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
