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closes #63; gene spans the scaffold #65

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closes #63; gene spans the scaffold #65

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8 changes: 5 additions & 3 deletions dna_features_viewer/BiopythonTranslator/BiopythonTranslatorBase.py
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Original file line number Diff line number Diff line change
Expand Up @@ -48,10 +48,12 @@ def translate_feature(self, feature):
other_properties = other_properties(feature)
properties.update(other_properties)

location = feature.location if feature.location_operator != 'join' else feature.location.parts[0]

return GraphicFeature(
start=feature.location.start,
end=feature.location.end,
strand=feature.location.strand,
start=location.start,
end=location.end,
strand=location.strand,
**properties
)

Expand Down
88 changes: 88 additions & 0 deletions tests/data/bad_first_gene_example.gb
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Original file line number Diff line number Diff line change
@@ -0,0 +1,88 @@
LOCUS Example 4720 bp DNA circular BCT 20-MAY-2020
DEFINITION .
ACCESSION Example
VERSION Example
KEYWORDS .
SOURCE .
ORGANISM .
.
FEATURES Location/Qualifiers
CDS complement(join(3831..3851,1..331))
/locus_tag="REFERENCE.1_000001"
/product="aminotransferase class I/II-fold pyridoxal
phosphate-dependent enzyme"
CDS complement(324..1691)
/locus_tag="REFERENCE.1_000002"
/product="FAD-dependent oxidoreductase"
CDS complement(1898..2263)
/locus_tag="REFERENCE.1_000003"
/product="hypothetical protein"
CDS complement(2767..3813)
/locus_tag="REFERENCE.1_000004"
/product="alanine racemase"
ORIGIN
1 cggtgtccgg atcgatatcc agaccgtaga agcgggcctg gtgagcggcg atcgcggtgc
61 gcaacgaggg attccggcag cggcgggtac tgattacggc ccgcggcgat ggcctcgcgg
121 cggcgtcgag cacctcgtgc ggccccggat cgtcggggaa cccctgcccg agattgagcg
181 cgccggtgct ggtggccagg gcggtcatct cggtgaagat cgtcggcgcc acccggccgt
241 cggctcccag cagcccggca ccggcggccg tgcggcgcca tgggccggtg acgggtgccg
301 gtgtgttgag atcctcggcg ttctcactca ttgacccagt gtctcaagcc ccagcatccc
361 ggccgcctgc cgttcactag atgaccggta ccgggtgatc cagcgagaca gccgctgatc
421 tgtggcgttc ttgtcccaga ccccccatgt ctcgctggtt tacccggcac acctcgggta
481 tgcgcaccgg gcaggcatcg gatcggggtc acagctcggc gaagggacct ccggatcggc
541 cagccggccg gatcgacggg cctgcgggcc gcgatgatcg gcttgacggc atcgatgaca
601 tcccagacgt tgacattcat caccgcggtg atgcggttcg cgtcgagcca gaaggccacg
661 aactcgcggg tgtcgaggct cccgcggatc accaggagtc ctcctccccg ggctgcccgt
721 agtactccat gccgacgtcg tactgatcgc tgaagaagta cggcagctca tcccagcggg
781 cctccccgcc gagcagattc gtcaccgcga tgcccggctg gttcagggcc gtggcccagt
841 gctccacccg gctcctggca cccagaaccg gatggtccac attgcgatgt cgccgacggc
901 gtagatgtcc gggtcgctgg tgtgcagccc ggcgtcgacg aggacgccgt tgtccacggc
961 cagcccggcg cctcggccag tgccacattc ggctcggcgc cgatccccac caggaccgcg
1021 tctgcccccg atcgtctctc cgttggtgag cctcaccccg gtcgcccggc cggccgtcgc
1081 ggtgatctcg gccaccgagg tccgcagctt gaaggtgacg ccgtgctcgc gatggagctt
1141 cgcgtagacg gtgcccatcc ggtcgccgag tgcattggcc aggggatggt ggacggggcg
1201 acgacggtga cgacgctgcc cttctcccgt gcgtggcggc cgcctcgaga ccgatccagc
1261 cggcgcgacc acgagacggc gtccctcgcc gaactcggcg cgcagcgtct cggcgtcctg
1321 cctggtccgc agcacatgga cccgctcggc gccggccccg gatacggtga gccgccgtgg
1381 cgtggatccg gtcgccagga ccagcttgtc gtagcgcaat ggggcccctc gtcgggtcac
1441 cgcatgcaca cctcgggtcg atcgcggtgg cccgggtgga cagccgaagg tcgacgtcgt
1501 gctcggtgta ccagtcgcgg gggtgggcgt cctcgaagga gtcgccgccg gccaggaatc
1561 ccttcgacag cggtggtctc tcgtagggca ggttcggctc cgcggcgatg aggtgatcga
1621 gccgtcgaaa ccctgttccc tcagcgcctc gacggtcttc gcccggccag gcctccgccg
1681 atgacaacga tctcgtggac tgctcatggg atctccttcg ctggtggttc gcgcgcgacc
1741 accggagagc cttgcgcgca catgccgacc ccacctcaga tcggcgacgg cattcaaagt
1801 tggcggcagt ggaataccaa tgccgccgcc agttttggat gccgtcgagg aatggagccc
1861 gggaggggga acgggtgcag gggaggggag aacgggttca gaggcccggg gcagagcccg
1921 gtcgccgagg accgactggt tccagtagtc gatgtcgtcg gggcggcgta ccgcgtcgta
1981 cttgttcagc ctccggcagc agccacaccc gctggtagag ctgcggatgc tgaggctgcc
2041 ggtgagctgc ccacaggaag aacacgagct cggcgagatc ggactcgatg acatagctca
2101 cccggccctg ctccgaattg cccaccatgg cgaactggcc ccgctggacc atctggccca
2161 ggtcgatgct ctgccagtcc caggtcacca gatccccggc cgtcagtagg tggaagccgt
2221 cgatgttgat gaagatccgc ccctggtcca gaggacgcca catccgggtg gcgtcggcct
2281 gggcggcatt cctgcgctgg gagttcccga tggccgggcg agcccgacgc cggccgtcag
2341 cgccaacccg tactcgccgg tggcgaagaa gaacccgttg tcatggacgt aggacgccgt
2401 ctccgccgcc tggaaggagt acagcgtgaa gggggctgtg cgatcaccgt tctggggaag
2461 tgtccggaac cgcgaagggc accgggatgc ccggcacctc gtcgaagtgg tcggtgagga
2521 tgcagtgcac cgcgaagcgg tgcgcagcag gactctcacg ggagtccacc ccaccccggc
2581 acgctgctcc ggtacgccca gtcgaatccg ctcacccgga catggtattc cgccgatgtc
2641 caggcccgac caggtggcgg atctcccgca gtcgggggtt ccgtccgccg accgaaaagg
2701 acgcccgtcg ggaatctcgt cccttcactc cacgatgatc cgtccgggtg gcggtggcgc
2761 gcatcgtcac ctcgagctcg tcgccgatcc gcaccgagcc gggcacccac agcaggctcg
2821 cctgcatgtg cggaggctcg gcgaagaaga gcttgtgtcc gccggccgag taggggacag
2881 gccatccggc ccgcctccat gacgccgttg ccacggtgtg cgcgatctgc cgggcgttgg
2941 ccgcagccgt cgggcctgca tggccacccc gttggcggtt ccccccgaga cgatcgccag
3001 ccggtggtga cgccgcccgg cccggcgctg ccagtacccg acgcgttccg agggcgcgac
3061 gtcgtggacg tcctggacgc tcgcccggta gtgcagggcg tcgtgggccc ccagccacag
3121 ctcggtgccg acgcgatggc gcacctcgac gtggaaggtc tgacgcagcc ggtccagatc
3181 ggcggcgctg aggtgggaga cccacagtgg agccgtgtag gccgacaggg cggcggtggc
3241 caggtcggtg gcctcgccca gatgctggcc gatcatcggc aggtggatgg tccagccgac
3301 gatctccagc ccctcggcgg ccgcgacggc ggcctcgaac tcgtctggcc gcatcccgta
3361 gcggcgcatg gaggtgagca cctccaggat cacccgcgct cccggacggg ccttcgcgac
3421 ggcggccaca tcctcgaggc gcgagagggt cgtgatgacg ccgggatcgg cgagcgccgc
3481 ctcggccacg gcgtcgccgg gacgccacgg ggtgaggacg acgacgtccc cctcgaatcc
3541 cggatgctcg gcgtccccgg cccggacatc gtgctcatca gcgctgccgc gcacctcgtg
3601 ctcatcagcg ctgccgcgca ccagcgccac ctcctcggcc gtgcccaccg ccaggcagcc
3661 cagcccgagt cgtgtcacct cgccggccag ccgggcaagc ccgaagccgt agccattgcc
3721 cttggccacc ggaacgatac ccggatcgcc ggccaccacc gaatcctgat gggcccgcca
3781 ggcggcgccg tcgacgtgga gcaccaggct catcgcgacc tccggttcat gtaccagtcg
3841 aagaccttgt agagcagcgg atcgatgacc agatcccact cgccgatgta ggagacggcc
16 changes: 13 additions & 3 deletions tests/test_basics.py
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Expand Up @@ -20,6 +20,7 @@
matplotlib.use("Agg")

