
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	498 ma_in_pip = requests.get(ma_query).json()
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	499 pages = ma_in_pip['page']['totalPages']
4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty andrea.furlani parents: diff changeset	500 max_elem = ma_in_pip['page']['totalElements']

0

4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty

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diff changeset

1 import sys

4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty

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2 import requests

4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty

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3 import pandas as pd

4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty

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diff changeset

4 import urllib.request as url

4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty

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5

4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty

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6 impc_api_url = "https://www.gentar.org/impc-dev-api/"

4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty

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7 impc_api_search_url = f"{impc_api_url}/genes"

4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty

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8 impc_api_gene_bundle_url = f"{impc_api_url}/geneBundles"

4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty

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9

4357848fb4e6 planemo upload commit 213f6eeb03f96bb13d0ace6e0c87e2562d37f728-dirty

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10

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11 def stop_err(msg):

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12 sys.exit(msg)

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13

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14

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15 def main():

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16 inp = str(sys.argv[1])

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17 query = str(sys.argv[3])

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18

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19 try:

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20 if query == '7':

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21 full_gene_table()

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22 sys.exit(0)

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23

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24 if str(sys.argv[5])=="txt":

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25 s = str(sys.argv[6])

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26 if s == "t":

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27 sep = "\t"

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28 elif s == "s":

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29 sep = " "

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30 elif s in ",;.":

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31 sep = s

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32 else:

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33 sys.exit("Separator not valid, please change it.")

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34 inp = pd.read_csv(inp, header=None, delimiter=sep)

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35 if len(inp.columns)==1:

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36 inp = str(inp[0].values[0]).replace("'","")

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37 else:

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38 inp = inp.to_string(header=False, index=False).replace(" ",",")

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39

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40 if query == '8':

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41 genes_in_pipeline(inp)

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42 sys.exit(0)

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43 elif query == '10': # it's here but not totally implemented

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44 par_pip_ma(inp)

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45 sys.exit(0)

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46 elif query == '11': # it's here but not totally implemented

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47 par_gen(inp)

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48 sys.exit(0)

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49 else:

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50 tmp = inp.split(",")

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51 final_list = []

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52 sym_list = []

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53 for i in tmp:

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54 if 'MGI:' in i or 'MP:' in i:

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55 final_list.append(i)

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56 else:

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57 sym_list.append(i)

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58 del(i)

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59 if len(sym_list) != 0:

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60 sym_list = ",".join(sym_list)

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61 biodbnet = f'https://biodbnet.abcc.ncifcrf.gov/webServices/rest.php/biodbnetRestApi.xml?method=db2db&format=row&input=genesymbol&inputValues={sym_list}&outputs=mgiid&taxonId=10090'

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62 u = url.urlopen(biodbnet)

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63 db = pd.read_xml(u, elems_only=True)

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64 if len(db) == 0 and len(final_list) == 0:

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65 stop_err("It was not possible to map the input.")

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66 else:

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67 for i in range(0,len(db)):

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68 final_list.append(db['MGIID'][i][4:])

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69

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70 inp= ",".join(final_list)

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71

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72

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73 if query == '1':

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74 get_pheno(inp)

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75 sys.exit(0)

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76 elif query == '2':

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77 get_genes(inp)

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78 sys.exit(0)

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79 elif query == '3':

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80 gene_set(inp)

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81 sys.exit(0)

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82 elif query == '4':

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83 extr_img(inp)

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84 sys.exit(0)

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85 elif query == '5':

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86 parameters(inp)

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87 sys.exit(0)

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88 elif query == '6':

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89 sign_par(inp)

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90 sys.exit(0)

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91 elif query == '9':

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92 sign_mp(inp)

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93 sys.exit(0)

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94 else:

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95 stop_err("Error, non-implemented query selected: " + query)

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96 except Exception as ex:

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97 stop_err('Error running get_pheno.py:\n' + str(ex))

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98

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99

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100 # 1-Given a gene id, retrieve all the phenotypes related to it (id and name)

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101 def get_pheno(inp):

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102 head = sys.argv[4]

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103 mgi_accession_id = inp

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104

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105 gene_url = f"{impc_api_search_url}/{mgi_accession_id}"

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106 gene_data = requests.get(gene_url).json()

