if __name__=="__main__": import sys from SAP.Bio.Alphabet import generic_protein from SAP.Bio import AlignIO from SAP.Bio.PDB import PDBParser if len(sys.argv) != 4: print("Expects three arguments,") print(" - FASTA alignment filename (expect two sequences)") print(" - PDB file one") print(" - PDB file two") sys.exit() # The alignment fa=AlignIO.read(open(sys.argv[1]), "fasta", generic_protein) pdb_file1=sys.argv[2] pdb_file2=sys.argv[3] # The structures p=PDBParser() s1=p.get_structure('1', pdb_file1) p=PDBParser() s2=p.get_structure('2', pdb_file2) # Get the models m1=s1[0] m2=s2[0] al=StructureAlignment(fa, m1, m2)
if __name__ == "__main__": import sys from SAP.Bio.Alphabet import generic_protein from SAP.Bio import AlignIO from SAP.Bio.PDB import PDBParser if len(sys.argv) != 4: print("Expects three arguments,") print(" - FASTA alignment filename (expect two sequences)") print(" - PDB file one") print(" - PDB file two") sys.exit() # The alignment fa = AlignIO.read(open(sys.argv[1]), "fasta", generic_protein) pdb_file1 = sys.argv[2] pdb_file2 = sys.argv[3] # The structures p = PDBParser() s1 = p.get_structure('1', pdb_file1) p = PDBParser() s2 = p.get_structure('2', pdb_file2) # Get the models m1 = s1[0] m2 = s2[0] al = StructureAlignment(fa, m1, m2)
for pos in sorted(summary_info.ic_vector): fout.write("%d %s %.3f\n" % (pos, rep_sequence[pos], summary_info.ic_vector[pos])) if __name__ == "__main__": print("Quick test") from SAP.Bio import AlignIO from SAP.Bio.Align.Generic import Alignment filename = "../../Tests/GFF/multi.fna" format = "fasta" expected = FreqTable.FreqTable({"A":0.25,"G":0.25,"T":0.25,"C":0.25}, FreqTable.FREQ, IUPAC.unambiguous_dna) alignment = AlignIO.read(open(filename), format) for record in alignment: print(record.seq) print("="*alignment.get_alignment_length()) summary = SummaryInfo(alignment) consensus = summary.dumb_consensus(ambiguous="N") print(consensus) consensus = summary.gap_consensus(ambiguous="N") print(consensus) print("") print(summary.pos_specific_score_matrix(chars_to_ignore=['-'], axis_seq=consensus)) print("") #Have a generic alphabet, without a declared gap char, so must tell #provide the frequencies and chars to ignore explicitly.
if __name__ == "__main__": print("Quick test") from SAP.Bio import AlignIO from SAP.Bio.Align.Generic import Alignment filename = "../../Tests/GFF/multi.fna" format = "fasta" expected = FreqTable.FreqTable({ "A": 0.25, "G": 0.25, "T": 0.25, "C": 0.25 }, FreqTable.FREQ, IUPAC.unambiguous_dna) alignment = AlignIO.read(open(filename), format) for record in alignment: print(record.seq) print("=" * alignment.get_alignment_length()) summary = SummaryInfo(alignment) consensus = summary.dumb_consensus(ambiguous="N") print(consensus) consensus = summary.gap_consensus(ambiguous="N") print(consensus) print("") print( summary.pos_specific_score_matrix(chars_to_ignore=['-'], axis_seq=consensus)) print("") #Have a generic alphabet, without a declared gap char, so must tell