Module Import alias Import alias ImportFrom alias ImportFrom alias alias alias ImportFrom alias alias alias ImportFrom alias ClassDef bases AttributeLoad NameLoad attr body FunctionDef arguments args NameParam defaults body Assign AttributeStore NameLoad attr ListComp Call NameLoad NameLoad comprehension NameStore ListLoad Str Str Str Str Str Str Str Str Str Assign AttributeStore NameLoad attr ListComp Call NameLoad NameLoad comprehension NameStore ListLoad Str Str Str Str Str Str Str Str Str Str Str decorator_list FunctionDef arguments args NameParam defaults body For NameStore AttributeLoad NameLoad attr body Expr Call AttributeLoad NameLoad attr Call NameLoad NameLoad TupleLoad NameLoad Dict decorator_list FunctionDef arguments args NameParam defaults body For NameStore AttributeLoad NameLoad attr body Expr Call AttributeLoad NameLoad attr Call NameLoad NameLoad TupleLoad NameLoad Dict decorator_list decorator_list ClassDef bases AttributeLoad NameLoad attr body FunctionDef arguments args NameParam defaults body Assign AttributeStore NameLoad attr ListLoad TupleLoad ListLoad Call NameLoad Str ListLoad TupleLoad Str Str TupleLoad Str Str TupleLoad Str Str TupleLoad ListLoad Call NameLoad Str ListLoad TupleLoad Str Str TupleLoad ListLoad Call NameLoad Str ListLoad TupleLoad Str Str TupleLoad ListLoad Call NameLoad Str Call NameLoad Str Call NameLoad Str Call NameLoad Str Call NameLoad Str ListLoad TupleLoad Str Str TupleLoad Str Str TupleLoad ListLoad Call NameLoad Str ListLoad TupleLoad Str Str TupleLoad Str Str TupleLoad Str Str TupleLoad Str Str TupleLoad Str Str TupleLoad Str Str Assign AttributeStore NameLoad attr Call NameLoad Call NameLoad NameLoad ListLoad Str Str Str Str Str Str Str Str Str Assign AttributeStore NameLoad attr ListComp TupleLoad Call NameLoad SubscriptLoad NameLoad Index Num SubscriptLoad NameLoad Index Num SubscriptLoad NameLoad Index Num comprehension NameStore ListLoad TupleLoad Str NameLoad Str TupleLoad Str NameLoad Str TupleLoad Str NameLoad Str TupleLoad Str NameLoad Str TupleLoad Str NameLoad Str TupleLoad Str NameLoad Str TupleLoad Str NameLoad Str TupleLoad Str NameLoad Str TupleLoad Str NameLoad Str TupleLoad Str NameLoad Str TupleLoad Str NameLoad Str TupleLoad Str NameLoad Str TupleLoad Str NameLoad Str TupleLoad Str NameLoad Str decorator_list FunctionDef arguments args NameParam defaults body For TupleStore NameStore NameStore NameStore AttributeLoad NameLoad attr body With Call AttributeLoad NameLoad attr NameLoad NameLoad body Expr Call NameLoad NameLoad keyword NameLoad decorator_list FunctionDef arguments args NameParam defaults body With Call AttributeLoad NameLoad attr NameLoad Str body Expr Call NameLoad Call NameLoad Str decorator_list FunctionDef arguments args NameParam defaults body For TupleStore NameStore NameStore AttributeLoad NameLoad attr body For NameStore NameLoad body Assign NameStore Call NameLoad NameLoad keyword NameLoad Assign NameStore ListLoad Assign NameStore ListLoad For TupleStore NameStore NameStore NameLoad body Expr Call AttributeLoad NameLoad attr Call NameLoad NameLoad Expr Call AttributeLoad NameLoad attr NameLoad Assign NameStore Call NameLoad NameLoad keyword NameLoad Expr Call AttributeLoad NameLoad attr NameLoad NameLoad decorator_list decorator_list ClassDef bases AttributeLoad NameLoad attr body FunctionDef arguments args NameParam defaults body Assign NameStore Call NameLoad ListLoad Call NameLoad Str keyword Dict Str Str Call NameLoad Str keyword Dict Str Str Call NameLoad Str keyword Dict Str Str keyword Str Assign NameStore Call NameLoad ListLoad Call NameLoad Str keyword Dict Str Str Call NameLoad Str keyword Dict Str Str Call NameLoad Str keyword Dict Str Str Call NameLoad Str keyword Dict Str Str Call NameLoad Str keyword Dict Str Str Call NameLoad Str keyword Dict Str Str keyword Str Assign NameStore Call NameLoad ListLoad Call NameLoad Str keyword Dict Str Str Call NameLoad Str keyword Dict Str Str keyword Str Assign NameStore Call NameLoad ListLoad Call NameLoad Str keyword Dict Str Str keyword Str Assign NameStore Call NameLoad ListLoad Call NameLoad Str