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Merge pull request #18 from andrewjpage/no_trans_table_for_rna
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No trans table for rna
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@andrewjpage
andrewjpage committed Jan 21, 2015
2 parents a335338 + 9e9f39f commit 5e412b7
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Showing 5 changed files with 13 additions and 67 deletions.
3 changes: 2 additions & 1 deletion gff3toembl/convert.py
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Original file line number Diff line number Diff line change
Expand Up @@ -129,7 +129,8 @@ def construct_feature(self, feature_type = None, start = None, end = None, stran
for attribute_key in feature_attributes.keys():
feature += self.construct_feature_attribute( attribute_key = attribute_key, attribute_value = feature_attributes[attribute_key])

feature += "FT /transl_table="+str(self.translation_table)+"\n"
if feature_type == 'CDS':
feature += "FT /transl_table="+str(self.translation_table)+"\n"
return feature

def update_locus_tag(self,attribute_value):
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11 changes: 10 additions & 1 deletion gff3toembl/tests/convert_test.py
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Expand Up @@ -132,15 +132,24 @@ def test_construct_feature(self):
FT /locus_tag="ABC123"
FT /EC_number="12"
FT /EC_number="34"
"""

def test_only_cds_has_translation_table(self):
converter = convert.Convert()
assert converter.construct_feature(feature_type = 'CDS', start = 174883, end = 174959, strand = '-',feature_attributes = {'locus_tag': 'ABC123','eC_number': '12,34' }) == """\
FT CDS complement(174883..174959)
FT /locus_tag="ABC123"
FT /EC_number="12"
FT /EC_number="34"
FT /transl_table=11
"""


def test_construct_feature_locus_tag_update(self):
converter = convert.Convert(locus_tag = 'new_locus_tag')
assert converter.construct_feature(feature_type = 'tRNA', start = 174883, end = 174959, strand = '+',feature_attributes = {'locus_tag': 'ABC_123' }) == """\
FT tRNA 174883..174959
FT /locus_tag="new_locus_tag_123"
FT /transl_table=11
"""

def test_hypo_search(self):
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2 changes: 0 additions & 2 deletions gff3toembl/tests/data/expected_16s.embl
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Original file line number Diff line number Diff line change
Expand Up @@ -119,7 +119,6 @@ FT /db_xref="PFAM:PF04452.8"
FT /locus_tag="6714_8#3_01232"
FT /EC_number="2.1.1.193"
FT /gene="rsmE"
FT /transl_table=11
FT CDS complement(90..100)
FT /product="rRNA-specific 5-methylcytidine transferase"
FT /inference="ab initio prediction:Prodigal:2.60"
Expand Down Expand Up @@ -175,7 +174,6 @@ FT rRNA complement(130..140)
FT /product="16S ribosomal RNA"
FT /inference="COORDINATES:profile:RNAmmer:1.2"
FT /locus_tag="6714_8#3_02005"
FT /transl_table=11
SQ Sequence 180 BP; 62 A; 29 C; 44 G; 45 T; 0 other;
