diff options
| -rw-r--r-- | SNPResolver.sc | 380 |
1 files changed, 190 insertions, 190 deletions
diff --git a/SNPResolver.sc b/SNPResolver.sc index 777349c..9f368f0 100644 --- a/SNPResolver.sc +++ b/SNPResolver.sc @@ -1,196 +1,196 @@ SNPResolver{ - var <fileEnd = ".json"; - var <idList = ""; - var <userID; - var <thisUser; - var <users; - var <usersWithGenotypes = 0; - var <file; - var <path; - var <>resolver; - //initialize with a path to write json files to (/tmp for example), with a minimum free disk space of ~17-25GB! - *new{ - arg aPath = "/tmp/theSoundOfPeople/", aID = 1; - ^super.new.init(aPath, aID); - } + var <fileEnd = ".json"; + var <idList = ""; + var <userID; + var <thisUser; + var <users; + var <usersWithGenotypes = 0; + var <file; + var <path; + var <>resolver; + //initialize with a path to write json files to (/tmp for example), with a minimum free disk space of ~17-25GB! + *new{ + arg aPath = "/tmp/theSoundOfPeople/", aID = 1; + ^super.new.init(aPath, aID); + } - init{ - arg aPath, aID; - path = aPath; - userID = aID.asInt; - if(File.exists(path++userID++"/").not, { - protect{ - File.mkdir(path++userID++"/"); - }{ - ("Oh noes. The directory '"++this.path++"' could not be created. Check if all parent dirs are there and you have write permission!").warn; - }; - }); -// this.downloadUserList; - } + init{ + arg aPath, aID; + path = aPath; + userID = aID.asInt; + if(File.exists(path++userID++"/").not, { + protect{ + File.mkdir(path++userID++"/"); + }{ + ("Oh noes. The directory '"++this.path++"' could not be created. Check if all parent dirs are there and you have write permission!").warn; + }; + }); +// this.downloadUserList; + } - downloadUserList{//download a new users.json and parse it for users with genotypes - var usersFinished = Condition.new(false); - var phenoFinished = Condition.new(false); - fork{ - ("Downloading user list to: "++path++userID.asString++"/"++"users"++fileEnd).postln; - ("curl -s -o "++path++userID.asString++"/"++"users"++fileEnd++" http://opensnp.org/users"++fileEnd).unixCmd({ - arg res,pid; - if(res.asInt!=0,{ - "Server down. Try again later!".postln - },{//if the download finished, resume with parsing - usersFinished.unhang; - }); - }, false);//save to file with user id as parentdir - usersFinished.hang; - "Extracting users with genotypes...".postln; - users = (path++userID.asString++"/"++"users"++fileEnd).asString.parseYAMLFile; - users.do({//retrieve the user IDs of users that uploaded genotypes - arg item, i; - if(users[i].at("genotypes")[0].notNil,{ - if(users[i].at("id").asInt!=userID, {//exclude the user we're currently working on - idList = idList ++ users[i].at("id").asString++","; - usersWithGenotypes = usersWithGenotypes + 1; - }); - }); - }); - idList.removeAt(idList.size-1);//remove the last "," - "Done".postln; - ("Downloading user phenotype information to: "++path++userID.asString++"/"++userID.asString++".phenotypes"++fileEnd).postln; - ("curl -s -o "++path++userID.asString++"/"++userID.asString++".phenotypes"++fileEnd++" http://opensnp.org/phenotypes/json/"++userID.asString++fileEnd.asString).unixCmd({ - arg res,pid; - if(res.asInt!=0,{ - "Server down. Try again later!".postln - },{//if the download finished, resume with parsing - phenoFinished.unhang; - }); - }, false);//save to file with user id as parentdir - phenoFinished.hang; - thisUser = (path++userID.asString++"/"++userID.asString++".phenotypes"++fileEnd).asString.parseYAMLFile; - ("Finished downloading phenotypes of "++thisUser.at("user").at("name").asString++".").postln; - } - } + downloadUserList{//download a new users.json and parse it for users with genotypes + var usersFinished = Condition.new(false); + var phenoFinished = Condition.new(false); + fork{ + ("Downloading user list to: "++path++userID.asString++"/"++"users"++fileEnd).postln; + ("curl -s -o "++path++userID.asString++"/"++"users"++fileEnd++" http://opensnp.org/users"++fileEnd).unixCmd({ + arg res,pid; + if(res.asInt!