Back to index

python-biopython  1.60
Variables
test_align Namespace Reference

Variables

tuple alignment = MultipleSeqAlignment([], Alphabet.generic_alphabet)
string letters = "AbcDefGhiJklMnoPqrStuVwxYz"
tuple test_dir = os.path.join(os.getcwd(), 'Clustalw')
list test_names = ['opuntia.aln', 'cw02.aln']
list test_files = []
tuple align_info = AlignInfo.SummaryInfo(alignment)
tuple consensus = align_info.dumb_consensus()
tuple ks = align_info.replacement_dictionary(['N'])
list second_seq = alignment[1]
dictionary e_freq
tuple e_freq_table
list chars_to_ignore = ['N']
tuple to_parse = os.path.join(os.curdir, 'Quality', 'example.fasta')

Variable Documentation

tuple test_align.align_info = AlignInfo.SummaryInfo(alignment)

Definition at line 84 of file test_align.py.

tuple test_align.alignment = MultipleSeqAlignment([], Alphabet.generic_alphabet)

Definition at line 26 of file test_align.py.

Definition at line 124 of file test_align.py.

tuple test_align.consensus = align_info.dumb_consensus()

Definition at line 85 of file test_align.py.

dictionary test_align.e_freq
Initial value:
00001 {'G' : 0.25,
00002           'C' : 0.25,
00003           'A' : 0.25,
00004           'T' : 0.25}

Definition at line 114 of file test_align.py.

Initial value:
00001 FreqTable.FreqTable(e_freq, FreqTable.FREQ,
00002                                    IUPAC.unambiguous_dna)

Definition at line 119 of file test_align.py.

tuple test_align.ks = align_info.replacement_dictionary(['N'])

Definition at line 91 of file test_align.py.

string test_align.letters = "AbcDefGhiJklMnoPqrStuVwxYz"

Definition at line 33 of file test_align.py.

Definition at line 104 of file test_align.py.

tuple test_align.test_dir = os.path.join(os.getcwd(), 'Clustalw')

Definition at line 59 of file test_align.py.

Definition at line 62 of file test_align.py.

list test_align.test_names = ['opuntia.aln', 'cw02.aln']

Definition at line 60 of file test_align.py.

tuple test_align.to_parse = os.path.join(os.curdir, 'Quality', 'example.fasta')

Definition at line 134 of file test_align.py.