tcatgaatca acttcaagat gtcatacaag gactggagaa ggaggtgata aagtccatcg 60
ttaatcggag atggactaga atgctttgtg aaagcagatg agtataagtc ctcgttttga 120
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62 changes: 0 additions & 62 deletions gff3toembl/tests/data/expected_large_annotation.embl
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Original file line number Diff line number Diff line change
Expand Up @@ -24,7 +24,6 @@ FT rRNA complement(170..1709)
FT /product="16S ribosomal RNA"
FT /inference="COORDINATES:profile:RNAmmer:1.2"
FT /locus_tag="8233_4#93_02127"
FT /transl_table=11
FT CDS complement(2718..3164)
FT /product="Peroxide stress regulator PerR%2C FUR family"
FT /inference="ab initio prediction:Prodigal:2.60"
Expand Down Expand Up @@ -1707,22 +1706,18 @@ FT rRNA complement(171464..171577)
FT /product="5S ribosomal RNA"
FT /inference="COORDINATES:profile:RNAmmer:1.2"
FT /locus_tag="8233_4#93_02309"
FT /transl_table=11
FT rRNA complement(171652..174572)
FT /product="23S ribosomal RNA"
FT /inference="COORDINATES:profile:RNAmmer:1.2"
FT /locus_tag="8233_4#93_02310"
FT /transl_table=11
FT tRNA complement(174789..174864)
FT /product="tRNA-Ala(tgc)"
FT /inference="COORDINATES:profile:Aragorn:1.2.34"
FT /locus_tag="8233_4#93_02311"
FT /transl_table=11
FT tRNA complement(174883..174959)
FT /product="tRNA-Ile(gat)"
FT /inference="COORDINATES:profile:Aragorn:1.2.34"
FT /locus_tag="8233_4#93_02312"
FT /transl_table=11
SQ Sequence 175120 BP; 55731 A; 31266 C; 25419 G; 62704 T; 0 other;
tctgacaatc gctttcttta aaaagaaact attgtcgaga atttgcatta gcaatatcac 60
tttgtcaaaa agatgtttga atgttaaata aacattcaaa actgaataca atatgtcacg 120
Expand Down Expand Up @@ -4670,37 +4665,30 @@ FT rRNA 2..108
FT /product="5S ribosomal RNA"
FT /inference="COORDINATES:profile:RNAmmer:1.2"
FT /locus_tag="8233_4#93_02313"
FT /transl_table=11
FT tRNA 118..192
FT /product="tRNA-Asn(gtt)"
FT /inference="COORDINATES:profile:Aragorn:1.2.34"
FT /locus_tag="8233_4#93_02314"
FT /transl_table=11
FT tRNA 193..266
FT /product="tRNA-Glu(ttc)"
FT /inference="COORDINATES:profile:Aragorn:1.2.34"
FT /locus_tag="8233_4#93_02315"
FT /transl_table=11
FT tRNA 273..348
FT /product="tRNA-Val(tac)"
FT /inference="COORDINATES:profile:Aragorn:1.2.34"
FT /locus_tag="8233_4#93_02316"
FT /transl_table=11
FT tRNA 370..453
FT /product="tRNA-Tyr(gta)"
FT /inference="COORDINATES:profile:Aragorn:1.2.34"
FT /locus_tag="8233_4#93_02317"
FT /transl_table=11
FT tRNA 463..537
FT /product="tRNA-Gln(ttg)"
FT /inference="COORDINATES:profile:Aragorn:1.2.34"
FT /locus_tag="8233_4#93_02318"
FT /transl_table=11
FT tRNA 541..614
FT /product="tRNA-Lys(ttt)"
FT /inference="COORDINATES:profile:Aragorn:1.2.34"
FT /locus_tag="8233_4#93_02319"
FT /transl_table=11
FT CDS 737..1645
FT /product="arginase"
FT /inference="ab initio prediction:Prodigal:2.60"
Expand Down Expand Up @@ -5779,12 +5767,10 @@ FT tRNA 108138..108220
FT /product="tRNA-Leu(gag)"
FT /inference="COORDINATES:profile:Aragorn:1.2.34"
