-require 'rubygems'
require 'bio'
-
-# creating a Bio::Sequence::NA object containing ambiguous alphabets
-#as = Bio::Sequence::NA.new("atgcyrwskmbdhvn")
-#print as.to_s
+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
-#print "\n"
+# Creates a multiple sequence alignment (possibly unaligned) named
+# 'seqs' from array 'seq_ary'.
+seqs = Bio::Alignment.new( seq_ary )
-#seq1 = Bio::Sequence::AA.new("gggggg")
+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.
+msa = report.alignment
+
+# Goes through all sequences in 'msa' and prints the
+# actual molecular sequence.
+msa.each do |entry|
+ # puts entry.seq
+end
+
+##############
+
+DEFAULT_PARSER = Bio::Alignment::MultiFastaFormat
+puts DEFAULT_PARSER.to_s
+
+#file = Bio::Alignment.readfiles('bcl2.fasta', Bio::Alignment::MultiFastaFormat)
+#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.
+ #puts entry.aaseq.composition # Gets the amino acid composition.
+#end
+#puts 'OK'
+#puts
+
+file = Bio::FastaFormat.open('bcl2.fasta')
+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.
+ # do something on each fasta sequence entry
+end
+
+
+##############
+
+# Creates a new file named "outfile.fasta" and writes
+# multiple sequence alignment 'msa' to it in fasta format.
+File.open('outfile.fasta', 'w') do |f|
+ f.write(msa.output(:fasta))
+end
+
+# 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
+
+
+
+#############
+
+seq1 = Bio::Sequence.auto("gggggg")
+
+
+puts seq1.output(:fasta)
#seq2 = Bio::Sequence::AA.new("ggggt")
#seq3 = Bio::Sequence::AA.new("ggt")
-seqs = [ "KMLFGVVFFFGG",
- "LMGGHHF",
- "GKKKKGHHHGHRRRGR",
- "KKKKGHHHGHRRRGR" ]
+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
#puts report.alignment.output_fasta.to_s
report.alignment.each { |x| puts x.to_s }
puts 'OK'
-puts
\ No newline at end of file
+puts
+
+file = Bio::FastaFormat.open('bcl2.fasta')
+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.
+ puts entry.aaseq.composition # Gets the amino acid composition.
+end
+puts 'OK'
+puts
+
+Bio::FlatFile.auto('bcl2.fasta') do |ff|
+ ff.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.
+ puts entry.aaseq.composition # Gets the amino acid composition.
+ end
+end
+puts 'OK'
+puts
+
+
+
+
+
+
git://source.jalview.org / jalview.git / blobdiff