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107

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108 p_list = []

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109 id_list = []

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110

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111 if gene_data['significantMpTerms'] == None:

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112 stop_err("No significant MP terms found for this gene")

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113 else:

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114 for x in gene_data['significantMpTerms']:

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115 p_list.append(x['mpTermId'])

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116 id_list.append(x['mpTermName'])

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117

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118 df = pd.DataFrame()

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119 df['MP term name'] = p_list

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120 df['MP term id'] = id_list

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121

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122 if head == 'True':

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123 df.to_csv(sys.argv[2], header=True, index=False, sep="\t", index_label=False)

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124 else:

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125 df.to_csv(sys.argv[2], header=False, index=False, sep="\t", index_label=False)

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126

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127

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128 # 3-Extract all genes having a particular phenotype or a set of phenotypes (e.g. relevant to a disease)

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129 def get_genes(inp):

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130 head = sys.argv[4]

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131 target_mp_terms = inp

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132

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133 ## All the data is paginated using the page and size parameters, by default the endpoint returns the first 20 hits

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134 gene_by_phenotypes_query = f"{impc_api_search_url}/search/findAllBySignificantMpTermIdsContains?mpTermIds={target_mp_terms}&page=0&size=20"

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135 genes_with_clinical_chemistry_phenotypes = requests.get(gene_by_phenotypes_query).json()

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136 print(f"Genes with {target_mp_terms}: {genes_with_clinical_chemistry_phenotypes['page']['totalElements']}")

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137 list_of_genes = pd.DataFrame(columns=['Gene accession id', 'Gene name', 'Gene bundle url'])

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138 acc = []

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139 name = []

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140 url = []

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141

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142 for gene in genes_with_clinical_chemistry_phenotypes['_embedded']['genes']:

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143 acc.append(gene['mgiAccessionId'])

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144 name.append(gene['markerName'])

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145 url.append(gene['_links']['geneBundle']['href'])

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146

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147 list_of_genes['Gene accession id'] = acc

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148 list_of_genes['Gene name'] = name

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149 list_of_genes['Gene bundle url'] = url

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150

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151 if head == 'True':

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152 list_of_genes.to_csv(sys.argv[2], header=True, index=False, sep="\t", index_label=False)

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153 else:

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154 list_of_genes.to_csv(sys.argv[2], header=False, index=False, sep="\t", index_label=False)

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155

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156 # 4. Extract all phenotypes which are present in a particular gene set (e.g. genes together in a pathway)

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157

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158 def gene_set(inp):

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159 head = sys.argv[4]

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160 target_genes = inp

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161

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162 genes_in_gene_list_query = f"{impc_api_search_url}/search/findAllByMgiAccessionIdIn?mgiAccessionIds={target_genes}"

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163

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164 genes_in_gene_list = requests.get(genes_in_gene_list_query).json()

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165 list_of_mp_terms_vs_gene_index = {}

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166

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167 for gene in genes_in_gene_list['_embedded']['genes']:

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168 mp_terms = gene['significantMpTerms']

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169 gene_acc_id = gene["mgiAccessionId"]

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170 if mp_terms is None:

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171 continue

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172 for mp_term_name in mp_terms:

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173 if mp_term_name['mpTermId'] not in list_of_mp_terms_vs_gene_index:

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174 list_of_mp_terms_vs_gene_index[mp_term_name['mpTermId']] = {"mp_term": mp_term_name['mpTermId'], "genes": []}

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175 list_of_mp_terms_vs_gene_index[mp_term_name['mpTermId']]["genes"].append(gene_acc_id)

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176 genes_by_mp_term = list(list_of_mp_terms_vs_gene_index.values())

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177

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178 df = pd.DataFrame()

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179 terms = []

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180 genes = []

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181 for i in genes_by_mp_term:

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182 terms.append(i['mp_term'])

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183 genes.append(i['genes'])

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184

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185 df['mp_term'] = terms

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186 df['genes'] = genes

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187

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188 if head == 'True':

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189 df.to_csv(sys.argv[2], header=True, index=False, sep="\t", index_label=False)

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190 else:

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191 df.to_csv(sys.argv[2], header=False, index=False, sep="\t", index_label=False)

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192

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193 # 7. Extract images with a particular phenotype or a set of phenotypes

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194

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195

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196 def extr_img(inp):