FT /locus_tag="8233_4#93_02420"
FT /transl_table=11
FT tRNA 108243..108316
FT /product="tRNA-Gly(tcc)"
FT /inference="COORDINATES:profile:Aragorn:1.2.34"
FT /locus_tag="8233_4#93_02421"
FT /transl_table=11
SQ Sequence 108420 BP; 39263 A; 15735 C; 20016 G; 33406 T; 0 other;
ctatagcaag gaggtcacac ctgttcccat gccgaacaca gaagttaagc tccttagcgt 60
cgatggtagt tggacttacg ttccgctaga gtagaacgtt gccaggctat atattattcc 120
Expand Down Expand Up @@ -7620,142 +7606,114 @@ FT rRNA 1..91
FT /product="5S ribosomal RNA"
FT /inference="COORDINATES:profile:RNAmmer:1.2"
FT /locus_tag="8233_4#93_02422"
FT /transl_table=11
FT tRNA 102..177
FT /product="tRNA-Val(tac)"
FT /inference="COORDINATES:profile:Aragorn:1.2.34"
FT /locus_tag="8233_4#93_02423"
FT /transl_table=11
FT tRNA 194..269
FT /product="tRNA-Thr(tgt)"
FT /inference="COORDINATES:profile:Aragorn:1.2.34"
FT /locus_tag="8233_4#93_02424"
FT /transl_table=11
FT tRNA 275..350
FT /product="tRNA-Lys(ttt)"
FT /inference="COORDINATES:profile:Aragorn:1.2.34"
FT /locus_tag="8233_4#93_02425"
FT /transl_table=11
FT tRNA 353..436
FT /product="tRNA-Leu(tag)"
FT /inference="COORDINATES:profile:Aragorn:1.2.34"
FT /locus_tag="8233_4#93_02426"
FT /transl_table=11
FT tRNA 439..513
FT /product="tRNA-Gly(gcc)"
FT /inference="COORDINATES:profile:Aragorn:1.2.34"
FT /locus_tag="8233_4#93_02427"
FT /transl_table=11
FT tRNA 525..613
FT /product="tRNA-Leu(taa)"
FT /inference="COORDINATES:profile:Aragorn:1.2.34"
FT /locus_tag="8233_4#93_02428"
FT /transl_table=11
FT tRNA 631..706
FT /product="tRNA-Arg(acg)"
FT /inference="COORDINATES:profile:Aragorn:1.2.34"
FT /locus_tag="8233_4#93_02429"
FT /transl_table=11
FT tRNA 715..788
FT /product="tRNA-Pro(tgg)"
FT /inference="COORDINATES:profile:Aragorn:1.2.34"
FT /locus_tag="8233_4#93_02430"
FT /transl_table=11
FT tRNA 806..881
FT /product="tRNA-Ala(tgc)"
FT /inference="COORDINATES:profile:Aragorn:1.2.34"
FT /locus_tag="8233_4#93_02431"
FT /transl_table=11
FT tRNA 902..976
FT /product="tRNA-Met(cat)"
FT /inference="COORDINATES:profile:Aragorn:1.2.34"
FT /locus_tag="8233_4#93_02432"
FT /transl_table=11
FT tRNA 1004..1077
FT /product="tRNA-Met(cat)"
FT /inference="COORDINATES:profile:Aragorn:1.2.34"
FT /locus_tag="8233_4#93_02433"
FT /transl_table=11
FT tRNA 1086..1177
FT /product="tRNA-Ser(tga)"
FT /inference="COORDINATES:profile:Aragorn:1.2.34"
FT /locus_tag="8233_4#93_02434"
FT /transl_table=11
FT tRNA 1187..1262
FT /product="tRNA-Asp(gtc)"
FT /inference="COORDINATES:profile:Aragorn:1.2.34"
FT /locus_tag="8233_4#93_02435"
FT /transl_table=11
FT tRNA 1301..1393
FT /product="tRNA-Ser(tga)"
FT /inference="COORDINATES:profile:Aragorn:1.2.34"
FT /locus_tag="8233_4#93_02436"
FT /transl_table=11
FT tRNA 1407..1482
FT /product="tRNA-Met(cat)"
FT /inference="COORDINATES:profile:Aragorn:1.2.34"
FT /locus_tag="8233_4#93_02437"
FT /transl_table=11
FT tRNA 1492..1567
FT /product="tRNA-Asp(gtc)"
FT /inference="COORDINATES:profile:Aragorn:1.2.34"
