#Very simple tests on an empty alignment
alignment = Alignment(Alphabet.generic_alphabet)
assert alignment.get_alignment_length() == 0
assert alignment.get_all_seqs() == []
del alignment
#Basic tests on simple three string alignment
alignment = Alignment(Alphabet.generic_alphabet)
letters = "AbcDefGhiJklMnoPqrStuVwxYz"
alignment.add_sequence("mixed", letters)
alignment.add_sequence("lower", letters.lower())
alignment.add_sequence("upper", letters.upper())
assert alignment.get_alignment_length() == 26
assert len(alignment.get_all_seqs()) == 3
assert alignment.get_seq_by_num(0).tostring() == letters
assert alignment.get_seq_by_num(1).tostring() == letters.lower()
assert alignment.get_seq_by_num(2).tostring() == letters.upper()
assert alignment.get_all_seqs()[0].description == "mixed"
assert alignment.get_all_seqs()[1].description == "lower"
assert alignment.get_all_seqs()[2].description == "upper"
for (col, letter) in enumerate(letters) :
assert alignment.get_column(col) == letter \
+ letter.lower() \
+ letter.upper()
#Check row extractions:
assert alignment[0].id == "mixed"
assert alignment[-1].id == "upper"
#Check sub-alignment extraction by row slicing:
assert isinstance(alignment[::-1], Alignment)
assert alignment[::-1][0].id == "upper"
#Very simple tests on an empty alignment
alignment = Alignment(Alphabet.generic_alphabet)
assert alignment.get_alignment_length() == 0
assert len(alignment) == 0
del alignment
#Basic tests on simple three string alignment
alignment = Alignment(Alphabet.generic_alphabet)
letters = "AbcDefGhiJklMnoPqrStuVwxYz"
alignment.add_sequence("mixed", letters)
alignment.add_sequence("lower", letters.lower())
alignment.add_sequence("upper", letters.upper())
assert alignment.get_alignment_length() == 26
assert len(alignment) == 3
assert alignment.get_seq_by_num(0).tostring() == letters
assert alignment.get_seq_by_num(1).tostring() == letters.lower()
assert alignment.get_seq_by_num(2).tostring() == letters.upper()
assert alignment[0].description == "mixed"
assert alignment[1].description == "lower"
assert alignment[2].description == "upper"
for (col, letter) in enumerate(letters):
assert alignment.get_column(col) == letter \
+ letter.lower() \
+ letter.upper()
#Check row extractions:
assert alignment[0].id == "mixed"
assert alignment[-1].id == "upper"
#Check sub-alignment extraction by row slicing:
assert isinstance(alignment[::-1], Alignment)
assert alignment[::-1][0].id == "upper"
print seqrec
#tipo de dato alineamiento de secuencias, guarda no procesa
from Bio.Align.Generic import Alignment
seq1='MHQAIFIYQIGYPLKSGYIQSIRSPEYDNW'
seq2='MH--IFIYQIGYALKSGYIQSIRSPEY-NW'
align=Alignment(Bio.Alphabet.Gapped(IUPAC.protein)) #instance of Alignment class
align.add_sequence('asp',seq1)
align.add_sequence('unk',seq2)
print align
#Alignment methods
#get_all_seqs: return all sequences in the alignment as a list of SeqRecord
for s in align.get_all_seqs(): #in align: (the same)
print '->',s.seq
#get_seq_by_num(n): return only the selected sequence by index
print str(align.get_seq_by_num(1)) #Seq object
print align[0] #SeqRecord object
print str(align[0].seq)
#get_alignment_length(): get length of alignment
print align.get_alignment_length()
#get_column(n): return a string with all the letters in the n column
print align.get_column(0)
print align.get_column(2)
#AlignInfo module: to extract info from alignment objects
from Bio.Align import AlignInfo
#print_info_content function
#SummaryInfo,PSSM classes
summary=AlignInfo.SummaryInfo(align)
print summary.information_content()
print summary.dumb_consensus()