example_genbank = os.path.join("tests", "data", "example_sequence.gb")
example_bad_first_gene = os.path.join("tests", "data", "bad_first_gene_example.gb")
example_gff = os.path.join("tests", "data", "example_record.gff")


Expand Down Expand Up @@ -83,7 +84,6 @@ def test_from_genbank_to_circular(tmpdir):


def test_plot_with_gc_content(tmpdir):

fig, (ax1, ax2) = plt.subplots(2, 1, figsize=(8, 4), sharex=True)

# Parse the genbank file, plot annotations
Expand All @@ -98,7 +98,7 @@ def gc_content(seq):
return 100.0 * len([c for c in seq if c in "GC"]) / len(seq)

yy = [
gc_content(record.seq[i : i + window_size])
gc_content(record.seq[i: i + window_size])
for i in range(len(record.seq) - window_size)
]
xx = np.arange(len(record.seq) - window_size) + 25
Expand Down Expand Up @@ -245,7 +245,6 @@ def test_gff():


def test_multiline_plot():

translator = BiopythonTranslator()
graphic_record = translator.translate_record(example_genbank)
subrecord = graphic_record.crop((1700, 2200))
Expand Down Expand Up @@ -303,3 +302,14 @@ def compute_feature_color(self, feature):
graphic_record = translator.translate_record(example_genbank)
ax, _ = graphic_record.plot()
graphic_record.plot_legend(ax=ax)


def test_first_gene(tmpdir):
# Github issue 63
# first gene spans from end to start of a circular genome
graphic_record = BiopythonTranslator().translate_record(example_bad_first_gene)
assert len(graphic_record.features) == 4
ax, _ = graphic_record.plot(figure_width=10)
ax.figure.tight_layout()
target_file = os.path.join(str(tmpdir), "first_gene.png")
ax.figure.savefig(target_file)