5 ff = Bio::FlatFile.auto('bcl2.fasta')
6 ff.each_entry do |entry|
8 puts entry.entry_id # prints the identifier of the entry
9 puts entry.definition # prints the definition of the entry
10 puts entry.seq # prints the sequence data of the entry
13 # Creates a multiple sequence alignment (possibly unaligned) named
14 # 'seqs' from array 'seq_ary'.
15 seqs = Bio::Alignment.new( seq_ary )
16 seqs.each { |seq| puts seq.to_s }
21 # Writes multiple sequence alignment (possibly unaligned) 'seqs'
22 # to a file in PHYLIP format.
23 File.open('out0.phylip', 'w') do |f|
24 f.write(seqs.output(:phylip))
27 File.open('out0.fasta', 'w') do |f|
28 f.write(seqs.output(:fasta))
34 # Reads in a FASTA-formatted multiple sequence alignment (which does
35 # not have to be aligned, though) and stores its sequences in
38 fasta_seqs = Bio::Alignment::MultiFastaFormat.new(File.open('bcl2.fasta').read)
39 fasta_seqs.entries.each do |seq|
43 # Creates a multiple sequence alignment (possibly unaligned) named
44 # 'seqs' from array 'seq_ary'.
45 seqs = Bio::Alignment.new( seq_ary )
46 seqs.each { |seq| puts seq.to_s }
51 # Writes multiple sequence alignment (possibly unaligned) 'seqs'
52 # to a file in PHYLIP format.
53 File.open('out1.phylip', 'w') do |f|
54 f.write(seqs.output(:phylip))
57 File.open('out1.fasta', 'w') do |f|
58 f.write(seqs.output(:fasta))
64 #ff = Bio::FlatFile.new(Bio::FastaFormat, 'bcl2.fasta')
66 # puts "definition : " + f.definition
67 # puts "nalen : " + f.nalen.to_s
68 # puts "naseq : " + f.naseq
73 Bio::FastaFormat.open('bcl2.fasta') do | file |
75 puts entry.entry_id # Gets the identifier, e.g. 'sp|O35147|BAD_RAT'.
76 # puts entry.definition # Gets the complete fasta description line.
77 #puts entry.seq # Gets the actual sequence.
81 seqs =Bio::Alignment.new( seq_ary )
82 seqs.each { |x| puts x }
89 #seqs =Bio::Alignment.readfiles(File.open('bcl2.fasta'))
90 #seqs.entries.each do |seq|
91 # puts seq.to_biosequence
101 seqs = Bio::Alignment::MultiFastaFormat.new(File.open('bcl2.fasta').read)
102 seqs.entries.each do |seq|
103 puts seq.to_seq.output(:genbank)
108 puts seqs.entries[0].to_seq.output(:genbank)
111 puts seqs.entries[0].to_seq.output(:fasta)
114 puts seqs.entries[0].to_seq.output(:embl)
117 puts seqs.entries[0].to_seq.output(:raw)
120 puts seqs.entries[0].to_seq.output(:fasta_ncbi)
123 puts seqs.entries[0].to_seq.output(:fastq)
126 puts seqs.entries[0].to_seq.output(:fastq_sanger)
129 puts seqs.entries[0].to_seq.output(:fastq_solexa)
132 puts seqs.entries[0].to_seq.output(:fastq_illumina)
135 puts seqs.entries[0].to_seq.output(:fasta_numeric)
138 puts seqs.entries[0].to_seq.output(:qual)
143 # Reads in a ClustalW formatted multiple sequence alignment
144 # from a file named "infile_clustalw.aln" and stores it in 'report'.
145 report = Bio::ClustalW::Report.new(File.read('infile_clustalw.aln'))
147 # Accesses the actual alignment.
148 msa = report.alignment
150 # Goes through all sequences in 'msa' and prints the
151 # actual molecular sequence.
158 DEFAULT_PARSER = Bio::Alignment::MultiFastaFormat
159 puts DEFAULT_PARSER.to_s
161 #file = Bio::Alignment.readfiles('bcl2.fasta', Bio::Alignment::MultiFastaFormat)
162 #file.each do |entry|
163 # puts entry.entry_id # Gets the identifier, e.g. 'sp|O35147|BAD_RAT'.
164 # puts entry.definition # Gets the complete fasta description line.
165 # puts entry.seq # Gets the actual sequence.
166 #puts entry.aaseq.composition # Gets the amino acid composition.
171 file = Bio::FastaFormat.open('bcl2.fasta')
173 puts entry.entry_id # Gets the identifier, e.g. 'sp|O35147|BAD_RAT'.
174 puts entry.definition # Gets the complete fasta description line.
175 puts entry.seq # Gets the actual sequence.
176 # do something on each fasta sequence entry
182 # Creates a new file named "outfile.fasta" and writes
183 # multiple sequence alignment 'msa' to it in fasta format.
184 File.open('outfile.fasta', 'w') do |f|
185 f.write(msa.output(:fasta))
189 File.open('outfile.clustal', 'w') do |f|
190 f.write(msa.output(:clustal))
192 File.open('outfile.phylip', 'w') do |f|
193 f.write(msa.output(:phylip))
195 File.open('outfile.phylipnon', 'w') do |f|
196 f.write(msa.output(:phylipnon))
198 File.open('outfile.msf', 'w') do |f|
199 f.write(msa.output(:msf))
201 File.open('outfile.molphy', 'w') do |f|
202 f.write(msa.output(:molphy))
209 seq1 = Bio::Sequence.auto("gggggg")
212 puts seq1.output(:fasta)
213 #seq2 = Bio::Sequence::AA.new("ggggt")
214 #seq3 = Bio::Sequence::AA.new("ggt")
218 seqs = ['MFQIPEFEPSEQEDSSSAER',
219 'MGTPKQPSLAPAHALGLRKS',
225 options = [ '--maxiterate', '1000', '--localpair' ]
226 mafft = Bio::MAFFT.new('mafft', options )
227 report = mafft.query_align( seqs)
229 # Accesses the actual alignment
230 align = report.alignment
232 # Prints each sequence to the console.
233 align.each { |s| puts s.to_s }
240 clustalw = Bio::ClustalW.new('/home/zma/SOFTWARE/clustalw-2.1/src/clustalw2' )
241 report = clustalw.query_align( seqs)
242 #puts report.alignment.output_fasta.to_s
243 report.alignment.each { |x| puts x.to_s }
248 options = [ '-quiet', '-maxiters', '64' ]
249 muscle = Bio::Muscle.new('/home/zma/SOFTWARE/muscle3.8.31/src/muscle', options )
250 report = muscle.query_align( seqs)
251 #puts report.alignment.output_fasta.to_s
252 report.alignment.each { |x| puts x.to_s }
256 file = Bio::FastaFormat.open('bcl2.fasta')
258 puts entry.entry_id # Gets the identifier, e.g. 'sp|O35147|BAD_RAT'.
259 puts entry.definition # Gets the complete fasta description line.
260 puts entry.seq # Gets the actual sequence.
261 puts entry.aaseq.composition # Gets the amino acid composition.
266 Bio::FlatFile.auto('bcl2.fasta') do |ff|
268 puts entry.entry_id # Gets the identifier, e.g. 'sp|O35147|BAD_RAT'.
269 puts entry.definition # Gets the complete fasta description line.
270 puts entry.seq # Gets the actual sequence.
271 puts entry.aaseq.composition # Gets the amino acid composition.