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=b27d913c0436a4593117695911ca62bfe7a1b838;hpb=b238db9423661e6271b54b2e50e56ecdd801a45b;p=jalview.git

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