From 53694c29c8deada091a88bbd201f6bb2034124fa Mon Sep 17 00:00:00 2001 From: "cmzmasek@gmail.com" Date: Wed, 9 Mar 2011 03:06:36 +0000 Subject: [PATCH] in progress... --- forester/ruby/scripts/bioruby_examples/msa_1.rb | 40 ++++++++++++++++++++--- 1 file changed, 36 insertions(+), 4 deletions(-) diff --git a/forester/ruby/scripts/bioruby_examples/msa_1.rb b/forester/ruby/scripts/bioruby_examples/msa_1.rb index b27d913..d39d810 100644 --- a/forester/ruby/scripts/bioruby_examples/msa_1.rb +++ b/forester/ruby/scripts/bioruby_examples/msa_1.rb @@ -7,9 +7,41 @@ seqs = Bio::Alignment::MultiFastaFormat.new(File.open('bcl2.fasta').read) seqs.entries.each do |seq| puts seq.to_seq.output(:genbank) end - - - +puts +puts +puts :genbank +puts seqs.entries[0].to_seq.output(:genbank) +puts +puts :fasta +puts seqs.entries[0].to_seq.output(:fasta) +puts +puts :embl +puts seqs.entries[0].to_seq.output(:embl) +puts +puts :raw +puts seqs.entries[0].to_seq.output(:raw) +puts +puts :fasta_ncbi +puts seqs.entries[0].to_seq.output(:fasta_ncbi) +puts +puts :fastq +puts seqs.entries[0].to_seq.output(:fastq) +puts +puts :fastq_sanger +puts seqs.entries[0].to_seq.output(:fastq_sanger) +puts +puts :fastq_solexa +puts seqs.entries[0].to_seq.output(:fastq_solexa) +puts +puts :fastq_illumina +puts seqs.entries[0].to_seq.output(:fastq_illumina) +puts +puts :fasta_numeric +puts seqs.entries[0].to_seq.output(:fasta_numeric) +puts +puts :qual +puts seqs.entries[0].to_seq.output(:qual) +exit ############## @@ -49,7 +81,7 @@ file.each do |entry| # do something on each fasta sequence entry end -exit + ############## # Creates a new file named "outfile.fasta" and writes -- 1.7.10.2