keyword Dict Str Str keyword Str Assign AttributeStore NameLoad attr ListLoad NameLoad NameLoad NameLoad NameLoad NameLoad Assign AttributeStore NameLoad attr Call NameLoad NameLoad ListLoad Str Str Str Str Str Assign AttributeStore NameLoad attr ListLoad TupleLoad Call NameLoad ListLoad Str TupleLoad Call NameLoad ListLoad Call NameLoad Str keyword Dict Str Str Call NameLoad Str keyword Dict Str Str Str TupleLoad Call NameLoad ListLoad Call NameLoad Str keyword Dict Str Str Call NameLoad Str keyword Dict Str Str keyword Str Str decorator_list FunctionDef arguments args NameParam defaults body For TupleStore NameStore NameStore Call NameLoad AttributeLoad NameLoad attr AttributeLoad NameLoad attr body Assign NameStore Call AttributeLoad NameLoad attr Expr Call NameLoad NameLoad NameLoad Assign NameStore Call AttributeLoad NameLoad attr Expr Call AttributeLoad NameLoad attr With Call AttributeLoad NameLoad attr NameLoad NameStore body Assign NameStore Call AttributeLoad NameLoad attr Expr Call AttributeLoad NameLoad attr NameLoad NameLoad decorator_list FunctionDef arguments args NameParam defaults body For TupleStore NameStore NameStore AttributeLoad NameLoad attr body Assign NameStore Call AttributeLoad NameLoad attr With Call AttributeLoad NameLoad attr NameLoad NameLoad body Expr Call NameLoad NameLoad NameLoad Assign NameStore Call AttributeLoad NameLoad attr Expr Call AttributeLoad NameLoad attr Expr Call AttributeLoad NameLoad attr NameLoad Str decorator_list decorator_list If CompareEq NameLoad Str body Expr Call AttributeLoad NameLoad attr
N/A N/A io N/A unittest skbio.io PhylipFormatError skbio.io.format.phylip _tabular_msa_to_phylip _phylip_to_tabular_msa _phylip_sniffer skbio TabularMSA DNA RNA skbio.util get_data_path TestSniffer N/A N/A unittest TestCase N/A setUp N/A N/A self N/A N/A N/A N/A self positives N/A N/A get_data_path e N/A e N/A phylip_dna_3_seqs phylip_single_seq_long phylip_single_seq_short phylip_two_chunks phylip_variable_length_ids phylip_varied_whitespace_in_seqs phylip_whitespace_in_header_1 phylip_whitespace_in_header_2 phylip_whitespace_in_header_3 N/A N/A self negatives N/A N/A get_data_path e N/A e N/A empty whitespace_only phylip_invalid_empty_line_after_header phylip_invalid_empty_line_before_header phylip_invalid_header_too_long phylip_invalid_header_too_short phylip_invalid_no_header phylip_invalid_seq_too_long phylip_invalid_seq_too_short phylip_invalid_zero_seq_len phylip_invalid_zero_seqs N/A test_positives N/A N/A self N/A N/A N/A fp N/A self positives N/A N/A N/A N/A self assertEqual N/A _phylip_sniffer fp N/A True N/A N/A test_negatives N/A N/A self N/A N/A N/A fp N/A self negatives N/A N/A N/A N/A self assertEqual N/A _phylip_sniffer fp N/A False N/A N/A N/A TestReaders N/A N/A unittest TestCase N/A setUp N/A N/A self N/A N/A N/A N/A self valid_configurations N/A N/A N/A N/A get_data_path phylip_dna_3_seqs N/A N/A ..ACC-GTTGG.. d1 N/A TTACCGGT-GGCC d2 N/A .-ACC-GTTGC-- d3 N/A N/A N/A get_data_path phylip_single_seq_long N/A N/A ..ACC-GTTGG..AATGC.C---- foo N/A N/A N/A get_data_path phylip_single_seq_short N/A N/A - N/A N/A N/A get_data_path phylip_two_chunks N/A get_data_path phylip_varied_whitespace_in_seqs N/A get_data_path phylip_whitespace_in_header_1 N/A get_data_path phylip_whitespace_in_header_2 N/A get_data_path phylip_whitespace_in_header_3 N/A N/A ..ACC-GTTGG..AATGC.C foo N/A TTACCGGT-GGCCTA-GCAT bar N/A N/A N/A get_data_path phylip_variable_length_ids N/A N/A .-ACGT N/A TGCA-. a N/A .ACGT- bb N/A TGCA-. 1 N/A AAAAAA abcdefghij N/A GGGGGG ab def42ij N/A N/A self positive_fps N/A list N/A map get_data_path N/A phylip_dna_3_seqs phylip_single_seq_long phylip_single_seq_short phylip_two_chunks phylip_variable_length_ids phylip_varied_whitespace_in_seqs phylip_whitespace_in_header_1 phylip_whitespace_in_header_2 phylip_whitespace_in_header_3 N/A N/A self invalid_files N/A N/A N/A get_data_path N/A e N/A 0 N/A e N/A 1 N/A e N/A 2 N/A e N/A N/A empty PhylipFormatError This file is empty. N/A whitespace_only PhylipFormatError Found non-header line .