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Update variantNamingPipeline.rb #1

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17 changes: 11 additions & 6 deletions variantNamingPipeline.rb
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Original file line number Diff line number Diff line change
Expand Up @@ -25,7 +25,7 @@

# THE LOGIN FILE PATH NEEDS TO BE MODIFIED TO FIT YOUR DIRECTORY PATH
# IT IS EXPECTING A LINE IN THE FILE WITH FORMAT AS [USER LOGIN]:[PASSWORD]
loginFile="/home/dc12/.AlleleRegistry"
loginFile=".AlleleRegistry"

# return response
# throw exceptions in case of errors
Expand Down Expand Up @@ -347,7 +347,8 @@ def sortVCF(data, outfileName)
infile = "#{outfileName}_input.txt"
outfile = "#{outfileName}_input_sorted.txt"
File.open(infile,"w") { |file| file.puts data}
`(grep ^"#" #{infile}; grep -v ^"#" #{infile} | sort -k1,1 -k2,2n) > #{outfile}`
#`(grep ^"#" #{infile}; grep -v ^"#" #{infile} | sort -k1,1 -k2,2n) > #{outfile}`
system("(grep ^'#' '#{infile}'; grep -v ^'#' '#{infile}' | sort -k1,1 -k2,2n) > '#{outfile}'")
File.delete(infile)
result = File.read(outfile)
File.delete(outfile)
Expand Down Expand Up @@ -477,7 +478,7 @@ def mergeIntermediateWithInput(options, tmpDir, ourFileName)
end
puts "[#{Time.now.strftime("%Y-%m-%dT%H:%M:%S")}] Merging *_CAid* intermediate files in: #{tmpDir}"
caIDs = Dir["#{tmpDir}/*tmp*_CAid*"]

end

def mergeIntermediateVcfFiles(options,tmpDir,outFileName)
Expand All @@ -491,12 +492,16 @@ def mergeIntermediateVcfFiles(options,tmpDir,outFileName)
puts "[#{Time.now.strftime("%Y-%m-%dT%H:%M:%S")}] Merging *_CAid* intermediate files in: #{tmpDir}"
caIDs = Dir["#{tmpDir}/*tmp*_CAid*"]
#puts "cat #{caIDs.join(" ")} > #{options[:out]}/#{caIdOutName}\n"
`cat #{caIDs.join(" ")} > #{options[:out]}/#{caIdOutName}`
#`cat #{caIDs.join(" ")} > #{options[:out]}/#{caIdOutName}`
#puts("cat \'#{caIDs.join("\' \'")}\' > \'#{options[:out]}/#{caIdOutName}\'")
system("cat \'#{caIDs.join("\' \'")}\' > \'#{options[:out]}/#{caIdOutName}\'")

puts "[#{Time.now.strftime("%Y-%m-%dT%H:%M:%S")}] Merging *_noCAid* intermediate files in: #{tmpDir}"
noCAids = Dir["#{tmpDir}/*tmp*_noCAid*"]
#puts "cat #{options[:notRegisteredFile]} #{noCAids.join(" ")} > #{options[:out]}/#{noCAidOutName}"
`cat #{options[:notRegisteredFile]} #{noCAids.join(" ")} > #{options[:out]}/#{noCAidOutName}`
#`cat #{options[:notRegisteredFile]} #{noCAids.join(" ")} > #{options[:out]}/#{noCAidOutName}`
#puts("cat \'#{options[:notRegisteredFile]}\' \'#{noCAids.join("\' \'")}\' > \'#{options[:out]}/#{noCAidOutName}\'")
system("cat \'#{options[:notRegisteredFile]}\' \'#{noCAids.join("\' \'")}\' > \'#{options[:out]}/#{noCAidOutName}\'")

if options[:summary]
summaries = "#{tmpDir}/*tmp*summary*"
Expand Down Expand Up @@ -672,4 +677,4 @@ def addCount(countHash, key, count)
#remove the intermediate files
#cleanTmpDirFiles(tmpDirFname)

puts "[#{Time.now.strftime("%Y-%m-%dT%H:%M:%S")}] finish"
puts "[#{Time.now.strftime("%Y-%m-%dT%H:%M:%S")}] finish"