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197 head = sys.argv[4]

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198 target_mp_terms = inp # ['MP:0002110', 'MP:0000559']

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199

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200 ## All the data is paginated using the page and size parameters, by default the endpoint returns the first 20 hits

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201 gene_by_phenotypes_query = f"{impc_api_search_url}/search/findAllBySignificantMpTermIdsContains?mpTermIds={target_mp_terms}&page=0&size=20"

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202 genes_with_morphology_mps = requests.get(gene_by_phenotypes_query).json()

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203 list_of_gene_bundle_urls = [gene["_links"]["geneBundle"]['href'] for gene in

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204 genes_with_morphology_mps['_embedded']['genes']]

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205

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206 gene_bundles = []

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207 for gene_bundle_url in list_of_gene_bundle_urls:

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208 gene_bundle = requests.get(gene_bundle_url).json()

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209 gene_bundles.append(gene_bundle)

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210

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211 images_with_morphology_mps = []

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212

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213 ## Doing just the first 20 and filtering out fields on the images

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214 display_fields = ['geneSymbol', 'parameterName', 'biologicalSampleGroup', 'colonyId', 'zygosity', 'sex',

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215 'downloadUrl', 'externalSampleId', 'thumbnailUrl']

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216

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217

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218 for gene_bundle in gene_bundles[:20]:

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219 if len(gene_bundle) == 4:

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220 continue

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221 if gene_bundle["geneImages"] is not None:

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222 images = gene_bundle["geneImages"]

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223 for image in images:

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224 display_image = {k: v for k, v in image.items() if k in display_fields}

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225 images_with_morphology_mps.append(display_image)

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226

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227 images_table = []

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228 print(f"Images related to phenotype {target_mp_terms}: {len(images_with_morphology_mps)}")

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229 ## Displaying just the first 20 images

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230 for i in images_with_morphology_mps[:20]:

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231 row = [f"<img src='{i['thumbnailUrl']}' />"] + list(i.values())

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232 images_table.append(row)

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233

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234 df = pd.DataFrame()

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235 externalSampleId = []

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236 geneSymbol = []

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237 biologicalSampleGroup = []

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238 sex = []

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239 colonyId = []

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240 zygosity = []

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241 parameterName = []

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242 downloadUrl = []

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243 thumbnailUrl = []

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244

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245 for i in images_table:

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246 externalSampleId.append(i[1])

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247 geneSymbol.append(i[2])

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248 biologicalSampleGroup.append(i[3])

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249 sex.append(i[4])

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250 colonyId.append(i[5])

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251 zygosity.append(i[6])

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252 parameterName.append(i[7])

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253 downloadUrl.append(i[8])

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254 thumbnailUrl.append(i[9])

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255

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256 df['externalSampleId'] = externalSampleId

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257 df['geneSymbol'] = geneSymbol

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258 df['biologicalSampleGroup'] = biologicalSampleGroup

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259 df['sex'] = sex

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260 df['colonyId'] = colonyId

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261 df['zygosity'] = zygosity

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262 df['parameterName'] = parameterName

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263 df['downloadUrl'] = downloadUrl

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264 df['thumbnailUrl'] = thumbnailUrl

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265

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266 if head == 'True':

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267 df.to_csv(sys.argv[2], header=True, index=False, sep="\t", index_label=False)

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268 else:

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269 df.to_csv(sys.argv[2], header=False, index=False, sep="\t", index_label=False)

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270

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271 # 11- Which parameters have been measured for a particular knockout EASY

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272

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273

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274 def parameters(inp):

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275 head = sys.argv[4]

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276 knockout = inp # "MGI:104636"

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277 gene_info = requests.get(impc_api_search_url + "/" + knockout).json()

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278

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279 if gene_info['phenotypingDataAvailable']:

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280 geneBundle = requests.get(gene_info['_links']['geneBundle']['href']).json()

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281 gen_imgs = geneBundle['geneImages']

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282 par_list = []

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283 l = {}

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284 for i in gen_imgs:

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285 l = {"Parameter Name": i['parameterName']}

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286 if l not in par_list:

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287 par_list.append(l)

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288 df = pd.DataFrame()

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289 l = []

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290

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291 for i in par_list:

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292 l.append(i['Parameter Name'])

