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from gtfparse import create_missing_features, parse_gtf_and_expand_attributes
from six import StringIO
# two lines from the Ensembl 54 human GTF containing only a stop_codon and
# exon features, but from which gene and transcript information could be
# inferred
GTF_TEXT = "\n".join([
"# seqname biotype feature start end score strand frame attribute",
"".join([
"""18\tprotein_coding\tstop_codon\t32630766\t32630768\t.\t-\t0\t""",
"""gene_id "ENSG00000134779"; transcript_id "ENST00000334295"; exon_number "7";"""
""" gene_name "C18orf10";""",
""" transcript_name "C18orf10-201";"""]),
"".join([
"""18\tprotein_coding\texon\t32663078\t32663157\t.\t+\t.\tgene_id "ENSG00000150477"; """,
"""transcript_id "ENST00000383055"; exon_number "1"; gene_name "KIAA1328"; """,
"""transcript_name "KIAA1328-202";"""]),
])
GTF_DATAFRAME = parse_gtf_and_expand_attributes(StringIO(GTF_TEXT))
def test_create_missing_features_identity():
df_should_be_same = create_missing_features(GTF_DATAFRAME, {})
assert len(GTF_DATAFRAME) == len(df_should_be_same), \
"GTF DataFrames should be same size"
def _check_expanded_dataframe(df):
assert "gene" in set(df["feature"]), \
"Extended GTF should contain gene feature"
assert "transcript" in set(df["feature"]), \
"Extended GTF should contain transcript feature"
C18orf10_201_transcript_mask = (
(df["feature"] == "transcript") &
(df["transcript_name"] == "C18orf10-201"))
assert len(df[C18orf10_201_transcript_mask]) == 1, \
"Expected only 1 gene entry for C18orf10-201, got %s" % (
df[C18orf10_201_transcript_mask],)
transcript_seqname = df[C18orf10_201_transcript_mask].seqname.iloc[0]
assert (transcript_seqname == "18"), \
"Wrong seqname for C18orf10-201: %s" % transcript_seqname
transcript_start = df[C18orf10_201_transcript_mask].start.iloc[0]
assert (transcript_start == 32630766), \
"Wrong start for C18orf10-201: %s" % transcript_start
transcript_end = df[C18orf10_201_transcript_mask].end.iloc[0]
assert (transcript_end == 32630768), \
"Wrong end for C18orf10-201: %s" % transcript_end
transcript_strand = df[C18orf10_201_transcript_mask].strand.iloc[0]
assert (transcript_strand == "-"), \
"Wrong strand for C18orf10-201: %s" % transcript_strand
KIAA1328_gene_mask = (
(df["feature"] == "gene") &
(df["gene_name"] == "KIAA1328"))
assert len(df[KIAA1328_gene_mask]) == 1, "Expected only 1 gene entry for KIAA1328"
gene_seqname = df[KIAA1328_gene_mask].seqname.iloc[0]
assert (gene_seqname == "18"), \
"Wrong seqname for KIAA1328: %s" % gene_seqname
gene_start = df[KIAA1328_gene_mask].start.iloc[0]
assert (gene_start == 32663078), \
"Wrong start for KIAA1328: %s" % (gene_start,)
gene_end = df[KIAA1328_gene_mask].end.iloc[0]
assert (gene_end == 32663157), \
"Wrong end for KIAA1328: %s" % (gene_end,)
gene_strand = df[KIAA1328_gene_mask].strand.iloc[0]
assert (gene_strand == "+"), \
"Wrong strand for KIAA1328: %s" % gene_strand
def test_create_missing_features():
assert "gene" not in set(GTF_DATAFRAME["feature"]), \
"Original GTF should not contain gene feature"
assert "transcript" not in set(GTF_DATAFRAME["feature"]), \
"Original GTF should not contain transcript feature"
df_extra_features = create_missing_features(
GTF_DATAFRAME,
unique_keys={
"gene": "gene_id",
"transcript": "transcript_id"
},
extra_columns={
"gene": {"gene_name"},
"transcript": {"gene_id", "gene_name", "transcript_name"},
})
_check_expanded_dataframe(df_extra_features)
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