X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fruby%2Fscripts%2Fbioruby_examples%2Fmsa_1.rb;h=d39d810515a6f654b9652c591a9103564d4f7719;hb=53694c29c8deada091a88bbd201f6bb2034124fa;hp=bb8210bf53b23c41a6e6da41e7a208a795b6d1c4;hpb=0b1f98e56d39ab1acd58da0f57fda383696d92c9;p=jalview.git

diff --git a/forester/ruby/scripts/bioruby_examples/msa_1.rb b/forester/ruby/scripts/bioruby_examples/msa_1.rb
index bb8210b..d39d810 100644
--- a/forester/ruby/scripts/bioruby_examples/msa_1.rb
+++ b/forester/ruby/scripts/bioruby_examples/msa_1.rb
@@ -3,6 +3,48 @@ require 'bio'
  
 #############
 
+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
+##############
+
+
 # Reads in a ClustalW formatted multiple sequence alignment
 # from a file named "infile_clustalw.aln" and stores it in 'report'.
 report = Bio::ClustalW::Report.new(File.read('infile_clustalw.aln'))
@@ -13,7 +55,7 @@ msa = report.alignment
 # Goes through all sequences in 'msa' and prints the
 # actual molecular sequence.
 msa.each do |entry|
-  puts entry.seq
+ # puts entry.seq
 end
 
 ##############
@@ -39,6 +81,7 @@ file.each do |entry|
   # do something on each fasta sequence entry
 end
 
+
 ##############
 
 # Creates a new file named "outfile.fasta" and writes