sequenceserver 0.6.9 → 0.7.1
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data/bin/sequenceserver
CHANGED
@@ -2,9 +2,31 @@
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require 'rubygems'
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require 'bundler/setup'
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+
require 'optparse'
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require 'sequenceserver'
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7
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# display name for tools like `ps`
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$PROGRAM_NAME = 'sequenceserver'
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# e.g:
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# sequenceserver --config .sequenceserver.conf format_database
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begin
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# parse command line till first non-option, removing parsed options from ARGV
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OptionParser.new do |opts|
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opts.on('-c', '--config CONFIG_FILE', 'Use the given configuration file') do |config_file|
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SequenceServer::App.config_file = File.expand_path(config_file)
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end
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end.order!
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# of the remaining items in ARGV, the first one must be a subcommand
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case ARGV.shift
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when 'format_database'
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require 'sequenceserver/database_formatter'
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exit
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end
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rescue OptionParser::InvalidOption =>e
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puts e
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exit
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end
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10
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SequenceServer::App.run!
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@@ -1,9 +1,10 @@
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-
#!/usr/bin/env ruby
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# copyright yannick . wurm at unil . ch
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# Finds files, reads first char. if its '>', read 500 lines. Guess sequence type, ask user for title to format as blast database.
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5
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-
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-
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# TODO: bring it under SequenceServer namespace
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# TODO: move the file to a 'command/' sub-directory (probably makes more sense if we have several subcommands)
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# TODO: needs more love (read refactoring) overall
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require 'ptools' # for File.binary?(file)
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require 'find'
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require 'logger'
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@@ -144,36 +145,32 @@ end
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OptionParser.new do |opts|
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opts.banner =<<BANNER
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-
NAME
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-
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+
SUMMARY
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prepare BLAST databases for SequenceServer
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-
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+
USAGE
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-
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sequenceserver format_database [--verbose] [blast_database_directory]
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Example:
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-
$
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-
$
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159
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+
$ sequenceserver format_database ~/db # explicitly specify a database directory
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$ sequenceserver format_database # use the database directory in config.yml
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DESCRIPTION
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-
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-
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Recursively scan the given 'blast_database_directory' for BLAST databases and
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formats them for use with SequenceServer.
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It automagically detects the database type, and ignores non-db files and
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pre-formatted databases. The 'parse_seqids' makeblastdb options is used.
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'blast_database_directory' can be passed as a command line parameter or
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-
through
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SequenceServer).
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-
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-
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Failing both, database_formatter will look for 'database' directory relative
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-
to the current working directory i.e ./database.
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-
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-
database_formatter can be used standalone too.
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through a configuration file by setting the 'database' key (the same option
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used by SequenceServer). Configuration file will be checked only if the
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command line parameter is missing.
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OPTIONS
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data/sequenceserver.gemspec
CHANGED
@@ -1,7 +1,7 @@
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Gem::Specification.new do |s|
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# meta
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s.name = 'sequenceserver'
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-
s.version = '0.
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s.version = '0.7.1'
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s.authors = ['Anurag Priyam', 'Ben J Woodcroft', 'Yannick Wurm']
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s.email = 'anurag08priyam@gmail.com'
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s.homepage = 'http://sequenceserver.com'
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@@ -22,7 +22,7 @@ DESC
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s.files = s.files + ['config.ru', 'example.config.yml']
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s.files = s.files + ['LICENSE.txt', 'README.txt']
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s.files = s.files + ['Gemfile', 'sequenceserver.gemspec']
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-
s.executables = ['sequenceserver'
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+
s.executables = ['sequenceserver']
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s.require_paths = ['lib']
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# post install information
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metadata
CHANGED
@@ -1,13 +1,13 @@
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--- !ruby/object:Gem::Specification
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name: sequenceserver
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version: !ruby/object:Gem::Version
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hash:
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hash: 1
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prerelease:
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segments:
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- 0
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-
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-
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version: 0.
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- 7
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- 1
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version: 0.7.1
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platform: ruby
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authors:
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- Anurag Priyam
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@@ -69,13 +69,13 @@ description: |
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email: anurag08priyam@gmail.com
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executables:
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- sequenceserver
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-
- database_formatter
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extensions: []
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extra_rdoc_files: []
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files:
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- lib/sequenceserver.rb
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+
- lib/sequenceserver/database_formatter.rb
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- lib/sequenceserver/sequencehelpers.rb
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- lib/sequenceserver/customisation.rb
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- lib/sequenceserver/helpers.rb
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@@ -107,7 +107,6 @@ files:
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- Gemfile
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- sequenceserver.gemspec
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- bin/sequenceserver
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-
- bin/database_formatter
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homepage: http://sequenceserver.com
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licenses:
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- SequenceServer (custom)
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