6 seqs = Bio::Alignment::MultiFastaFormat.new(File.open('bcl2.fasta').read)
7 seqs.entries.each do |seq|
8 puts seq.to_seq.output(:genbank)
13 puts seqs.entries[0].to_seq.output(:genbank)
16 puts seqs.entries[0].to_seq.output(:fasta)
19 puts seqs.entries[0].to_seq.output(:embl)
22 puts seqs.entries[0].to_seq.output(:raw)
25 puts seqs.entries[0].to_seq.output(:fasta_ncbi)
28 puts seqs.entries[0].to_seq.output(:fastq)
31 puts seqs.entries[0].to_seq.output(:fastq_sanger)
34 puts seqs.entries[0].to_seq.output(:fastq_solexa)
37 puts seqs.entries[0].to_seq.output(:fastq_illumina)
40 puts seqs.entries[0].to_seq.output(:fasta_numeric)
43 puts seqs.entries[0].to_seq.output(:qual)
48 # Reads in a ClustalW formatted multiple sequence alignment
49 # from a file named "infile_clustalw.aln" and stores it in 'report'.
50 report = Bio::ClustalW::Report.new(File.read('infile_clustalw.aln'))
52 # Accesses the actual alignment.
53 msa = report.alignment
55 # Goes through all sequences in 'msa' and prints the
56 # actual molecular sequence.
63 DEFAULT_PARSER = Bio::Alignment::MultiFastaFormat
64 puts DEFAULT_PARSER.to_s
66 #file = Bio::Alignment.readfiles('bcl2.fasta', Bio::Alignment::MultiFastaFormat)
68 # puts entry.entry_id # Gets the identifier, e.g. 'sp|O35147|BAD_RAT'.
69 # puts entry.definition # Gets the complete fasta description line.
70 # puts entry.seq # Gets the actual sequence.
71 #puts entry.aaseq.composition # Gets the amino acid composition.
76 file = Bio::FastaFormat.open('bcl2.fasta')
78 puts entry.entry_id # Gets the identifier, e.g. 'sp|O35147|BAD_RAT'.
79 puts entry.definition # Gets the complete fasta description line.
80 puts entry.seq # Gets the actual sequence.
81 # do something on each fasta sequence entry
87 # Creates a new file named "outfile.fasta" and writes
88 # multiple sequence alignment 'msa' to it in fasta format.
89 File.open('outfile.fasta', 'w') do |f|
90 f.write(msa.output(:fasta))
94 File.open('outfile.clustal', 'w') do |f|
95 f.write(msa.output(:clustal))
97 File.open('outfile.phylip', 'w') do |f|
98 f.write(msa.output(:phylip))
100 File.open('outfile.phylipnon', 'w') do |f|
101 f.write(msa.output(:phylipnon))
103 File.open('outfile.msf', 'w') do |f|
104 f.write(msa.output(:msf))
106 File.open('outfile.molphy', 'w') do |f|
107 f.write(msa.output(:molphy))
114 seq1 = Bio::Sequence.auto("gggggg")
117 puts seq1.output(:fasta)
118 #seq2 = Bio::Sequence::AA.new("ggggt")
119 #seq3 = Bio::Sequence::AA.new("ggt")
123 seqs = ['MFQIPEFEPSEQEDSSSAER',
124 'MGTPKQPSLAPAHALGLRKS',
130 options = [ '--maxiterate', '1000', '--localpair' ]
131 mafft = Bio::MAFFT.new('mafft', options )
132 report = mafft.query_align( seqs)
134 # Accesses the actual alignment
135 align = report.alignment
137 # Prints each sequence to the console.
138 align.each { |s| puts s.to_s }
145 clustalw = Bio::ClustalW.new('/home/zma/SOFTWARE/clustalw-2.1/src/clustalw2' )
146 report = clustalw.query_align( seqs)
147 #puts report.alignment.output_fasta.to_s
148 report.alignment.each { |x| puts x.to_s }
153 options = [ '-quiet', '-maxiters', '64' ]
154 muscle = Bio::Muscle.new('/home/zma/SOFTWARE/muscle3.8.31/src/muscle', options )
155 report = muscle.query_align( seqs)
156 #puts report.alignment.output_fasta.to_s
157 report.alignment.each { |x| puts x.to_s }
161 file = Bio::FastaFormat.open('bcl2.fasta')
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 Bio::FlatFile.auto('bcl2.fasta') do |ff|
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 puts entry.aaseq.composition # Gets the amino acid composition.