FT /locus_tag="8233_4#93_02438"
FT /transl_table=11
FT tRNA 1585..1659
FT /product="tRNA-Phe(gaa)"
FT /inference="COORDINATES:profile:Aragorn:1.2.34"
FT /locus_tag="8233_4#93_02439"
FT /transl_table=11
FT tRNA 1666..1741
FT /product="tRNA-Thr(tgt)"
FT /inference="COORDINATES:profile:Aragorn:1.2.34"
FT /locus_tag="8233_4#93_02440"
FT /transl_table=11
FT tRNA 1748..1830
FT /product="tRNA-Tyr(gta)"
FT /inference="COORDINATES:profile:Aragorn:1.2.34"
FT /locus_tag="8233_4#93_02441"
FT /transl_table=11
FT tRNA 1842..1915
FT /product="tRNA-Trp(cca)"
FT /inference="COORDINATES:profile:Aragorn:1.2.34"
FT /locus_tag="8233_4#93_02442"
FT /transl_table=11
FT tRNA 1918..1991
FT /product="tRNA-His(gtg)"
FT /inference="COORDINATES:profile:Aragorn:1.2.34"
FT /locus_tag="8233_4#93_02443"
FT /transl_table=11
FT tRNA 2002..2073
FT /product="tRNA-Gln(ttg)"
FT /inference="COORDINATES:profile:Aragorn:1.2.34"
FT /locus_tag="8233_4#93_02444"
FT /transl_table=11
FT tRNA 2079..2152
FT /product="tRNA-Cys(gca)"
FT /inference="COORDINATES:profile:Aragorn:1.2.34"
FT /locus_tag="8233_4#93_02445"
FT /transl_table=11
FT tRNA 2160..2234
FT /product="tRNA-Gly(tcc)"
FT /inference="COORDINATES:profile:Aragorn:1.2.34"
FT /locus_tag="8233_4#93_02446"
FT /transl_table=11
FT tRNA 2252..2326
FT /product="tRNA-Gly(tcc)"
FT /inference="COORDINATES:profile:Aragorn:1.2.34"
FT /locus_tag="8233_4#93_02447"
FT /transl_table=11
FT tRNA 2340..2414
FT /product="tRNA-Gly(tcc)"
FT /inference="COORDINATES:profile:Aragorn:1.2.34"
FT /locus_tag="8233_4#93_02448"
FT /transl_table=11
FT tRNA 2453..2536
FT /product="tRNA-Leu(caa)"
FT /inference="COORDINATES:profile:Aragorn:1.2.34"
FT /locus_tag="8233_4#93_02449"
FT /transl_table=11
FT CDS 2804..3865
FT /product="Regulatory protein"
FT /inference="ab initio prediction:Prodigal:2.60"
Expand Down Expand Up @@ -8057,42 +8015,34 @@ FT tRNA 33592..33665
FT /product="tRNA-Met(cat)"
FT /inference="COORDINATES:profile:Aragorn:1.2.34"
FT /locus_tag="8233_4#93_02479"
FT /transl_table=11
FT tRNA 33681..33756
FT /product="tRNA-Asp(gtc)"
FT /inference="COORDINATES:profile:Aragorn:1.2.34"
FT /locus_tag="8233_4#93_02480"
FT /transl_table=11
FT tRNA 33773..33845
FT /product="tRNA-Phe(gaa)"
FT /inference="COORDINATES:profile:Aragorn:1.2.34"
FT /locus_tag="8233_4#93_02481"
FT /transl_table=11
FT tRNA 33859..33934
FT /product="tRNA-His(gtg)"
FT /inference="COORDINATES:profile:Aragorn:1.2.34"
FT /locus_tag="8233_4#93_02482"
FT /transl_table=11
FT tRNA 33950..34023
FT /product="tRNA-Gly(tcc)"
FT /inference="COORDINATES:profile:Aragorn:1.2.34"
FT /locus_tag="8233_4#93_02483"
FT /transl_table=11
FT tRNA 34040..34114
FT /product="tRNA-Asn(gtt)"
FT /inference="COORDINATES:profile:Aragorn:1.2.34"
FT /locus_tag="8233_4#93_02484"
FT /transl_table=11
FT tRNA 34115..34188
FT /product="tRNA-Glu(ttc)"
FT /inference="COORDINATES:profile:Aragorn:1.2.34"
FT /locus_tag="8233_4#93_02485"
FT /transl_table=11
FT tRNA 34242..34330
FT /product="tRNA-Ser(gga)"
