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Commit 18274535 authored by Enza Colonna's avatar Enza Colonna
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REPEATED COMMIT made readme for vepAllInOne.py, I know it is not the best name... 

REPEATED COMMIT made readme for vepAllInOne.py, I know it is not the best name ever, fell free to change it :)
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associations/README.md
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......@@ -34,3 +34,19 @@ python opentargets.py -o orphan_id [-s threshold_score]
- The threshold score is by default set to 0 (although OpenTargets recommend 0.6 as a reasonable
threshold).
## Ensembl
The script [vepAllInOne.py](bh19-rare-diseases/associations/vepmining) retrives information about (allele frequencies)[https://en.wikipedia.org/wiki/Allele\_frequency] in several populations available in the (Ensembl)[http://www.ensembl.org/index.html] databse. This is done throug (this endpoint)[https://rest.ensembl.org/documentation/info/vep\_id\_post] of the Ensembl API.
```commandline
python3 vepAllInOne.py -f <single column of rsid input file > -t < float, allele frequency threshold below with variant is retained >
```
It takes as *input* a file with a single column of rs# and give as *output* in the standard out a single column of rs#.
In the output there are the variants from the input that are either not described in the genomic databses contained in Ensembl or for which there is at least one population with allele frequency >= the threshold indicated in the command line. As an example, using a threshold of 0.10 will filter out form the input file all variants that have minor allele frequency eqaul to or greater than 10\% in at least one population among those described in Ensembl. Also variant not present in Ensembl are filtered out under the assumption that they have never been described so far.
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associations/vepmining/cicci.json deleted 100644 → 0
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['rs1060501114\n', 'rs1060501127\n', 'rs1060501130\n', 'rs1060501135\n']
[
[
"rs1060501114",
{}
],
[
"rs1060501127",
{}
],
[
"rs1060501130",
{}
],
[
"rs1060501135",
{}
],
[
"rs1060501136",
{}
],
[
"rs1060501142",
{}
],
[
"rs1060501145",
{}
],
[
"rs1064792926",
{}
],
[
"rs1131691708",
{}
]
]
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import requests, sys, json , argparse
listOfDict=[]
listOfrsid=["rs10494366", "rs1060501114", "rs1060501127", "rs1060501130"]
server = "https://rest.ensembl.org"
ext = "/vep/human/id"
headers={ "Content-Type" : "application/json", "Accept" : "application/json"}
strOfDataDictionary=json.dumps({"ids" : listOfrsid })
res = requests.post(server+ext, headers=headers, data=strOfDataDictionary)
#return json.loads(res.text)
decoded = res.json() # a python dictionary
for elem in decoded:
#freq_dict={}
for var in elem["colocated_variants"]:
if 'frequencies' in var:#freq_dict=var["frequencies"]
listOfDict.append(var["frequencies"] )
return listOfDict
#print (len(decoded) )
#print(json.dumps(decoded, indent=2))
associations/vepmining/vepAllInOne.py
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import requests, sys, json , argparse
"""
USAGE: python3 vep.py -t <threshold below with variant is retained> -f <disgenet.test.out>
send a request to https://rest.ensembl.org/documentation/info/vep_id_post to retrive information about allele frequencies in the general population (if available) for a list of rsid
INPUT: an output file form disgenet.py or in general any file that contains rsid in the form
"rs1060501145",
(one or more rsid per line, rsdi must have quotes
USAGE: python3 vepAllInOne.py -f <single column of rsid input file > -t < allele frequency threshold below with variant is retained >
OUTPUT: a single column text file with rsids of variants that are either not described in the genomic databses contained in VEP or for which there is at least one population described in VEP with allele frequency >= the threshold indicated in the command line
INPUT: single column of rsid input file
OUTPUT: in the standard out, a single column of rsids of variants that are either not described in the genomic databses contained in VEP or for which there is at least one population described in VEP with allele frequency >= the threshold indicated in the command line
"""
def compareFreq (dictionary, threshold):
variantIsCommon=0; retain=True
for elem in dictionary:
......@@ -60,15 +61,19 @@ def main():
with open(args.f) as myf:
allrsId = myf.readlines()
#thislist=["rs12720452", "rs1060501130"]
result = getfreqfromVEPbulck(allrsId[1:100])
for rsinfo in result:
rsdict=rsinfo[1]; rsname=rsinfo[0]
if not any(rsdict): print (rsname) #, rsdict, "RARE")
elif compareFreq(rsdict, args.t ): print(rsname) #, rsdict, "YAY, RARE" )
#else: print(rsname, rsdict, "DISCARDED")
maxNumbRsIdForRequest=200 # there is a limit in the VEP rest
while len(allrsId) > 0 :
sublist=allrsId[0:maxNumbRsIdForRequest]
allrsId=allrsId[maxNumbRsIdForRequest:]
result = getfreqfromVEPbulck(sublist)
for rsinfo in result:
rsdict=rsinfo[1]; rsname=rsinfo[0]
if not any(rsdict): print (rsname) #, rsdict, "RARE")
elif compareFreq(rsdict, args.t ): print(rsname) #, rsdict, "YAY, RARE" )
#else: print(rsname, rsdict, "DISCARDED")
#print(json.dumps(result, indent=2))
#print (result)
#print(json.dumps(result, indent=2))
#print (result)
if __name__ == "__main__":
main()
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rs1060501114
rs1060501127
rs1060501130
rs1060501135
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rs1060501142
rs1060501145
rs1064792926
rs1131691708
rs12720452
rs137854600
rs137854601
rs137854602
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rs137854604
rs137854606
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rs137854609
rs137854611
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rs185492581
rs185638763
rs193922726
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