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[jalview.git] / forester / ruby / scripts / bioruby_examples / msa_1.rb

diff --git a/forester/ruby/scripts/bioruby_examples/msa_1.rb b/forester/ruby/scripts/bioruby_examples/msa_1.rb
index ed5d473..d39d810 100644 (file)
--- a/forester/ruby/scripts/bioruby_examples/msa_1.rb
+++ b/forester/ruby/scripts/bioruby_examples/msa_1.rb
@@ -3,17 +3,59 @@ 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'))
 
 # Accesses the actual alignment.
-align = report.alignment
+msa = report.alignment
 
-# Goes through all sequences in 'align' and prints the
+# Goes through all sequences in 'msa' and prints the
 # actual molecular sequence.
-align.each do |entry|
-  puts entry.seq
+msa.each do |entry|
+ # puts entry.seq
 end
 
 ##############
@@ -39,19 +81,33 @@ file.each do |entry|
   # do something on each fasta sequence entry
 end
 
+
 ##############
 
 # Creates a new file named "outfile.fasta" and writes
-# multiple sequence alignment 'align' to it in fasta format.
+# multiple sequence alignment 'msa' to it in fasta format.
 File.open('outfile.fasta', 'w') do |f|
-  f.write(align.output(:fasta))
+  f.write(msa.output(:fasta))
 end
 
-# Creates a new file named "outfile.aln" and writes
-# multiple sequence alignment 'align' to it in clustal format.
-File.open('outfile.aln', 'w') do |f|
-  f.write(align.output(:clustal))
+# Other formats
+File.open('outfile.clustal', 'w') do |f|
+  f.write(msa.output(:clustal))
 end
+File.open('outfile.phylip', 'w') do |f|
+  f.write(msa.output(:phylip))
+end
+File.open('outfile.phylipnon', 'w') do |f|
+  f.write(msa.output(:phylipnon))
+end
+File.open('outfile.msf', 'w') do |f|
+  f.write(msa.output(:msf))
+end
+File.open('outfile.molphy', 'w') do |f|
+  f.write(msa.output(:molphy))
+end
+
+
 
 #############
 
@@ -64,15 +120,15 @@ puts seq1.output(:fasta)
 
 
 
-seqs = [ "MFQIPEFEPSEQEDSSSAER",
-         "MGTPKQPSLAPAHALGLRKS",
-         "PKQPSLAPAHALGLRKS",
-         "MCSTSGCDLE" ] 
+seqs = ['MFQIPEFEPSEQEDSSSAER',
+        'MGTPKQPSLAPAHALGLRKS',
+        'PKQPSLAPAHALGLRKS',
+        'MCSTSGCDLE'] 
 
 
 # MAFFT
 options = [ '--maxiterate', '1000', '--localpair' ]
-mafft = Bio::MAFFT.new('/home/zma/SOFTWARE/mafft-6.847-without-extensions/scripts/mafft', options )
+mafft = Bio::MAFFT.new('mafft', options )
 report = mafft.query_align( seqs)
 
 # Accesses the actual alignment