Testing and annotation are fixed

Testing the application is now fixed and works with recent versions of BLAST+ (2.4.0+ and 2.5.0+)

• Had to remove some of the default columns as the result is different pending on the version
• Tested with version 2.5.0+ and 2.4.0+ (other versions can output not equal results)

Annotation fix

• Fixed bug that created infinite number of columns

Almost ready to be published

Too many changes to overview, can now test functionalities

• b054ed4 - forgot about adding folder - André Veríssimo (HEAD -> master, tag: v0.9.11, origin/master)
• c078b2a - missed byebug -_- - André Veríssimo
• d7b23a9 - could not use report.csv, as it has local path - André Veríssimo
• e638c9d - annotation dir is optional - André Veríssimo
• 8fa7e54 - wrong files copied.. oops - André Veríssimo
• c8e2206 - corrects all tests and defines bootstrap as requirement - André Veríssimo
• dddc269 - add rake to gemfile! - André Veríssimo
• 2d0245b - reduces size of testing - André Veríssimo
• c21d49a - remove byebug - André Veríssimo
• b8936c4 - removes byebug -_- - André Veríssimo
• 6d5c4a6 - add testing script - André Veríssimo
• 3f0580a - adds warning when blast returns no hits - André Veríssimo
• b004c68 - update tests - André Veríssimo
• 515ef42 - change fvesca to blackberry - André Veríssimo
• 62b0456 - validates configuration file - André Veríssimo
• 35cbe0a - update minimum codon to 120 - André Veríssimo

Correction on fasta files

• corrects import fastas to take empty argument as nucl
• doesn't add empty seqs to fasta files and alwyas writes intermediate files
• corrects fasta files generation (origin of the bug: copy/paste of expressions)
• removes task option, use default in blast engines that require
• corrects annotation and custom alignment search
• corrects variable config generation that was being changed in parallel

Annotation, multithreading when separate_db and better

Some major improvements with only one new functionality: annotation

• Adds external annotation via csv files -- see user.yml for more information
• Multithreading jobs when separating databases
• Implemented benchmarking in script.rb (see src/script.rb to add benchmarking)
• Better documentation of config files
• All paths in user.yml are relative to this file
• Adds origin sequence from BLAST db (in addition to aligned portion)
• Download taxonomy only for working dir in scripts
• Searches databases by calling blastdbcmd instead of looking for files with extensions *.nhr and *.phr

Adds BLASTP engine

New features:

• Adds BLASTP engine
• Adds windows script to import fasta files to BLAST databases
• Import fasta files to databases as protein databases

Newest ORF Finder and better logging

New features:

• Uses version 0.1.4 of ORF Finder (previous release had bug)
• Logs error messages from BLAST commands
• Adds a separate_db option that will process each db into a separate folder

First pre-release of MassBlast

Almost production ready!