=0,{ + "Server down. Try again later!".postln + },{//if the download finished, resume with parsing + usersFinished.unhang; + }); + }, false);//save to file with user id as parentdir + usersFinished.hang; + "Extracting users with genotypes...".postln; + users = (path++userID.asString++"/"++"users"++fileEnd).asString.parseYAMLFile; + users.do({//retrieve the user IDs of users that uploaded genotypes + arg item, i; + if(users[i].at("genotypes")[0].notNil,{ + if(users[i].at("id").asInt!=userID, {//exclude the user we're currently working on + idList = idList ++ users[i].at("id").asString++","; + usersWithGenotypes = usersWithGenotypes + 1; + }); + }); + }); + idList.removeAt(idList.size-1);//remove the last "," + "Done".postln; + ("Downloading user phenotype information to: "++path++userID.asString++"/"++userID.asString++".phenotypes"++fileEnd).postln; + ("curl -s -o "++path++userID.asString++"/"++userID.asString++".phenotypes"++fileEnd++" http://opensnp.org/phenotypes/json/"++userID.asString++fileEnd.asString).unixCmd({ + arg res,pid; + if(res.asInt!=0,{ + "Server down. Try again later!".postln + },{//if the download finished, resume with parsing + phenoFinished.unhang; + }); + }, false);//save to file with user id as parentdir + phenoFinished.hang; + thisUser = (path++userID.asString++"/"++userID.asString++".phenotypes"++fileEnd).asString.parseYAMLFile; + ("Finished downloading phenotypes of "++thisUser.at("user").at("name").asString++".").postln; + } + } - downloadResolver{//get a resolver for an ID (of a base pair at a certain position) from opensnp.org - arg id; - var state = false; //, downloadFinished = Condition.new(false); - if(File.exists(path++userID.asString++"/"++id.asString++fileEnd).not,{ - ("Downloading JSON file for "++id).postln; - ("curl -s -o "++path++userID.asString++"/"++id.asString++fileEnd++" http://opensnp.org/snps/"++id.asString++fileEnd).unixCmd({ - arg res,pid; - if(res.asInt!=0,{ - "Failed! Retry later.".postln; - },{ - "Success!".postln; - }); - },false);//save to file with user id as parent directory - state = true; - },{ - state = true; - }); - ^state; - } - - retrieveResolver{//parse a downloaded JSON file and retrieve a resolver for a given base (pair) with an ID. Returns resolver base or \none - arg snp, id; - var baseCase = 0; - if(File.exists(path++userID.asString++"/"++id.asString++fileEnd),{//if the json file exists, parse it and return the resolver (if found) - var matchHunt = 0, huntOver = false, jsonReturn, resolver, jsonFile; - jsonFile = (path++userID.asString++"/"++id.asString++fileEnd); - try{ - jsonReturn = jsonFile.parseYAMLFile;//parse the JSON file - while({ matchHunt < size(jsonReturn) && huntOver.not },{//iterate the parsed JSON for a combo match - if(jsonReturn[matchHunt].includesKey("error").not,{//if error, skip this one - if(size(jsonReturn[matchHunt].at("user").at("genotypes"))!