#############
+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'))
# Goes through all sequences in 'msa' and prints the
# actual molecular sequence.
msa.each do |entry|
- puts entry.seq
+ # puts entry.seq
end
##############
# do something on each fasta sequence entry
end
+
##############
# Creates a new file named "outfile.fasta" and writes