*: "" N/A phylip_invalid_empty_line_after_header PhylipFormatError Empty lines are not allowed. N/A phylip_invalid_empty_line_before_header PhylipFormatError Found non-header line .*: "" N/A phylip_invalid_empty_line_between_seqs PhylipFormatError Empty lines are not allowed. N/A phylip_invalid_header_too_long PhylipFormatError Found non-header line .*: "2 20 extra_text" N/A phylip_invalid_header_too_short PhylipFormatError Found non-header line .*: " 20" N/A phylip_invalid_no_header PhylipFormatError Found non-header line .*: "foo .*" N/A phylip_invalid_seq_too_long PhylipFormatError The length of sequence foo is not 20 as specified .*. N/A phylip_invalid_seq_too_short PhylipFormatError The length of sequence foo is not 20 as specified .*. N/A phylip_invalid_too_few_seqs PhylipFormatError The number of sequences is not .* as specified .*. N/A phylip_invalid_too_many_seqs PhylipFormatError The number of sequences is not .* as specified in the header. N/A phylip_invalid_zero_seq_len PhylipFormatError The number of sequences and the length must be positive. N/A phylip_invalid_zero_seqs PhylipFormatError The number of sequences and the length must be positive. N/A test_phylip_to_tabular_msa_invalid_files N/A N/A self N/A N/A N/A N/A fp error_type error_msg_regex N/A self invalid_files N/A N/A N/A N/A self assertRaisesRegex error_type error_msg_regex N/A N/A N/A _phylip_to_tabular_msa fp constructor DNA N/A test_phylip_to_tabular_msa_no_constructor N/A N/A self N/A N/A N/A N/A N/A self assertRaisesRegex ValueError `constructor` N/A N/A N/A _phylip_to_tabular_msa N/A get_data_path phylip_dna_3_seqs N/A test_phylip_to_tabular_msa_valid_files N/A N/A self N/A N/A N/A N/A valid_files components N/A self valid_configurations N/A N/A valid valid_files N/A N/A observed N/A _phylip_to_tabular_msa valid constructor DNA N/A expected_seqs N/A N/A expected_index N/A N/A N/A seq ID components N/A N/A N/A N/A expected_seqs append N/A DNA seq N/A N/A N/A expected_index append ID N/A expected N/A TabularMSA expected_seqs index expected_index N/A N/A N/A self assertEqual observed expected N/A N/A TestWriters N/A N/A unittest TestCase N/A setUp N/A N/A self N/A N/A N/A dna_3_seqs N/A TabularMSA N/A N/A DNA ..ACC-GTTGG.. metadata N/A id d1 N/A DNA TTACCGGT-GGCC metadata N/A id d2 N/A DNA .-ACC-GTTGC-- metadata N/A id d3 minter id N/A variable_length_ids N/A TabularMSA N/A N/A DNA .-ACGT metadata N/A id N/A DNA TGCA-. metadata N/A id a N/A DNA .ACGT- metadata N/A id bb N/A DNA TGCA-. metadata N/A id 1 N/A DNA AAAAAA metadata N/A id abcdefghij N/A DNA GGGGGG metadata N/A id ab def42ij minter id N/A two_chunks N/A TabularMSA N/A N/A DNA ..ACC-GTTGG..AATGC.C metadata N/A id foo N/A DNA TTACCGGT-GGCCTA-GCAT metadata N/A id bar minter id N/A single_seq_long N/A TabularMSA N/A N/A DNA ..ACC-GTTGG..AATGC.C---- metadata N/A id foo minter id N/A single_seq_short N/A TabularMSA N/A N/A DNA - metadata N/A id minter id N/A N/A self objs N/A dna_3_seqs variable_length_ids two_chunks single_seq_long single_seq_short N/A N/A self fps N/A map get_data_path N/A phylip_dna_3_seqs phylip_variable_length_ids phylip_two_chunks phylip_single_seq_long phylip_single_seq_short N/A N/A self invalid_objs N/A N/A N/A TabularMSA N/A one sequence N/A N/A TabularMSA N/A N/A DNA metadata N/A id d1 N/A DNA metadata N/A id d2 one position N/A N/A TabularMSA N/A N/A RNA ACGU metadata N/A id foo N/A RNA UGCA metadata N/A id alongsequenceid minter id 10.*alongsequenceid N/A test_write N/A N/A self N/A N/A N/A N/A fp obj N/A zip N/A self fps N/A self objs N/A N/A fh N/A N/A io StringIO N/A N/A _tabular_msa_to_phylip obj fh N/A obs N/A N/A fh getvalue N/A N/A N/A fh close N/A N/A N/A io open fp fh N/A N/A exp N/A N/A fh read N/A N/A N/A self assertEqual obs exp N/A test_write_invalid_alignment N/A N/A self N/A N/A N/A N/A invalid_obj error_msg_regexp N/A self invalid_objs N/A N/A fh N/A N/A io StringIO N/A N/A N/A self assertRaisesRegex PhylipFormatError error_msg_regexp N/A N/A N/A _tabular_msa_to_phylip invalid_obj fh N/A obs N/A N/A fh getvalue N/A N/A N/A fh close N/A N/A N/A self assertEqual obs N/A N/A N/A N/A __name__ __main__ N/A N/A N/A N/A unittest main