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"""
Test cases used for the nosetest generator over in parser_test.py.
Each item is a 3-tuple. The first two items are the attribute string and the
expected parsed dictionary. The third, if not None, is a reconstructed string
that is acceptable -- this is needed for cases like this:
name "fgenesh1_pg.C_chr_1000007"; transcriptId 873
where there is not consistency in the quoting of values. So, in this case, the
following would be an acceptable recontructed string (with quotes around the
873):
name "fgenesh1_pg.C_chr_1000007"; transcriptId "873"
"""
attrs = [
# c_elegans_WS199_shortened_gff.txt
(
"count=1;gene=amx-2;sequence=SAGE:ggcagagtcttttggca;" "transcript=B0019.1",
{
"count": ["1"],
"gene": ["amx-2"],
"sequence": ["SAGE:ggcagagtcttttggca"],
"transcript": ["B0019.1"],
},
None,
),
# ensembl_gtf.txt
(
'gene_id "Y74C9A.6"; transcript_id "Y74C9A.6"; exon_number "1"; '
'gene_name "Y74C9A.6"; transcript_name "NR_001477.2";',
{
"gene_id": ["Y74C9A.6"],
"transcript_id": ["Y74C9A.6"],
"exon_number": ["1"],
"gene_name": ["Y74C9A.6"],
"transcript_name": ["NR_001477.2"],
},
None,
),
# F3-unique-3.v2.gff
(
"g=A3233312322232122211;i=1;p=1.000;q=23,12,18,17,10,24,19,14,27,9,23"
",9,16,20,11,7,8,4,4,14;u=0,0,0,1",
{
"g": ["A3233312322232122211"],
"i": ["1"],
"p": ["1.000"],
"q": [
"23",
"12",
"18",
"17",
"10",
"24",
"19",
"14",
"27",
"9",
"23",
"9",
"16",
"20",
"11",
"7",
"8",
"4",
"4",
"14",
],
"u": ["0", "0", "0", "1"],
},
None,
),
# glimmer_nokeyval.gff3
(
"ID=GL0000006;Name=GL0000006;Lack 3'-end;",
{"ID": ["GL0000006"], "Name": ["GL0000006"], "Lack 3'-end": []},
None,
),
# hybrid1.gff3
(
"ID=A00469;Dbxref=AFFX-U133:205840_x_at,Locuslink:2688,Genbank-mRNA:"
"A00469,Swissprot:P01241,PFAM:PF00103,AFFX-U95:1332_f_at,Swissprot:"
"SOMA_HUMAN;Note=growth%20hormone%201;Alias=GH1",
{
"ID": ["A00469"],
"Dbxref": [
"AFFX-U133:205840_x_at",
"Locuslink:2688",
"Genbank-mRNA:A00469",
"Swissprot:P01241",
"PFAM:PF00103",
"AFFX-U95:1332_f_at",
"Swissprot:SOMA_HUMAN",
],
"Note": ["growth hormone 1"],
"Alias": ["GH1"],
},
"ID=A00469;Dbxref=AFFX-U133:205840_x_at,Locuslink:2688,Genbank-mRNA:"
"A00469,Swissprot:P01241,PFAM:PF00103,AFFX-U95:1332_f_at,Swissprot:"
"SOMA_HUMAN;Note=growth hormone 1;Alias=GH1",
),
# jgi_gff2.txt
#
# This file is inconsitent with how it quotes values -- integers are not
# quoted but string values are. Only way to make this be invariant is to
# keep track of the "flavor" of each attribute; not sure it's worth the
# effort / processing time.
(
'name "fgenesh1_pg.C_chr_1000007"; transcriptId 873',
{"name": ["fgenesh1_pg.C_chr_1000007"], "transcriptId": ["873"]},
'name "fgenesh1_pg.C_chr_1000007"; transcriptId "873"',
),
# mouse_extra_comma.gff3: extra comma line
#
# Note extra empty string in the dictionary's "Parent" field.
#
(
"Name=CDS:NC_000083.5:LOC100040603;Parent=XM_001475631.1,",
{"Name": ["CDS:NC_000083.5:LOC100040603"], "Parent": ["XM_001475631.1", ""]},
None,
),
# mouse_extra_comma.gff3
#
# Note the empty ID field. Compare with the "Lack 3'-end" attribute of
# glimmer_nokeyval.gff3 above. Presumably the "Lack 3'-end" field should
# be interpreted as "True", but an empty ID should be interpreted as "None"
# or something.
#
# Furthermore, the "Lack 3'-end" has no trailing "=", but the "ID" field
# here does.
#
# In both cases, the dictionary entry is simply an empty list; it's just in
# the reconstruction where things get tricky.
(
"ID=;Parent=XM_001475631.1",
{"ID": [], "Parent": ["XM_001475631.1"]},
"ID;Parent=XM_001475631.1",
),
# ncbi_gff3.txt
(
"ID=NC_008596.1:speB:unknown_transcript_1;Parent=NC_008596.1:speB;"
"locus_tag=MSMEG_1072;EC_number=3.5.3.11;note=identified%20by%20mat"
"ch%20to%20protein%20family%20HMM%20PF00491%3B%20match%20to%20prote"
"in%20family%20HMM%20TIGR01230;transl_table=11;product=agmatinase;p"
"rotein_id=YP_885468.1;db_xref=GI:118469242;db_xref=GeneID:4535378;"
"exon_number=1",
{
"ID": ["NC_008596.1:speB:unknown_transcript_1"],
"Parent": ["NC_008596.1:speB"],
"locus_tag": ["MSMEG_1072"],
"EC_number": ["3.5.3.11"],
"note": [
"identified by match to protein family HMM P"
"F00491; match to protein family HMM TIGR01"
"230"
],
"transl_table": ["11"],
"product": ["agmatinase"],
"protein_id": ["YP_885468.1"],
"db_xref": ["GI:118469242", "GeneID:4535378"],
"exon_number": ["1"],
},
"ID=NC_008596.1:speB:unknown_transcript_1;Parent=NC_008596.1:speB;"
"locus_tag=MSMEG_1072;EC_number=3.5.3.11;note=identified by mat"
"ch to protein family HMM PF00491%3B match to prote"
"in family HMM TIGR01230;transl_table=11;product=agmatinase;p"
"rotein_id=YP_885468.1;db_xref=GI:118469242;db_xref=GeneID:4535378;"
"exon_number=1",
),
# wormbase_gff2_alt.txt
#
(
'CDS "cr01.sctg102.wum.2.1"',
{"CDS": ["cr01.sctg102.wum.2.1"]},
None,
),
]
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