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293

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294 df['Parameter'] = l

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295 if head == 'True':

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296 df.to_csv(sys.argv[2], header=True, index=False, sep="\t", index_label=False)

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297 else:

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298 df.to_csv(sys.argv[2], header=False, index=False, sep="\t", index_label=False)

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299

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300 else:

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301 stop_err("No parameters available for this knockout gene")

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302

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303

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304 # 12- Which parameters identified a significant finding for a particular knockout line (colony) EASY

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305 def sign_par(inp):

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306 head = sys.argv[4]

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307 knockout = inp # "MGI:104636"

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308

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309 gene_info = requests.get(f"{impc_api_url}statisticalResults/search/findAllByMarkerAccessionIdIsAndSignificantTrue?mgiAccessionId=" + knockout).json()

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310 gene_stats = gene_info['_embedded']['statisticalResults']

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311

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312 if len(gene_stats) == 0:

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313 stop_err("No statistically relevant parameters found for this knockout gene")

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314 else:

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315 df = pd.DataFrame()

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316 n = []

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317 p = []

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318 for g in gene_stats:

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319 n.append(g['parameterName'])

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320 p.append(g['pvalue'])

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321

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322 df['Parameter name'] = n

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323 df['p-value'] = p

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324 if head == 'True':

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325 df.to_csv(sys.argv[2], header=True, index=False, sep="\t", index_label=False)

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326 else:

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327 df.to_csv(sys.argv[2], header=False, index=False, sep="\t", index_label=False)

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328

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329

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330 # 13- List of genes names and ID measured in a pipeline

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331 def genes_in_pipeline(inp):

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332 head = sys.argv[4]

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333 pip = inp

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334

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335 g_in_p_query = f"{impc_api_search_url}/search/findAllByTestedPipelineId?pipelineId={pip}&page=0&size=1000"

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336 genes_in_pip = requests.get(g_in_p_query).json()

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337 pages = genes_in_pip['page']['totalPages']

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338 max_elem = genes_in_pip['page']['totalElements']

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339

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340 print(f"Genes with {pip}: {genes_in_pip['page']['totalElements']}")

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341 d ={ }

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342 list_d = []

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343 list_of_genes = pd.DataFrame(columns=['Gene accession id', 'Gene name'])

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344 acc = []

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345 name = []

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346

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347 if max_elem > 1000:

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348 g_in_p_query = genes_in_pip['_embedded']['genes']

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349 for i in range(1,pages):

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350 gl = requests.get(f'{impc_api_search_url}/search/findAllByTestedPipelineId?pipelineId={pip}&page={i}&size=1000').json()['_embedded']['genes']

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351 g_in_p_query += gl

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352 else:

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353 g_in_p_query = genes_in_pip['_embedded']['genes']

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354

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355 for g in g_in_p_query:

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356 d = {"Gene Accession ID": g['mgiAccessionId'], "Gene Name": g['markerName']}

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357 list_d.append(d)

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358

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359 for i in list_d:

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360 acc.append(i['Gene Accession ID'])

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361 name.append(i['Gene Name'])

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362

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363 list_of_genes['Gene accession id'] = acc

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364 list_of_genes['Gene name'] = name

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365

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366 if head == 'True':

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367 list_of_genes.to_csv(sys.argv[2], header=True, index=False, sep="\t", index_label=False)

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368 else:

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369 list_of_genes.to_csv(sys.argv[2], header=False, index=False, sep="\t", index_label=False)

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370

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371

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372 # 14- Extract all genes and corresponding phenotypes related to a particular organ system(eg: significatMPTerm)

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373 def sign_mp(inp):

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374 head = sys.argv[4]

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375 mp_term = inp # ['MP:0005391']

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376

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377 gene_by_mpterm_query = f"{impc_api_search_url}/search/findAllBySignificantMpTermIdsContains?mpTermIds={mp_term}&size=1000"

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378 genes_with_mpterm = requests.get(gene_by_mpterm_query).json()

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379

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380 pages = genes_with_mpterm['page']['totalPages']

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381 genes_info = genes_with_mpterm['_embedded']['genes']

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382

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383 for pn in range(1,pages):

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384 pq = f"{impc_api_search_url}/search/findAllBySignificantMpTermIdsContains?mpTermIds={mp_term}&page={pn}&size=1000"

