diff --git a/tests/test_transcript_structure.py b/tests/test_transcript_structure.py
index 3535d8fcc228f0f79687f05ffdb2f72af5ae8622..b28f71ad32662715a163e49aa33b7ab50f55a81e 100644
--- a/tests/test_transcript_structure.py
+++ b/tests/test_transcript_structure.py
@@ -22,7 +22,7 @@ P_INTRON_1: float = 1
)
def test_csv_2_dict(test_input):
builder = Gts.BuildTranscriptStructure(test_input[0], test_input[1], test_input[2])
- builder.__csv_2_dict()
+ builder._csv_2_dict()
with open(TEST_CSV_TITLE) as csv:
csv_lines = csv.readlines()
first_line = csv_lines[0].split(',')
@@ -38,7 +38,7 @@ def test_csv_2_dict(test_input):
def test_gtf_2_dict():
builder = Gts.BuildTranscriptStructure(TEST_CSV_TITLE, GENE_COORDS, P_INTRON_0)
- builder.__gtf_2_dict()
+ builder._gtf_2_dict()
assert len(builder.gene_sequences_dict) == 2 # Two genes read in the dictionary.
assert len(builder.gene_sequences_dict[GENE_KEYS[0]]) == 5
assert len(builder.gene_sequences_dict[GENE_KEYS[1]]) == 5
@@ -63,9 +63,9 @@ def test_gtf_2_dict():
)
def test_make_new_transcripts(test_input):
builder = Gts.BuildTranscriptStructure(test_input[0], test_input[1], test_input[2])
- builder.__csv_2_dict() # Generates dictionary from gene count csv file.
- builder.__gtf_2_dict() # Generates dictionary from gtf file.
- builder.__make_new_transcripts() # Generates the differently spliced transcripts.
+ builder._csv_2_dict() # Generates dictionary from gene count csv file.
+ builder._gtf_2_dict() # Generates dictionary from gtf file.
+ builder._make_new_transcripts() # Generates the differently spliced transcripts.
numb_trans_dict = 0
numb_trans_csv = 10
@@ -86,10 +86,10 @@ def test_make_new_transcripts(test_input):
)
def test_make_gtf_lines(test_input):
builder = Gts.BuildTranscriptStructure(test_input[0], test_input[1], test_input[2])
- builder.__csv_2_dict() # Generates dictionary from gene count csv file.
- builder.__gtf_2_dict() # Generates dictionary from gtf file.
- builder.__make_new_transcripts() # Generates the differently spliced transcripts.
- builder.__make_gtf_info()
+ builder._csv_2_dict() # Generates dictionary from gene count csv file.
+ builder._gtf_2_dict() # Generates dictionary from gtf file.
+ builder._make_new_transcripts() # Generates the differently spliced transcripts.
+ builder._make_gtf_info()
for line in builder.gtf_lines:
columns = line.split('\t')
assert columns[3] < columns[4] # Tests that the coordinates are increasing.
@@ -104,10 +104,10 @@ def test_make_gtf_lines(test_input):
)
def test_sort_gtf_lines(test_input):
builder = Gts.BuildTranscriptStructure(test_input[0], test_input[1], test_input[2])
- builder.__csv_2_dict() # Generates dictionary from gene count csv file.
- builder.__gtf_2_dict() # Generates dictionary from gtf file.
- builder.__make_new_transcripts() # Generates the differently spliced transcripts.
- builder.__make_gtf_info()
+ builder._csv_2_dict() # Generates dictionary from gene count csv file.
+ builder._gtf_2_dict() # Generates dictionary from gtf file.
+ builder._make_new_transcripts() # Generates the differently spliced transcripts.
+ builder._make_gtf_info()
starts_before = [] # Verifies that the function actually has to sort.
for line in builder.gtf_lines:
@@ -116,9 +116,9 @@ def test_sort_gtf_lines(test_input):
starts_before.append(columns[3])
for ii in range(len(starts_before)-1):
assert starts_before[ii] > starts_before[ii+1]
- builder.__sort_gtf_lines()
+ builder._sort_gtf_lines()
- builder.__sort_gtf_lines()
+ builder._sort_gtf_lines()
starts_after = [] # Verifies that the function sorted.
for line in builder.gtf_lines:
columns = line.split('\t')
@@ -126,7 +126,6 @@ def test_sort_gtf_lines(test_input):
starts_after.append(columns[3])
for ii in range(len(starts_before)-1):
assert starts_after[ii] < starts_after[ii+1]
- builder.__sort_gtf_lines()
def test_write_gtf():
diff --git a/transcript_structure/Generate_transcript_structure.py b/transcript_structure/Generate_transcript_structure.py
index bf491701edc078cd4a630c53d6726742f2e6b27e..31fc77a33ca0555051a45d1cf49edf2ca5fbf328 100644
--- a/transcript_structure/Generate_transcript_structure.py
+++ b/transcript_structure/Generate_transcript_structure.py
@@ -52,14 +52,14 @@ class BuildTranscriptStructure:
def generate_transcript_structure(self):
"""Computes distribution and gene coordinates of differently spliced mRNA."""
- self.__csv_2_dict() # Generates dictionary from gene count csv file.
- self.__gtf_2_dict() # Generates dictionary from gtf file.
- self.__make_new_transcripts() # Generates the differently spliced transcripts.
- self.__make_gtf_info() # Builds the gtf file of all newly created transcripts.
- self.__sort_gtf_lines() # Sorts the gtf file by gene occurrence in sequence.
+ self._csv_2_dict() # Generates dictionary from gene count csv file.
+ self._gtf_2_dict() # Generates dictionary from gtf file.
+ self._make_new_transcripts() # Generates the differently spliced transcripts.
+ self._make_gtf_info() # Builds the gtf file of all newly created transcripts.
+ self._sort_gtf_lines() # Sorts the gtf file by gene occurrence in sequence.
self._transcripts_generated = True # Adapts state variable.
- def __csv_2_dict(self) -> None:
+ def _csv_2_dict(self) -> None:
"""Converts the csv file with gene count into a dictionary."""
with open(self.gene_count) as g_c:
lines = g_c.readlines()
@@ -72,7 +72,7 @@ class BuildTranscriptStructure:
line_entries = line.split(',')
self.gene_count_dict[line_entries[0]] = int(line_entries[1])
- def __gtf_2_dict(self) -> None:
+ def _gtf_2_dict(self) -> None:
"""Converts the gtf file into a nested dictionary."""
with open(self.input_coords) as c_g: # Reads coordinates from .gtf file.
lines = c_g.readlines()
@@ -109,7 +109,7 @@ class BuildTranscriptStructure:
gene_info['exon_seq'] = coordinates
self.gene_sequences_dict[gene_name] = gene_info
- def __make_new_transcripts(self) -> None:
+ def _make_new_transcripts(self) -> None:
""" Generates the differently spliced transcripts."""
for gene in self.gene_count_dict:
@@ -135,7 +135,7 @@ class BuildTranscriptStructure:
self.gene_transcript_dict[gene] = transcript_numbers
- def __make_gtf_info(self) -> None:
+ def _make_gtf_info(self) -> None:
""" Writes the lines of the new gtf file for the differently spliced transcripts."""
for gene in self.gene_transcript_dict: # Iterates over all genes required.
self.gtf_lines.append(self.gene_sequences_dict[gene]['gene_line']) # Add gene line to list.
@@ -188,7 +188,7 @@ class BuildTranscriptStructure:
exon_lines.reverse()
self.gtf_lines.extend(exon_lines)
- def __sort_gtf_lines(self) -> None:
+ def _sort_gtf_lines(self) -> None:
""" Sorts the gtf lines by the position of the genes (increasing) and returns it."""