/bioinformatics

First project for Bioinformatic course at ITBA. Year 2013.

Primary LanguageRuby

Bioinformatics

First project for Bioinformatics course at ITBA. Year 2013.

Instructions

  • Ex1.rb Generates a Fasta sequence file from a GenBank input file

    • ruby src/Ex1.rb input_file_path output_file_path
    • input_file_path is the file path for a GenBank input file
    • output_file_path is the file path for the fasta output file
    • Example: ruby src/Ex1.rb files/genbank/tritricum_globulin.gbk outputs/Ex1.fas

  • Ex2.rb Generates a Blast report from a Fasta file

    • ruby src/Ex2.rb input_file_path output_file_path type
    • input_file_path is the file path for the fasta input file
    • output_file_path is the file path for the blast report output file
    • type is either --prot or --nuc
    • Example: ruby src/Ex2.rb files/fasta/maize_globulin.fas outputs/Ex2.out --nuc

  • Ex3.rb Parses a Blast report and shows the hits that matches a pattern.

    • ruby src/Ex3.rb input_file_path output_file_path pattern type
    • input_file_path is the file path for the blast report input file
    • output_file_path is the file path for the blast parsed output file
    • type is either --prot or --nuc
    • pattern is the pattern that will match a description
    • Example: ruby src/Ex3.rb files/blast/maize_globulin.xml outputs/Ex3.out mays --nuc

  • Ex4.rb Runs the EMBOSS Water command for two proteins.

    • ruby src/Ex4.rb output_file_path
    • output_file_path is the file path for the water command result output file
    • For OSX EMBOSS installation http://nodens.ceab.csic.es/t-rfpred/mac#EMB
    • Example: ruby src/Ex4.rb outputs/Ex4.out

  • files folder contains blast, fasta and genbank example input files

  • outputs folder contains some output example files

  • src folder contains the different scripts