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385 g = requests.get(pq).json()['_embedded']['genes']

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386 genes_info += g

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387

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388 list_d=[]

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389 d={}

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390 for g in genes_info:

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391 names=[]

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392 ids=[]

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393 for s in g['significantMpTerms']:

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394 names.append(s['mpTermName'])

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395 ids.append(s['mpTermId'])

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396 d={'Gene':g['mgiAccessionId'], 'mpTermId': ids, 'mpTermName':names}

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397 list_d.append(d)

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398

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399

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400 g = []

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401 ids = []

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402 names = []

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403 for i in list_d:

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404 g.append(i['Gene'])

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405 ids.append(i['mpTermId'])

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406 names.append(i['mpTermName'])

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407

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408 df = pd.DataFrame()

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409 df['Gene Id']=g

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410 df['Significant MP terms Ids']=ids

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411 df['Significant MP terms Names']=names

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412

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413 if head == 'True':

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414 df.to_csv(sys.argv[2], header=True, index=False, sep="\t", index_label=False)

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415 else:

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416 df.to_csv(sys.argv[2], header=False, index=False, sep="\t", index_label=False)

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417

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418

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419 # 16- Full table of genes and all identified phenotypes

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420

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421 def full_gene_table():

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422 head = sys.argv[4]

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423 gene_list = requests.get(impc_api_search_url + '?page=0&size=1000').json()

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424 pages = gene_list['page']['totalPages']

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425 genes_info = gene_list['_embedded']['genes']

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426

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427 for pn in range(1,pages):

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428 gp = requests.get(impc_api_search_url + f'?page={pn}&size=1000').json()['_embedded']['genes']

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429 genes_info += gp

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430

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431 d = {}

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432 list_d=[]

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433

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434 for i in genes_info:

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435 l = []

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436 if i['significantMpTerms'] is None:

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437 d={"Gene": i['mgiAccessionId'], "Identified phenotypes": "None"}

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diff changeset

438 else:

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439 d = {"Gene": i['mgiAccessionId'], "Identified phenotypes": [sub['mpTermId'] for sub in i['significantMpTerms']]}

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440 list_d.append(d)

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441

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442 df = pd.DataFrame()

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443 g = []

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444 p = []

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445 for i in list_d:

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446 g.append(i['Gene'])

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447 p.append(i['Identified phenotypes'])

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448

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449 df['MGI id'] = g

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450 df['MP term list'] = p

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451

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452 for i in range(0, len(df)):

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453 if df['MP term list'][i] != "None":

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454 df['MP term list'][i] = str(df['MP term list'][i])[1:-1].replace("'", "")

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455

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456 if str(sys.argv[1]) == 'True':

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457 if head == 'True':

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458 df.to_csv(sys.argv[2], header=True, index=False, sep="\t", index_label=False)

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459 else:

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460 df.to_csv(sys.argv[2], header=False, index=False, sep="\t", index_label=False)

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461 else:

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462 df = df[df['MP term list'] != "None"]

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463 df.reset_index(drop=True, inplace=True)

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464 if head == 'True':

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465 df.to_csv(sys.argv[2], header=True, index=False, sep="\t", index_label=False)

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466 else:

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467 df.to_csv(sys.argv[2], header=False, index=False, sep="\t", index_label=False)

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468

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469 # Old method, chech which is faster

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470 # max_elem = gene_list['page']['totalElements']

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471 # d = {}

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472 # list_d = []

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473 # for i in range(0, pages):

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474 # gl = requests.get(impc_api_search_url + '?page=' + str(i) + '&size=' + str(max_elem)).json()

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diff changeset

475 # for g in gl['_embedded']['genes']:

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476 # if g['significantMpTerms'] is None:

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477 # d = {"Gene": g['mgiAccessionId'], "Identified phenotypes": "None"}

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478 # else:

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479 # d = {"Gene": g['mgiAccessionId'], "Identified phenotypes": [ sub['mpTermId'] for sub in g['significantMpTerms'] ]}

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480 # list_d.append(d)

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481

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482

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483

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484

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485 # 18- Extract measurements and analysis for a parameter or pipeline

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486

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487 def par_pip_ma(inp):

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488 head = sys.argv[4]

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489 id = inp

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490

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491 if id[0:4] == "IMPC":