=0,{//if there is no data, skip this one - if(jsonReturn[matchHunt].at("user").at("genotypes")[0].at("local_genotype").asString != "--",{//if it's invalid (too), skip this one - if(SNPInfo.isBase(snp),{//check if single base or base pair - baseCase = 1; - }); - switch(baseCase, - 0,{//base pair lookup - if(jsonReturn[matchHunt].at("user").at("genotypes")[0].at("local_genotype").asString != snp.asString && SNPInfo.isBasePair(jsonReturn[matchHunt].at("user").at("genotypes")[0].at("local_genotype")),{//check if it's member of base pair and not the same base pair - ("SUCCESS: Different base found for "++id.asString++" in ("++(matchHunt+1).asString++"/"++jsonReturn.size.asString++")!").post; - (snp.asString++" -> "++jsonReturn[matchHunt].at("user").at("genotypes")[0].at("local_genotype").asString).postln; - resolver = this.calcResolverPair(snp, jsonReturn[matchHunt].at("user").at("genotypes")[0].at("local_genotype").asSymbol); - huntOver = true; - }); - }, - 1,{//single base lookup - if(jsonReturn[matchHunt].at("user").at("genotypes")[0].at("local_genotype").asString != snp.asString && SNPInfo.isBase(jsonReturn[matchHunt].at("user").at("genotypes")[0].at("local_genotype")),{//check if it's member of base pair and not the same base pair - ("SUCCESS: Different base found for "++id.asString++" in ("++(matchHunt+1).asString++"/"++jsonReturn.size.asString++")!").post; - (snp.asString++" -> "++jsonReturn[matchHunt].at("user").at("genotypes")[0].at("local_genotype").asString).postln; - resolver = [jsonReturn[matchHunt].at("user").at("genotypes")[0].at("local_genotype").asSymbol]; - huntOver = true; - }); - } - ); - }); - }); - }); - matchHunt = matchHunt + 1; - }); - jsonReturn = nil; - if(resolver.isNil,{//if no resolver was found return none - switch(baseCase, - 0,{^SNPInfo.emptyBasePair}, - 1,{^SNPInfo.emptyBase} - ); - },{ - ^resolver; - }); - }{ - ("FAILED: Parsing not possible, file corrupt: "++id.asString++fileEnd).postln; - ("Skipping for now and removing.").postln; - File.delete(path++userID.asString++"/"++id.asString++fileEnd); - } - },{//file is not there yet, download it? something like that... - ("FAILED: Resolver file for "++id.asString++" not available yet. Download it.").postln; -// this.downloadResolver(id); - }); - } + downloadResolver{//get a resolver for an ID (of a base pair at a certain position) from opensnp.org + arg id; + var state = false; //, downloadFinished = Condition.new(false); + if(File.exists(path++userID.asString++"/"++id.asString++fileEnd).not,{ + ("Downloading JSON file for "++id).postln; + ("curl -s -o "++path++userID.asString++"/"++id.asString++fileEnd++" http://opensnp.org/snps/"++id.asString++fileEnd).unixCmd({ + arg res,pid; + if(res.asInt!=0,{ + "Failed! Retry later.".postln; + },{ + "Success!".postln; + }); + },false);//save to file with user id as parent directory + state = true; + },{ + state = true; + }); + ^state; + } - calcResolverPair{//calculate upper/lower ends of resolver pairs - arg base, resolver; - switch(base, - \AA,{ - switch(resolver, - \AC,{^[resolver,\CC]}, - \CC,{^[\AC,resolver]}, - \AG,{^[resolver,\GG]}, - \GG,{^[\AG,resolver]}, - \AT,{^[resolver,\TT]}, - \TT,{^[\AT,resolver]} - ); - }, - \CC,{ - switch(resolver, - \AA,{^[resolver,\AC]}, - \AC,{^[\AA,resolver]}, - \CG,{^[resolver,\GG]}, - \GG,{^[\CG,resolver]}, - \CT,{^[resolver,\TT]}, - \TT,{^[\CT,resolver]} - ); - }, - \GG,{ - switch(resolver, - \AA,{^[resolver,\AG]}, - \AG,{^[\AA,resolver]}, - \CG,{^[\CC,resolver]}, - \CC,{^[resolver,\CG]}, - \GT,{^[resolver,\TT]}, - \TT,{^[\GT,resolver]} - ); - }, - \TT,{ - switch(resolver, - \AA,{^[resolver,\AT]}, - \AT,{^[\AA,resolver]}, - \CT,{^[\CC,resolver]}, - \CC,{^[resolver,\CT]}, - \GT,{^[\GG,resolver]}, - \GG,{^[resolver,\GT]} - ); - } - ); - } + retrieveResolver{//parse a downloaded JSON file and retrieve a resolver for a given base (pair) with an ID. Returns resolver base or \none + arg snp, id; + var baseCase = 0; + if(File.exists(path++userID.asString++"/"++id.asString++fileEnd),{//if the json file exists, parse it and return the resolver (if found) + var matchHunt = 0, huntOver = false, jsonReturn, resolver, jsonFile; + jsonFile = (path++userID.asString++"/"++id.asString++fileEnd); + try{ + jsonReturn = jsonFile.parseYAMLFile;//parse the JSON file + while({ matchHunt < size(jsonReturn) && huntOver.not },{//iterate the parsed JSON for a combo match + if(jsonReturn[matchHunt].includesKey("error").not,{//if error, skip this one + if(size(jsonReturn[matchHunt].at("user").at("genotypes"))!