FT /inference="COORDINATES:profile:Aragorn:1.2.34"
FT /locus_tag="8233_4#93_02486"
FT /transl_table=11
FT CDS complement(35452..36240)
FT /product="Prophage protein"
FT /inference="ab initio prediction:Prodigal:2.60"
Expand Down Expand Up @@ -9205,7 +9155,6 @@ FT tRNA complement(9103..9195)
FT /product="tRNA-Ser(tga)"
FT /inference="COORDINATES:profile:Aragorn:1.2.34"
FT /locus_tag="8233_4#93_02511"
FT /transl_table=11
FT CDS complement(9473..10936)
FT /product="Glutamate synthase [NADPH] small chain"
FT /inference="ab initio prediction:Prodigal:2.60"
Expand Down Expand Up @@ -10447,7 +10396,6 @@ FT rRNA 107..220
FT /product="5S ribosomal RNA"
FT /inference="COORDINATES:profile:RNAmmer:1.2"
FT /locus_tag="8233_4#93_02549"
FT /transl_table=11
FT CDS 731..2068
FT /product="Orn/Lys/Arg decarboxylase family protein"
FT /inference="ab initio prediction:Prodigal:2.60"
Expand Down Expand Up @@ -10889,47 +10837,38 @@ FT rRNA 38392..38505
FT /product="5S ribosomal RNA"
FT /inference="COORDINATES:profile:RNAmmer:1.2"
FT /locus_tag="8233_4#93_02587"
FT /transl_table=11
FT tRNA 38516..38591
FT /product="tRNA-Val(tac)"
FT /inference="COORDINATES:profile:Aragorn:1.2.34"
FT /locus_tag="8233_4#93_02588"
FT /transl_table=11
FT tRNA 38608..38683
FT /product="tRNA-Thr(tgt)"
FT /inference="COORDINATES:profile:Aragorn:1.2.34"
FT /locus_tag="8233_4#93_02589"
FT /transl_table=11
FT tRNA 38689..38763
FT /product="tRNA-Lys(ttt)"
FT /inference="COORDINATES:profile:Aragorn:1.2.34"
FT /locus_tag="8233_4#93_02590"
FT /transl_table=11
FT tRNA 38796..38870
FT /product="tRNA-Gly(gcc)"
FT /inference="COORDINATES:profile:Aragorn:1.2.34"
FT /locus_tag="8233_4#93_02591"
FT /transl_table=11
FT tRNA 38878..38966
FT /product="tRNA-Leu(taa)"
FT /inference="COORDINATES:profile:Aragorn:1.2.34"
FT /locus_tag="8233_4#93_02592"
FT /transl_table=11
FT tRNA 38972..39048
FT /product="tRNA-Arg(acg)"
FT /inference="COORDINATES:profile:Aragorn:1.2.34"
FT /locus_tag="8233_4#93_02593"
FT /transl_table=11
FT tRNA 39069..39142
FT /product="tRNA-Pro(tgg)"
FT /inference="COORDINATES:profile:Aragorn:1.2.34"
FT /locus_tag="8233_4#93_02594"
FT /transl_table=11
FT tRNA 39165..39240
FT /product="tRNA-Ala(tgc)"
FT /inference="COORDINATES:profile:Aragorn:1.2.34"
FT /locus_tag="8233_4#93_02595"
FT /transl_table=11
SQ Sequence 39433 BP; 14273 A; 5313 C; 7870 G; 11977 T; 0 other;
gacgaatact aatcgatcga agacttaatc aaaataaatg ttttgcgaag caaaatcact 60
tttacttact atctagtttt gaatgtataa tctacattcg tatgtctggt gactatagca 120
Expand Down Expand Up @@ -12427,7 +12366,6 @@ FT tRNA complement(370..446)
FT /product="tRNA-Ile(gat)"
FT /inference="COORDINATES:profile:Aragorn:1.2.34"
FT /locus_tag="8233_4#93_02634"
FT /transl_table=11
SQ Sequence 656 BP; 184 A; 154 C; 100 G; 218 T; 0 other;
aagcatatcg tcgttagtaa cgtccttcat cggcttctag tgccaaggca tccaccgtgc 60
gcccttaata acttaatcta tgtttccacc atttttacaa gtcaaacgct cacatactgt 120
Expand Down
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