diff --git a/tests/.DS_Store b/tests/.DS_Store
new file mode 100644
index 0000000000000000000000000000000000000000..5008ddfcf53c02e82d7eee2e57c38e5672ef89f6
Binary files /dev/null and b/tests/.DS_Store differ
diff --git a/tests/resources/.DS_Store b/tests/resources/.DS_Store
new file mode 100644
index 0000000000000000000000000000000000000000..7ad1176167dc0ba71da2384413b97af9cb814803
Binary files /dev/null and b/tests/resources/.DS_Store differ
diff --git a/tests/resources/test_transcript_structure/RP1_RIK.gtf b/tests/resources/test_transcript_structure/RP1_RIK.gtf
new file mode 100644
index 0000000000000000000000000000000000000000..d8e59e5114bfabdec1abb86b7b83748d70b5bf5f
--- /dev/null
+++ b/tests/resources/test_transcript_structure/RP1_RIK.gtf
@@ -0,0 +1,12 @@
+1 ensembl_havana gene 3999557 4409241 . - . gene_id "ENSMUSG00000025900"; gene_version "12"; gene_name "Rp1"; gene_source "ensembl_havana"; gene_biotype "protein_coding";
+1 havana transcript 4290846 4409241 . - . gene_id "ENSMUSG00000025900"; gene_version "12"; transcript_id "ENSMUST00000208793"; transcript_version "1"; gene_name "Rp1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Rp1-204"; transcript_source "havana"; transcript_biotype "retained_intron"; transcript_support_level "1";
+1 havana exon 4409170 4409241 . - . gene_id "ENSMUSG00000025900"; gene_version "12"; transcript_id "ENSMUST00000208793"; transcript_version "1"; exon_number "1"; gene_name "Rp1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Rp1-204"; transcript_source "havana"; transcript_biotype "retained_intron"; exon_id "ENSMUSE00001379779"; exon_version "1"; transcript_support_level "1";
+1 havana exon 4352202 4352837 . - . gene_id "ENSMUSG00000025900"; gene_version "12"; transcript_id "ENSMUST00000208793"; transcript_version "1"; exon_number "2"; gene_name "Rp1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Rp1-204"; transcript_source "havana"; transcript_biotype "retained_intron"; exon_id "ENSMUSE00001377400"; exon_version "1"; transcript_support_level "1";
+1 havana exon 4351910 4352081 . - . gene_id "ENSMUSG00000025900"; gene_version "12"; transcript_id "ENSMUST00000208793"; transcript_version "1"; exon_number "3"; gene_name "Rp1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Rp1-204"; transcript_source "havana"; transcript_biotype "retained_intron"; exon_id "ENSMUSE00001380148"; exon_version "1"; transcript_support_level "1";
+1 havana exon 4290846 4293012 . - . gene_id "ENSMUSG00000025900"; gene_version "12"; transcript_id "ENSMUST00000208793"; transcript_version "1"; exon_number "4"; gene_name "Rp1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Rp1-204"; transcript_source "havana"; transcript_biotype "retained_intron"; exon_id "ENSMUSE00001345123"; exon_version "1"; transcript_support_level "1";
+1 havana gene 9747648 9791924 . + . gene_id "ENSMUSG00000097893"; gene_version "8"; gene_name "1700034P13Rik"; gene_source "havana"; gene_biotype "lncRNA";
+1 havana transcript 9747648 9791922 . + . gene_id "ENSMUSG00000097893"; gene_version "8"; transcript_id "ENSMUST00000181821"; transcript_version "7"; gene_name "1700034P13Rik"; gene_source "havana"; gene_biotype "lncRNA"; transcript_name "1700034P13Rik-202"; transcript_source "havana"; transcript_biotype "lncRNA"; transcript_support_level "1";
+1 havana exon 9747648 9748604 . + . gene_id "ENSMUSG00000097893"; gene_version "8"; transcript_id "ENSMUST00000181821"; transcript_version "7"; exon_number "1"; gene_name "1700034P13Rik"; gene_source "havana"; gene_biotype "lncRNA"; transcript_name "1700034P13Rik-202"; transcript_source "havana"; transcript_biotype "lncRNA"; exon_id "ENSMUSE00001104564"; exon_version "1"; transcript_support_level "1";
+1 havana exon 9752449 9752564 . + . gene_id "ENSMUSG00000097893"; gene_version "8"; transcript_id "ENSMUST00000181821"; transcript_version "7"; exon_number "2"; gene_name "1700034P13Rik"; gene_source "havana"; gene_biotype "lncRNA"; transcript_name "1700034P13Rik-202"; transcript_source "havana"; transcript_biotype "lncRNA"; exon_id "ENSMUSE00001144804"; exon_version "1"; transcript_support_level "1";
+1 havana exon 9789656 9789780 . + . gene_id "ENSMUSG00000097893"; gene_version "8"; transcript_id "ENSMUST00000181821"; transcript_version "7"; exon_number "3"; gene_name "1700034P13Rik"; gene_source "havana"; gene_biotype "lncRNA"; transcript_name "1700034P13Rik-202"; transcript_source "havana"; transcript_biotype "lncRNA"; exon_id "ENSMUSE00001175967"; exon_version "1"; transcript_support_level "1";
+1 havana exon 9791125 9791922 . + . gene_id "ENSMUSG00000097893"; gene_version "8"; transcript_id "ENSMUST00000181821"; transcript_version "7"; exon_number "4"; gene_name "1700034P13Rik"; gene_source "havana"; gene_biotype "lncRNA"; transcript_name "1700034P13Rik-202"; transcript_source "havana"; transcript_biotype "lncRNA"; exon_id "ENSMUSE00001174858"; exon_version "1"; transcript_support_level "1";
\ No newline at end of file
diff --git a/tests/resources/test_transcript_structure/Rik_5_Rp1_5_no_title.csv b/tests/resources/test_transcript_structure/Rik_5_Rp1_5_no_title.csv
new file mode 100644
index 0000000000000000000000000000000000000000..6add2b68a03c19802e0165c5efb5b45eba521454
--- /dev/null
+++ b/tests/resources/test_transcript_structure/Rik_5_Rp1_5_no_title.csv
@@ -0,0 +1,2 @@
+1700034P13Rik,5
+Rp1,5
\ No newline at end of file
diff --git a/tests/resources/test_transcript_structure/Rik_5_Rp1_5_title.csv b/tests/resources/test_transcript_structure/Rik_5_Rp1_5_title.csv
new file mode 100644
index 0000000000000000000000000000000000000000..b6be973a2fcec97d9ed65dc4e600ded43d94b7db
--- /dev/null
+++ b/tests/resources/test_transcript_structure/Rik_5_Rp1_5_title.csv
@@ -0,0 +1,3 @@
+GeneID,count
+1700034P13Rik,5
+Rp1,5
\ No newline at end of file
diff --git a/tests/test_transcript_structure.py b/tests/test_transcript_structure.py
new file mode 100644
index 0000000000000000000000000000000000000000..523db757f4036fd86766e203f88175f195f53e47
--- /dev/null
+++ b/tests/test_transcript_structure.py
@@ -0,0 +1,135 @@
+import pytest
+from transcript_structure import Generate_transcript_structure as Gts
+
+TEST_CSV_TITLE = './tests/resources/test_transcript_structure/Rik_5_Rp1_5_title.csv'
+TEST_CSV_NO_TITLE = './tests/resources/test_transcript_structure/Rik_5_Rp1_5_no_title.csv'
+
+GENE_COORDS = './tests/resources/RP1_RIK.gtf'
+GENE_KEYS = ['Rp1', '1700034P13Rik']
+
+P_INTRON_0: float = 0
+P_INTRON_0_2 = 0.2
+P_INTRON_1: float = 1
+
+
+@pytest.mark.parametrize(
+ "test_input",
+ [(TEST_CSV_TITLE, GENE_COORDS, P_INTRON_0),
+ (TEST_CSV_NO_TITLE, GENE_COORDS, P_INTRON_0)
+ ],
+)
+def test_csv_2_dict(test_input):
+ builder = Gts.BuildTranscriptStructure(test_input[0], test_input[1], test_input[2])
+ builder.csv_2_dict()
+ with open(TEST_CSV_TITLE) as csv:
+ csv_lines = csv.readlines()
+ first_line = csv_lines[0].split(',')
+ if not first_line[1].isnumeric():
+ del(csv_lines[0]) # Removes title.
+ csv_lines[-1] = ''.join([csv_lines[-1], '\n']) # Adds \n to last line of csv.
+
+ keys = list(builder.gene_count_dict.keys())
+ for index, line in enumerate(csv_lines):
+ dic_line = ''.join([keys[index], ',', str(builder.gene_count_dict[keys[index]]), '\n'])
+ assert line == dic_line
+
+
+def test_gtf_2_dict():
+ builder = Gts.BuildTranscriptStructure(TEST_CSV_TITLE, GENE_COORDS, P_INTRON_0)
+ 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
+ gene_line_rik = ('1\thavana\tgene\t9747648\t9791924\t.\t+\t.\tgene_id "ENSMUSG00000097893"; gene_version "8"; '
+ 'gene_name "1700034P13Rik"; gene_source "havana"; gene_biotype "lncRNA";\n')
+ assert gene_line_rik == builder.gene_sequences_dict[GENE_KEYS[1]]['gene_line']
+
+ with open(GENE_COORDS) as gtf:
+ lines = gtf.readlines()
+ numb_exons_gtf = len(lines) - 4 # 2x exon + transcript line
+ numb_exons_dict = 0
+ for gene_key in GENE_KEYS:
+ numb_exons_dict += len(builder.gene_sequences_dict[gene_key]['exon_seq'])
+ assert numb_exons_gtf == numb_exons_dict
+
+
+@pytest.mark.parametrize(
+ "test_input",
+ [(TEST_CSV_TITLE, GENE_COORDS, P_INTRON_0),
+ (TEST_CSV_TITLE, GENE_COORDS, P_INTRON_1)
+ ],
+)
+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.
+
+ numb_trans_dict = 0
+ numb_trans_csv = 10
+ for gene_key in GENE_KEYS:
+ for trans_id in builder.gene_transcript_dict[gene_key]:
+ numb_trans_dict += builder.gene_transcript_dict[gene_key][trans_id]
+ assert numb_trans_csv == numb_trans_csv
+
+ for gene_key in GENE_KEYS:
+ assert len(builder.gene_transcript_dict[gene_key]) == 1 # All have identical transcript IDs.
+
+
+@pytest.mark.parametrize(
+ "test_input",
+ [(TEST_CSV_TITLE, GENE_COORDS, P_INTRON_0),
+ (TEST_CSV_TITLE, GENE_COORDS, P_INTRON_1)
+ ],
+)
+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()
+ for line in builder.gtf_lines:
+ columns = line.split('\t')
+ assert columns[3] < columns[4] # Tests that the coordinates are increasing.
+ pass
+
+
+@pytest.mark.parametrize(
+ "test_input",
+ [(TEST_CSV_TITLE, GENE_COORDS, P_INTRON_0),
+ (TEST_CSV_TITLE, GENE_COORDS, P_INTRON_1)
+ ],
+)
+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()
+
+ starts_before = [] # Verifies that the function actually has to sort.
+ for line in builder.gtf_lines:
+ columns = line.split('\t')
+ if columns[2] == 'gene':
+ 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()
+ starts_after = [] # Verifies that the function sorted.
+ for line in builder.gtf_lines:
+ columns = line.split('\t')
+ if columns[2] == 'gene':
+ 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():
+ pass
+
+
+def test_write_csv():
+ pass
diff --git a/transcript_structure/.DS_Store b/transcript_structure/.DS_Store
new file mode 100644
index 0000000000000000000000000000000000000000..9c75cefce1c0973c30df5a9d9edb641571a6d60e
Binary files /dev/null and b/transcript_structure/.DS_Store differ
diff --git a/transcript_structure/Generate_transcript_structure.py b/transcript_structure/Generate_transcript_structure.py
new file mode 100644
index 0000000000000000000000000000000000000000..82558f451126c67bcc0a20f27c85fecf22b8be3f
--- /dev/null
+++ b/transcript_structure/Generate_transcript_structure.py
@@ -0,0 +1,268 @@
+import random
+import csv
+import copy
+
+
+class BuildTranscriptStructure:
+
+ """Creates differently spliced transcripts.
+
+ Args:
+ input_gene_count(str): Path to csv file of type "geneID", number to sample.
+ input_coordinates(str): Path to gtf file of relevant genes.
+ p_intron(float): Probability to include each intron in the mRNA sequence.
+
+ Attributes:
+ gene_count_dict(dict): Dictionary of format {"gene_ID": number_of_samplings}
+ gene_sequences_dict(dict): Nested dictionary with information about each gene.
+ Format: {"gene_ID": {"gene_line": gene_gtf_line,
+ "transcript_line": transcript_gtf_line,
+ "exon_line": exemplary_exon_line,
+ "exon_seq": [[start_exon1, end_exon1],[start_exon2, end_exon2],...]
+ }
+ }
+ gene_transcript_dict(dict): Nested dictionary with amount of each differently spliced transcript.
+ Format: {"gene_ID": {"transcript_ID": n_copies}}
+ The transcript ID is a binary code, signifying whether a certain intron is included or not.
+ E.g. gene with 4 exons:
+ transcript code 001: The 1. and 2. introns are not included (spliced away), the 3. is included.
+ The transcript will therefore have 3 exons (exon 3 and 4 are combined).
+ For sequences with negative strand senses, the exon numbering is determining the direction the transcript
+ code is to be applied, and not the occurrence in the gene sequence (inverted by convention).
+ E.g. '01' means the intron between original (fully spliced) exon 1 and exon 2 was spliced away,
+ but the intron between exon 2 and exon 3 is included in the transcript.
+ gtf_lines(list): List with all newly created gtf lines.
+ """
+
+ def __init__(self,
+ input_gene_count: str,
+ input_coordinates: str,
+ p_intron: float,
+ ) -> None:
+ """Class constructor."""
+ self.gene_count = input_gene_count
+ self.input_coords = input_coordinates
+ self.p_intron = p_intron
+ self.gene_count_dict = {}
+ self.gene_sequences_dict = {}
+ self.gene_transcript_dict = {}
+ self.gtf_lines = []
+
+ 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.
+
+ 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()
+
+ first_line = lines[0].split(',') # Removes the first line if it is a title.
+ if not first_line[1][0].isnumeric():
+ del lines[0]
+
+ for line in lines:
+ line_entries = line.split(',')
+ self.gene_count_dict[line_entries[0]] = int(line_entries[1])
+
+ 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()
+ lines = [i for i in lines if i[0] != '#'] # Exclude comments
+
+ for gene_line in range(len(lines)):
+ gene_info = {} # Dictionary with information of a single gene.
+ line_entries = lines[gene_line].split('\t')
+ if line_entries[2] == 'gene': # The line indeed describes a gene.
+ attribute = line_entries[8].split(';')
+ gene_name = attribute[2][12:-1] # Extracts the gene name from the attributes.
+ gene_info['gene_line'] = lines[gene_line]
+ gene_info['transcript_line'] = lines[gene_line + 1]
+ gene_info['exon_line'] = lines[gene_line + 2] # Exemplary line of an exon.
+ gene_info['strand_sense'] = line_entries[6] == '+' # Strand sense.
+
+ coordinates = []
+ exon_line = []
+ line_offset = 2 # Lines after the gene line (+1 is transcript description).
+ while True:
+ try: # Avoids error at end of list.
+ exon_line = lines[gene_line + line_offset].split('\t')
+ except IndexError: # End of gtf file reached: The job is finished.
+ break
+ if exon_line[2] != 'exon': # End of exon list of this gene is reached.
+ break
+ else: # The line is an exon.
+ coordinates.append([int(exon_line[3]), int(exon_line[4])])
+ line_offset += 1 # Move to next line.
+
+ if exon_line[6] == '-': # Strands with sense (-)
+ coordinates.reverse()
+
+ gene_info['exon_seq'] = coordinates
+ self.gene_sequences_dict[gene_name] = gene_info
+
+ def make_new_transcripts(self) -> None:
+ """ Generates the differently spliced transcripts."""
+ for gene in self.gene_count_dict:
+
+ # Computes the intron splicing for each transcript.
+ transcript_ids = []
+ for _ in range(self.gene_count_dict[gene]):
+ i_d = []
+ for __ in range(len(self.gene_sequences_dict[gene]['exon_seq']) - 1):
+ if random.random() > self.p_intron: # Intron spliced away.
+ i_d.append('0')
+ else: # Intron not spliced away.
+ i_d.append('1')
+ transcript_ids.append(''.join(i_d)) # Combine all transcript IDs in one list.
+
+ # Counts how often each transcript is is the list.
+ transcript_numbers = {}
+ while True:
+ i_d = transcript_ids.pop()
+ transcript_numbers['-'.join([gene, i_d])] = 1 + transcript_ids.count(i_d)
+ transcript_ids = [not_current_iD for not_current_iD in transcript_ids if not_current_iD != i_d]
+ if not transcript_ids: # Leaves loop once all codes were scanned for.
+ break
+
+ self.gene_transcript_dict[gene] = transcript_numbers
+
+ def write_csv(self,
+ output_transcript_count: str
+ ) -> None:
+
+ """ Writes a csv file containing the number of differently spliced transcripts.
+
+ Args:
+ output_transcript_count(str): Path and name of the output cvs file: "transcript_ID", "gene_ID", count.
+ """
+
+ with open(output_transcript_count, 'w', newline='') as file:
+ writer = csv.writer(file)
+ writer.writerow(['Transcript_ID', 'Gene_ID', 'count'])
+ for gene in self.gene_transcript_dict:
+ for transcript_ID in self.gene_transcript_dict[gene]:
+ writer.writerow([transcript_ID, gene, self.gene_transcript_dict[gene][transcript_ID]])
+
+ 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.
+ sense = self.gene_sequences_dict[gene]['strand_sense']
+
+ for transcript_ID in self.gene_transcript_dict[gene]: # Iterates over all occurring types of splicings.
+ # Modifies the transcript line according to the splicing.
+ transcript_line = self.gene_sequences_dict[gene]['transcript_line'].split('\t')
+ attribute = transcript_line[8].split(';')
+ attribute[7] = ''.join(['transcript_name "', transcript_ID, '"'])
+ transcript_line[8] = '; '.join(attribute)
+ self.gtf_lines.append('\t'.join(transcript_line))
+
+ start_id = len(gene)
+ i_d = list(map(int, transcript_ID[start_id + 1:])) # Extract the splicing coding as int.
+ i_d_pop = copy.copy(i_d)
+ if sense:
+ i_d_pop.reverse()
+ numb_introns = sum(i_d) # Adds up the transcription ID as int.
+ numb_exons = len(self.gene_sequences_dict[gene]['exon_seq']) - numb_introns
+
+ n_unspliced = 0 # Count of number of unspliced introns.
+ exon_lines = []
+ for exon in range(numb_exons):
+ exon_line = self.gene_sequences_dict[gene]['exon_line'].split('\t') # Initializes exon line.
+ exon_line[2] = 'exon'
+ attribute = exon_line[8].split(';')
+ if sense:
+ attribute[4] = ''.join(['exon_number "', str(exon + 1), '"'])
+ else:
+ attribute[4] = ''.join(['exon_number "', str(numb_exons - exon), '"'])
+ attribute[8] = ''.join(['transcript_name "', transcript_ID, '"'])
+ exon_line[8] = '; '.join(attribute)
+ exon_line[3] = str(self.gene_sequences_dict[gene]['exon_seq'][exon + n_unspliced][0])
+ exon_line[4] = str(self.gene_sequences_dict[gene]['exon_seq'][exon + n_unspliced][1])
+
+ try:
+ while i_d_pop.pop():
+ n_unspliced += 1
+ if sense:
+ exon_line[4] = str(self.gene_sequences_dict[gene]['exon_seq'][exon + n_unspliced][1])
+ else:
+ exon_line[3] = str(self.gene_sequences_dict[gene]['exon_seq'][exon + n_unspliced][0])
+ except IndexError: # End of ID reached
+ pass
+
+ exon_lines.append('\t'.join(exon_line))
+
+ if not self.gene_sequences_dict[gene]['strand_sense']: # Negative strand sense need reversed order.
+ exon_lines.reverse()
+ self.gtf_lines.extend(exon_lines)
+
+ def sort_gtf_lines(self) -> None:
+
+ """ Sorts the gtf lines by the position of the genes (increasing) and returns it."""
+
+ # Builds and uses a dictionary with the start of the gene as key, and all lines related to this gene as value:
+ # {start_gene(int): [[gene_line],[transcript_line],[exon_line1],[exon_line2],...]}
+
+ gene_lines_dict = {}
+ gene_start = 0 # Validation: This key should remain unused, as every gtf file starts with a gene.
+ for index, line in enumerate(self.gtf_lines):
+ line_content = line.split('\t')
+ if line_content[2] == 'gene': # This is the next gene line. Initializes dictionary entry.
+ gene_start = line_content[3] # Extract the key = start of gene.
+ gene_lines_dict[gene_start] = []
+ gene_lines_dict[gene_start].append(line) # Append all lines related to this gene.
+
+ sorted_keys = sorted(gene_lines_dict) # Sorts the keys by their values.
+ sorted_gtf_lines = []
+ for key in sorted_keys:
+ sorted_gtf_lines.extend(gene_lines_dict[key]) # Creates a new list of the gtf lines in the correct order.
+
+ self.gtf_lines = sorted_gtf_lines
+
+ def write_gtf(self,
+ output_coords: str
+ ) -> None:
+
+ """ Writes a gtf file with the information about the differently spliced transcripts.
+
+ Args:
+ output_coords(str): Path and name of the output gtf file with the information of all relevant transcripts.
+ """
+ with open(output_coords, 'w') as gtf_file:
+ gtf_file.writelines(self.gtf_lines)
+
+
+def main():
+ """ Main Function."""
+ # Inputs
+ # gene_count = 'gene_count/Rik_5.csv' # Strand with + sense
+ # gene_count = 'gene_count/Rp1_5.csv' # Strand with - sense.
+ gene_count = 'gene_count/Rik_5_Rp1_5.csv' # Both strand senses combined
+ coordinates_genes = 'gtf/coordinates.gtf'
+ p_intron = 0.3
+
+ # Output paths and names.
+ name_csv_output = 'Outputs/csv_new.csv'
+ name_gtf_output = 'Outputs/gtf_new.gtf'
+
+ random.seed(10) # Initializes seed for random functions for reproducibility.
+
+ bts = BuildTranscriptStructure(gene_count, coordinates_genes, p_intron)
+ bts.csv_2_dict() # Generates dictionary from gene count csv file.
+ bts.gtf_2_dict() # Generates dictionary from gtf file.
+ bts.make_new_transcripts() # Generates the differently spliced transcripts.
+ bts.make_gtf_info() # Builds the gtf file of all newly created transcripts.
+ bts.sort_gtf_lines() # Sorts the gtf file by gene occurrence in sequence.
+ bts.write_gtf(name_gtf_output) # Writes the new gtf file.
+ bts.write_csv(name_csv_output) # Writes the new csv file with the count of the transcripts.
+
+
+if __name__ == '__main__':
+ main()
+ print('process completed')
diff --git a/transcript_structure/Outputs/.DS_Store b/transcript_structure/Outputs/.DS_Store
new file mode 100644
index 0000000000000000000000000000000000000000..5008ddfcf53c02e82d7eee2e57c38e5672ef89f6
Binary files /dev/null and b/transcript_structure/Outputs/.DS_Store differ
diff --git a/transcript_structure/Outputs/csv_new.csv b/transcript_structure/Outputs/csv_new.csv
new file mode 100644
index 0000000000000000000000000000000000000000..88a301674c9709792b1fa39ba3b721fb76dcf010
--- /dev/null
+++ b/transcript_structure/Outputs/csv_new.csv
@@ -0,0 +1,8 @@
+Transcript_ID,Gene_ID,count
+1700034P13Rik-010,1700034P13Rik,3
+1700034P13Rik-100,1700034P13Rik,1
+1700034P13Rik-000,1700034P13Rik,1
+Rp1-111,Rp1,1
+Rp1-000,Rp1,2
+Rp1-010,Rp1,1
+Rp1-001,Rp1,1
diff --git a/transcript_structure/Outputs/gtf_new.gtf b/transcript_structure/Outputs/gtf_new.gtf
new file mode 100644
index 0000000000000000000000000000000000000000..e80579574e8088396d34b4d736efcbfaf8322d88
--- /dev/null
+++ b/transcript_structure/Outputs/gtf_new.gtf
@@ -0,0 +1,30 @@
+1 ensembl_havana gene 3999557 4409241 . - . gene_id "ENSMUSG00000025900"; gene_version "12"; gene_name "Rp1"; gene_source "ensembl_havana"; gene_biotype "protein_coding";
+1 havana transcript 4290846 4409241 . - . gene_id "ENSMUSG00000025900"; gene_version "12"; transcript_id "ENSMUST00000208793"; transcript_version "1"; gene_name "Rp1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Rp1-111"; transcript_source "havana"; transcript_biotype "retained_intron"; transcript_support_level "1";
+1 havana exon 4409170 4293012 . - . gene_id "ENSMUSG00000025900"; gene_version "12"; transcript_id "ENSMUST00000208793"; transcript_version "1"; exon_number "1"; gene_name "Rp1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Rp1-111"; transcript_source "havana"; transcript_biotype "retained_intron"; exon_id "ENSMUSE00001379779"; exon_version "1"; transcript_support_level "1";
+1 havana transcript 4290846 4409241 . - . gene_id "ENSMUSG00000025900"; gene_version "12"; transcript_id "ENSMUST00000208793"; transcript_version "1"; gene_name "Rp1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Rp1-000"; transcript_source "havana"; transcript_biotype "retained_intron"; transcript_support_level "1";
+1 havana exon 4409170 4409241 . - . gene_id "ENSMUSG00000025900"; gene_version "12"; transcript_id "ENSMUST00000208793"; transcript_version "1"; exon_number "1"; gene_name "Rp1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Rp1-000"; transcript_source "havana"; transcript_biotype "retained_intron"; exon_id "ENSMUSE00001379779"; exon_version "1"; transcript_support_level "1";
+1 havana exon 4352202 4352837 . - . gene_id "ENSMUSG00000025900"; gene_version "12"; transcript_id "ENSMUST00000208793"; transcript_version "1"; exon_number "2"; gene_name "Rp1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Rp1-000"; transcript_source "havana"; transcript_biotype "retained_intron"; exon_id "ENSMUSE00001379779"; exon_version "1"; transcript_support_level "1";
+1 havana exon 4351910 4352081 . - . gene_id "ENSMUSG00000025900"; gene_version "12"; transcript_id "ENSMUST00000208793"; transcript_version "1"; exon_number "3"; gene_name "Rp1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Rp1-000"; transcript_source "havana"; transcript_biotype "retained_intron"; exon_id "ENSMUSE00001379779"; exon_version "1"; transcript_support_level "1";
+1 havana exon 4290846 4293012 . - . gene_id "ENSMUSG00000025900"; gene_version "12"; transcript_id "ENSMUST00000208793"; transcript_version "1"; exon_number "4"; gene_name "Rp1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Rp1-000"; transcript_source "havana"; transcript_biotype "retained_intron"; exon_id "ENSMUSE00001379779"; exon_version "1"; transcript_support_level "1";
+1 havana transcript 4290846 4409241 . - . gene_id "ENSMUSG00000025900"; gene_version "12"; transcript_id "ENSMUST00000208793"; transcript_version "1"; gene_name "Rp1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Rp1-010"; transcript_source "havana"; transcript_biotype "retained_intron"; transcript_support_level "1";
+1 havana exon 4409170 4409241 . - . gene_id "ENSMUSG00000025900"; gene_version "12"; transcript_id "ENSMUST00000208793"; transcript_version "1"; exon_number "1"; gene_name "Rp1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Rp1-010"; transcript_source "havana"; transcript_biotype "retained_intron"; exon_id "ENSMUSE00001379779"; exon_version "1"; transcript_support_level "1";
+1 havana exon 4352202 4352081 . - . gene_id "ENSMUSG00000025900"; gene_version "12"; transcript_id "ENSMUST00000208793"; transcript_version "1"; exon_number "2"; gene_name "Rp1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Rp1-010"; transcript_source "havana"; transcript_biotype "retained_intron"; exon_id "ENSMUSE00001379779"; exon_version "1"; transcript_support_level "1";
+1 havana exon 4290846 4293012 . - . gene_id "ENSMUSG00000025900"; gene_version "12"; transcript_id "ENSMUST00000208793"; transcript_version "1"; exon_number "3"; gene_name "Rp1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Rp1-010"; transcript_source "havana"; transcript_biotype "retained_intron"; exon_id "ENSMUSE00001379779"; exon_version "1"; transcript_support_level "1";
+1 havana transcript 4290846 4409241 . - . gene_id "ENSMUSG00000025900"; gene_version "12"; transcript_id "ENSMUST00000208793"; transcript_version "1"; gene_name "Rp1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Rp1-001"; transcript_source "havana"; transcript_biotype "retained_intron"; transcript_support_level "1";
+1 havana exon 4409170 4409241 . - . gene_id "ENSMUSG00000025900"; gene_version "12"; transcript_id "ENSMUST00000208793"; transcript_version "1"; exon_number "1"; gene_name "Rp1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Rp1-001"; transcript_source "havana"; transcript_biotype "retained_intron"; exon_id "ENSMUSE00001379779"; exon_version "1"; transcript_support_level "1";
+1 havana exon 4352202 4352837 . - . gene_id "ENSMUSG00000025900"; gene_version "12"; transcript_id "ENSMUST00000208793"; transcript_version "1"; exon_number "2"; gene_name "Rp1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Rp1-001"; transcript_source "havana"; transcript_biotype "retained_intron"; exon_id "ENSMUSE00001379779"; exon_version "1"; transcript_support_level "1";
+1 havana exon 4351910 4293012 . - . gene_id "ENSMUSG00000025900"; gene_version "12"; transcript_id "ENSMUST00000208793"; transcript_version "1"; exon_number "3"; gene_name "Rp1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Rp1-001"; transcript_source "havana"; transcript_biotype "retained_intron"; exon_id "ENSMUSE00001379779"; exon_version "1"; transcript_support_level "1";
+1 havana gene 9747648 9791924 . + . gene_id "ENSMUSG00000097893"; gene_version "8"; gene_name "1700034P13Rik"; gene_source "havana"; gene_biotype "lncRNA";
+1 havana transcript 9747648 9791922 . + . gene_id "ENSMUSG00000097893"; gene_version "8"; transcript_id "ENSMUST00000181821"; transcript_version "7"; gene_name "1700034P13Rik"; gene_source "havana"; gene_biotype "lncRNA"; transcript_name "1700034P13Rik-010"; transcript_source "havana"; transcript_biotype "lncRNA"; transcript_support_level "1";
+1 havana exon 9747648 9748604 . + . gene_id "ENSMUSG00000097893"; gene_version "8"; transcript_id "ENSMUST00000181821"; transcript_version "7"; exon_number "1"; gene_name "1700034P13Rik"; gene_source "havana"; gene_biotype "lncRNA"; transcript_name "1700034P13Rik-010"; transcript_source "havana"; transcript_biotype "lncRNA"; exon_id "ENSMUSE00001104564"; exon_version "1"; transcript_support_level "1";
+1 havana exon 9752449 9789780 . + . gene_id "ENSMUSG00000097893"; gene_version "8"; transcript_id "ENSMUST00000181821"; transcript_version "7"; exon_number "2"; gene_name "1700034P13Rik"; gene_source "havana"; gene_biotype "lncRNA"; transcript_name "1700034P13Rik-010"; transcript_source "havana"; transcript_biotype "lncRNA"; exon_id "ENSMUSE00001104564"; exon_version "1"; transcript_support_level "1";
+1 havana exon 9791125 9791922 . + . gene_id "ENSMUSG00000097893"; gene_version "8"; transcript_id "ENSMUST00000181821"; transcript_version "7"; exon_number "3"; gene_name "1700034P13Rik"; gene_source "havana"; gene_biotype "lncRNA"; transcript_name "1700034P13Rik-010"; transcript_source "havana"; transcript_biotype "lncRNA"; exon_id "ENSMUSE00001104564"; exon_version "1"; transcript_support_level "1";
+1 havana transcript 9747648 9791922 . + . gene_id "ENSMUSG00000097893"; gene_version "8"; transcript_id "ENSMUST00000181821"; transcript_version "7"; gene_name "1700034P13Rik"; gene_source "havana"; gene_biotype "lncRNA"; transcript_name "1700034P13Rik-100"; transcript_source "havana"; transcript_biotype "lncRNA"; transcript_support_level "1";
+1 havana exon 9747648 9752564 . + . gene_id "ENSMUSG00000097893"; gene_version "8"; transcript_id "ENSMUST00000181821"; transcript_version "7"; exon_number "1"; gene_name "1700034P13Rik"; gene_source "havana"; gene_biotype "lncRNA"; transcript_name "1700034P13Rik-100"; transcript_source "havana"; transcript_biotype "lncRNA"; exon_id "ENSMUSE00001104564"; exon_version "1"; transcript_support_level "1";
+1 havana exon 9789656 9789780 . + . gene_id "ENSMUSG00000097893"; gene_version "8"; transcript_id "ENSMUST00000181821"; transcript_version "7"; exon_number "2"; gene_name "1700034P13Rik"; gene_source "havana"; gene_biotype "lncRNA"; transcript_name "1700034P13Rik-100"; transcript_source "havana"; transcript_biotype "lncRNA"; exon_id "ENSMUSE00001104564"; exon_version "1"; transcript_support_level "1";
+1 havana exon 9791125 9791922 . + . gene_id "ENSMUSG00000097893"; gene_version "8"; transcript_id "ENSMUST00000181821"; transcript_version "7"; exon_number "3"; gene_name "1700034P13Rik"; gene_source "havana"; gene_biotype "lncRNA"; transcript_name "1700034P13Rik-100"; transcript_source "havana"; transcript_biotype "lncRNA"; exon_id "ENSMUSE00001104564"; exon_version "1"; transcript_support_level "1";
+1 havana transcript 9747648 9791922 . + . gene_id "ENSMUSG00000097893"; gene_version "8"; transcript_id "ENSMUST00000181821"; transcript_version "7"; gene_name "1700034P13Rik"; gene_source "havana"; gene_biotype "lncRNA"; transcript_name "1700034P13Rik-000"; transcript_source "havana"; transcript_biotype "lncRNA"; transcript_support_level "1";
+1 havana exon 9747648 9748604 . + . gene_id "ENSMUSG00000097893"; gene_version "8"; transcript_id "ENSMUST00000181821"; transcript_version "7"; exon_number "1"; gene_name "1700034P13Rik"; gene_source "havana"; gene_biotype "lncRNA"; transcript_name "1700034P13Rik-000"; transcript_source "havana"; transcript_biotype "lncRNA"; exon_id "ENSMUSE00001104564"; exon_version "1"; transcript_support_level "1";
+1 havana exon 9752449 9752564 . + . gene_id "ENSMUSG00000097893"; gene_version "8"; transcript_id "ENSMUST00000181821"; transcript_version "7"; exon_number "2"; gene_name "1700034P13Rik"; gene_source "havana"; gene_biotype "lncRNA"; transcript_name "1700034P13Rik-000"; transcript_source "havana"; transcript_biotype "lncRNA"; exon_id "ENSMUSE00001104564"; exon_version "1"; transcript_support_level "1";
+1 havana exon 9789656 9789780 . + . gene_id "ENSMUSG00000097893"; gene_version "8"; transcript_id "ENSMUST00000181821"; transcript_version "7"; exon_number "3"; gene_name "1700034P13Rik"; gene_source "havana"; gene_biotype "lncRNA"; transcript_name "1700034P13Rik-000"; transcript_source "havana"; transcript_biotype "lncRNA"; exon_id "ENSMUSE00001104564"; exon_version "1"; transcript_support_level "1";
+1 havana exon 9791125 9791922 . + . gene_id "ENSMUSG00000097893"; gene_version "8"; transcript_id "ENSMUST00000181821"; transcript_version "7"; exon_number "4"; gene_name "1700034P13Rik"; gene_source "havana"; gene_biotype "lncRNA"; transcript_name "1700034P13Rik-000"; transcript_source "havana"; transcript_biotype "lncRNA"; exon_id "ENSMUSE00001104564"; exon_version "1"; transcript_support_level "1";
diff --git a/transcript_structure/__init__.py b/transcript_structure/__init__.py
new file mode 100644
index 0000000000000000000000000000000000000000..db9c290dedfc90e7b0fdd03739ac23cc90d5d051
--- /dev/null
+++ b/transcript_structure/__init__.py
@@ -0,0 +1,2 @@
+# Transcript Structure root package
+__version__ = "1.1.0"
diff --git a/transcript_structure/gene_count/.DS_Store b/transcript_structure/gene_count/.DS_Store
new file mode 100644
index 0000000000000000000000000000000000000000..5008ddfcf53c02e82d7eee2e57c38e5672ef89f6
Binary files /dev/null and b/transcript_structure/gene_count/.DS_Store differ
diff --git a/transcript_structure/gene_count/Rik_5.csv b/transcript_structure/gene_count/Rik_5.csv
new file mode 100644
index 0000000000000000000000000000000000000000..d437d8ec85888623dbc16f18beec306929a4c38f
--- /dev/null
+++ b/transcript_structure/gene_count/Rik_5.csv
@@ -0,0 +1,2 @@
+GeneID,count
+1700034P13Rik,5
\ No newline at end of file
diff --git a/transcript_structure/gene_count/Rik_5_Rp1_5.csv b/transcript_structure/gene_count/Rik_5_Rp1_5.csv
new file mode 100644
index 0000000000000000000000000000000000000000..b6be973a2fcec97d9ed65dc4e600ded43d94b7db
--- /dev/null
+++ b/transcript_structure/gene_count/Rik_5_Rp1_5.csv
@@ -0,0 +1,3 @@
+GeneID,count
+1700034P13Rik,5
+Rp1,5
\ No newline at end of file
diff --git a/transcript_structure/gene_count/Rp1_5.csv b/transcript_structure/gene_count/Rp1_5.csv
new file mode 100644
index 0000000000000000000000000000000000000000..e7bedd16273dbb4e829a16d37f9b60f654115b1f
--- /dev/null
+++ b/transcript_structure/gene_count/Rp1_5.csv
@@ -0,0 +1,2 @@
+GeneID,count
+Rp1,5
\ No newline at end of file
diff --git a/transcript_structure/gtf/.DS_Store b/transcript_structure/gtf/.DS_Store
new file mode 100644
index 0000000000000000000000000000000000000000..5008ddfcf53c02e82d7eee2e57c38e5672ef89f6
Binary files /dev/null and b/transcript_structure/gtf/.DS_Store differ
diff --git a/transcript_structure/gtf/coordinates.gtf b/transcript_structure/gtf/coordinates.gtf
new file mode 100644
index 0000000000000000000000000000000000000000..cb15d1672584996c6468f4e08d555a0c2ff30818
Binary files /dev/null and b/transcript_structure/gtf/coordinates.gtf differ
diff --git a/transcript_structure/gtf/gtf_explained.xlsx b/transcript_structure/gtf/gtf_explained.xlsx
new file mode 100644
index 0000000000000000000000000000000000000000..5cc4a71bb5c7db6720aa43375fc9c45c8441581f
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