progress_meter |
analyze_seq |
analyze_vals -k GC%,HARD_MASK%,SOFT_MASK% |
- write_tab -co #{@anal_file} -x"
+ write_tab -o #{@anal_file} -x"
)
STDERR.puts "done.\n"
end
def parse_analyze_vals
File.open(@anal_file, "r") do |ios|
while not ios.eof?
- line = ios.readline.chomp
-
- case line
- when /COUNT\s+(\d+)/ then @count = $1
- when /MIN\s+(\d+)/ then @min = $1
- when /MAX\s+(\d+)/ then @max = $1
- when /MEAN\s+(\d+)/ then @mean = $1
- when /SUM\s+(\d+)/ then @bases = $1
- when /GC%_MEAN:\s+(.+)/ then @gc = $1
- when /HARD_MASK%_MEAN:\s+(.+)/ then @hard = $1
- when /SOFT_MASK%_MEAN:\s+(.+)/ then @soft = $1
- end
- end
- end
- end
-
- def parse_mean_vals
- File.open(@out2_file, "r") do |ios|
- while not ios.eof?
- line = ios.readline.chomp
-
- case line
- when /GC%_MEAN: (.+)/; then @gc = $1
- when /HARD_MASK%_MEAN: (.+)/; then @hard = $1
- when /SOFT_MASK%_MEAN: (.+)/; then @soft = $1
+ line = ios.readline.chomp
+ fields = line.split("\t")
+
+ case fields.first
+ when "SEQ" then @count, @min, @max, @sum, @mean = fields[2], fields[3], fields[4], fields[5], fields[6]
+ when "GC%" then @gc = fields[6]
+ when "HARD_MASK%" then @hard = fields[6]
+ when "SOFT_MASK%" then @soft = fields[6]
end
end
end