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492 par = True

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493 ma_query = f"{impc_api_search_url}/search/findAllByTestedParameterId?parameterId={id}&page=0&size=1000"

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494 else:

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495 ma_query = f"{impc_api_search_url}/search/findAllByTestedPipelineId?pipelineId={id}&page=0&size=1000"

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496 par = False

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497

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498 ma_in_pip = requests.get(ma_query).json()

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499 pages = ma_in_pip['page']['totalPages']

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500 max_elem = ma_in_pip['page']['totalElements']

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501

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502 print(f"Genes with {id}: {ma_in_pip['page']['totalElements']}")

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503 d = {}

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504 list_d = []

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505 list_of_genes = pd.DataFrame(columns=['Measurements', 'Analysis'])

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506 mes = []

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507 an = []

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508

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509 if max_elem > 1000:

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510

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511 ma_in_pip = ma_in_pip['_embedded']['genes']

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512 for pn in range(1, pages):

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513 if par:

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514 pip = requests.get(f"{impc_api_search_url}/search/findAllByTestedParameterId?parameterId={id}&page={pn}&size=1000").json()['_embedded']['genes']

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515 else:

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516 pip = requests.get(f"{impc_api_search_url}/search/findAllByTestedPipelineId?pipelineId={id}&page={pn}&size=1000").json()['_embedded']['genes']

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517 ma_in_pip += pip

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518

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519 else:

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520 ma_in_pip = ma_in_pip['_embedded']['genes']

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521

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522 for g in ma_in_pip:

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523 d = {"Measurements": g[''], "Analysis": g['']}

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524 list_d.append(d)

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525

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526 for i in list_d:

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527 mes.append(i[''])

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528 an.append(i[''])

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529

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530 list_of_genes['Analysis'] = an

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531 list_of_genes['Measurements'] = mes

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532

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533 if head == 'True':

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534 list_of_genes.to_csv(sys.argv[2], header=True, index=False, sep="\t", index_label=False)

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diff changeset

535 else:

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536 list_of_genes.to_csv(sys.argv[2], header=False, index=False, sep="\t", index_label=False)

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537

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538

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539 # 19- Get all genes and measured values for a particular parameter

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540 def par_gen(inp):

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541 head = sys.argv[4]

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542 id = inp

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543

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544 pa_query = f"{impc_api_search_url}/search/findAllByTestedParameterId?parameterId={id}&page=0&size=1000"

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545

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546 gm_par = requests.get(pa_query).json()

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547 pages = gm_par['page']['totalPages']

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548 max_elem = gm_par['page']['totalElements']

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549

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550 print(f"Genes with {id}: {gm_par['page']['totalElements']}")

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551 d = {}

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552 list_d = []

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553 list_of_genes = pd.DataFrame(columns=['Genes', 'Measured Values'])

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554 gen = []

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555 mes = []

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556

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557 if max_elem > 1000:

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558

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559 gm_par = gm_par['_embedded']['genes']

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560

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561 for pn in range(1, pages):

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diff changeset

562 pip = requests.get(f"{impc_api_search_url}/search/findAllByTestedParameterId?parameterId={id}&page={pn}&size=1000").json()['_embedded']['genes']

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563 gm_par += pip

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564

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565 else:

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566 gm_par = gm_par['_embedded']['genes']

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567

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568

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569 for g in gm_par:

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diff changeset

570 d = {"Genes": g['mgiAccessionId'], "Measured Values": g['']}

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571 list_d.append(d)

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572

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573 for i in list_d:

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diff changeset

574 gen.append(i['Genes'])

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575 mes.append(i['Measured Values'])

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576

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577 list_of_genes['Genes'] = gen

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578 list_of_genes['Measured Values'] = mes

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579

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580 if head == 'True':

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diff changeset

581 list_of_genes.to_csv(sys.argv[2], header=True, index=False, sep="\t", index_label=False)

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diff changeset

582 else:

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583 list_of_genes.to_csv(sys.argv[2], header=False, index=False, sep="\t", index_label=False)

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diff changeset

584

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585

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diff changeset

586 if __name__ == "__main__":

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parents:

diff changeset

587 main()

Mercurial > repos > andrea.furlani > impc_tools

annotate impc_tool.py @ 0:4357848fb4e6 draft default tip