rbbt-util 5.17.45 → 5.17.46

checksums.yaml

@@ -1,7 +1,7 @@
 ---
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-  data.tar.gz: 22292e4bfb285b76dfb507ccea4e28587b3245f9
+  metadata.gz: 343bf453468db2fccabfac2f4bdc61766d5a13dc
+  data.tar.gz: 99da330d0c5b25fb5c641356b8bb6db857b2631a
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+  metadata.gz: 740316fe25f986440370d4f3fb0bb5178f442deee5b02d5e7ad1b0129e1174846371669c0f6bf39bfc18ce24582ae69319be36521f715d242140ff4f70cb5206
+  data.tar.gz: 854f65081846e9830d4d62318d4dd5884f8421bcfb35d432c22d90c49f31f04b4df3c8ca42933fed8023991ac478ee484054f92af200b05340c8cba536b949a3

data/bin/rbbt

@@ -32,7 +32,7 @@ Log.nocolor = true if ARGV.include? "--nocolor"
 options = SOPT.setup <<EOF
 Ruby bioinformatics toolkit
 
-$ rbbt <command> <subcommand> ... -a --arg1 --arg2='value' --arg3 'another-value'"
+$ rbbt <command> <subcommand> ... -a --arg1 --arg2='value' --arg3 'another-value'
 
 
 --log*                  #{Log.color :yellow, "Log level from 0 (debug) 6 (errors)"}

data/lib/rbbt/util/log/progress/report.rb

@@ -83,7 +83,7 @@ module Log
       str = Log.color :magenta, desc
       if @ticks == 0
         if @max
-          return str << " " << Log.color(:yellow, "waiting on #{@max} #{bytes ? 'bytes' : 'items'} - #{Process.pid}") 
+          return str << " " << Log.color(:yellow, "waiting on #{@max} #{bytes ? 'bytes' : 'items'}") 
         else
           return str << " " << Log.color(:yellow, "waiting - #{Process.pid}") 
         end

data/share/rbbt_commands/tsv/sort

@@ -13,6 +13,7 @@ $ rbbt tsv sort file.tsv
 Display summary information. Works with Tokyocabinet HDB and BDB as well.
 
 -hh--header_hash* Change the character used to mark the header line (defaults to #)
+-f--field* Field to sort by (name or number)
 -h--help Help
 EOF
 
@@ -22,7 +23,15 @@ file = ARGV.shift
 
 file = STDIN if file == '-' or file.nil?
 
-rest = ARGV.inject(""){|acc,e| acc << " '#{e}'" }
+
+field = options[:field]
+if field =~ /^\d+$/
+  field_pos = field.to_i
+else
+  field_pos = TSV.parse_header(file).all_fields.index(field) + 1
+end
+
+rest = ARGV.inject("-t\"\t\" -g -k#{field_pos}"){|acc,e| acc << " '#{e}'" }
 
 file_io = TSV.get_stream(file)
 stream = Misc.sort_stream(file_io, options[:header_hash] || "#", rest)

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.17.45
+  version: 5.17.46
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2015-06-09 00:00:00.000000000 Z
+date: 2015-06-11 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake