-require 'rubygems'
require 'bio'
-
+
+seq_ary = Array.new
+ff = Bio::FlatFile.auto('bcl2.fasta')
+ff.each_entry do |entry|
+ seq_ary.push(entry)
+ puts entry.entry_id # prints the identifier of the entry
+ puts entry.definition # prints the definition of the entry
+ puts entry.seq # prints the sequence data of the entry
+end
+
+# Creates a multiple sequence alignment (possibly unaligned) named
+# 'seqs' from array 'seq_ary'.
+seqs = Bio::Alignment.new( seq_ary )
+
+
+seqs.each { |seq| puts seq.to_s }
+
+
+puts seqs.consensus
+
+# Writes multiple sequence alignment (possibly unaligned) 'seqs'
+# to a file in PHYLIP format.
+File.open('out0.phylip', 'w') do |f|
+ f.write(seqs.output(:phylip))
+end
+
+File.open('out0.fasta', 'w') do |f|
+ f.write(seqs.output(:fasta))
+end
+
+exit
#############
+# Reads in a FASTA-formatted multiple sequence alignment (which does
+# not have to be aligned, though) and stores its sequences in
+# array 'seq_ary'.
+seq_ary = Array.new
+fasta_seqs = Bio::Alignment::MultiFastaFormat.new(File.open('bcl2.fasta').read)
+fasta_seqs.entries.each do |seq|
+ seq_ary.push( seq )
+end
+
+# Creates a multiple sequence alignment (possibly unaligned) named
+# 'seqs' from array 'seq_ary'.
+seqs = Bio::Alignment.new( seq_ary )
+seqs.each { |seq| puts seq.to_s }
+
+
+puts seqs.consensus
+
+# Writes multiple sequence alignment (possibly unaligned) 'seqs'
+# to a file in PHYLIP format.
+File.open('out1.phylip', 'w') do |f|
+ f.write(seqs.output(:phylip))
+end
+
+File.open('out1.fasta', 'w') do |f|
+ f.write(seqs.output(:fasta))
+end
+
+exit
+#################
+
+#ff = Bio::FlatFile.new(Bio::FastaFormat, 'bcl2.fasta')
+#ff.each_entry do |f|
+# puts "definition : " + f.definition
+# puts "nalen : " + f.nalen.to_s
+# puts "naseq : " + f.naseq
+#end
+#exit
+
+seq_ary = Array.new
+Bio::FastaFormat.open('bcl2.fasta') do | file |
+ file.each do |entry|
+ puts entry.entry_id # Gets the identifier, e.g. 'sp|O35147|BAD_RAT'.
+ # puts entry.definition # Gets the complete fasta description line.
+ #puts entry.seq # Gets the actual sequence.
+ seq_ary.push( entry )
+ end
+end
+seqs =Bio::Alignment.new( seq_ary )
+seqs.each { |x| puts x }
+puts seqs.consensus
+exit
+
+
+
+#will be obsolete!
+#seqs =Bio::Alignment.readfiles(File.open('bcl2.fasta'))
+#seqs.entries.each do |seq|
+# puts seq.to_biosequence
+#end
+
+#Bio::Alignment.
+
+
+
+#exit
+#############
+
+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
##############
# 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
+
+
#############
-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
git://source.jalview.org / jalview.git / blobdiff