=0,{//if there is no data, skip this one + if(jsonReturn[matchHunt].at("user").at("genotypes")[0].at("local_genotype").asString != "--",{//if it's invalid (too), skip this one + if(SNPInfo.isBase(snp),{//check if single base or base pair + baseCase = 1; + }); + switch(baseCase, + 0,{//base pair lookup + if(jsonReturn[matchHunt].at("user").at("genotypes")[0].at("local_genotype").asString != snp.asString && SNPInfo.isBasePair(jsonReturn[matchHunt].at("user").at("genotypes")[0].at("local_genotype")),{//check if it's member of base pair and not the same base pair + ("SUCCESS: Different base found for "++id.asString++" in ("++(matchHunt+1).asString++"/"++jsonReturn.size.asString++")!").post; + (snp.asString++" -> "++jsonReturn[matchHunt].at("user").at("genotypes")[0].at("local_genotype").asString).postln; + resolver = this.calcResolverPair(snp, jsonReturn[matchHunt].at("user").at("genotypes")[0].at("local_genotype").asSymbol); + huntOver = true; + }); + }, + 1,{//single base lookup + if(jsonReturn[matchHunt].at("user").at("genotypes")[0].at("local_genotype").asString != snp.asString && SNPInfo.isBase(jsonReturn[matchHunt].at("user").at("genotypes")[0].at("local_genotype")),{//check if it's member of base pair and not the same base pair + ("SUCCESS: Different base found for "++id.asString++" in ("++(matchHunt+1).asString++"/"++jsonReturn.size.asString++")!").post; + (snp.asString++" -> "++jsonReturn[matchHunt].at("user").at("genotypes")[0].at("local_genotype").asString).postln; + resolver = [jsonReturn[matchHunt].at("user").at("genotypes")[0].at("local_genotype").asSymbol]; + huntOver = true; + }); + } + ); + }); + }); + }); + matchHunt = matchHunt + 1; + }); + jsonReturn = nil; + if(resolver.isNil,{//if no resolver was found return none + switch(baseCase, + 0,{^SNPInfo.emptyBasePair}, + 1,{^SNPInfo.emptyBase} + ); + },{ + ^resolver; + }); + }{ + ("FAILED: Parsing not possible, file corrupt: "++id.asString++fileEnd).postln; + ("Skipping for now and removing.").postln; + File.delete(path++userID.asString++"/"++id.asString++fileEnd); + } + },{//file is not there yet, download it? something like that... + ("FAILED: Resolver file for "++id.asString++" not available yet. Download it.").postln; +// this.downloadResolver(id); + }); + } + + calcResolverPair{//calculate upper/lower ends of resolver pairs + arg base, resolver; + switch(base, + \AA,{ + switch(resolver, + \AC,{^[resolver,\CC]}, + \CC,{^[\AC,resolver]}, + \AG,{^[resolver,\GG]}, + \GG,{^[\AG,resolver]}, + \AT,{^[resolver,\TT]}, + \TT,{^[\AT,resolver]} + ); + }, + \CC,{ + switch(resolver, + \AA,{^[resolver,\AC]}, + \AC,{^[\AA,resolver]}, + \CG,{^[resolver,\GG]}, + \GG,{^[\CG,resolver]}, + \CT,{^[resolver,\TT]}, + \TT,{^[\CT,resolver]} + ); + }, + \GG,{ + switch(resolver, + \AA,{^[resolver,\AG]}, + \AG,{^[\AA,resolver]}, + \CG,{^[\CC,resolver]}, + \CC,{^[resolver,\CG]}, + \GT,{^[resolver,\TT]}, + \TT,{^[\GT,resolver]} + ); + }, + \TT,{ + switch(resolver, + \AA,{^[resolver,\AT]}, + \AT,{^[\AA,resolver]}, + \CT,{^[\CC,resolver]}, + \CC,{^[resolver,\CT]}, + \GT,{^[\GG,resolver]}, + \GG,{^[resolver,\GT]} + ); + } + ); + } } |