diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 704ad66d4bb39fc389e8464f80374132ead95d01..906cfa26c05a62a1c0b8ceac7c8b1146d85c5fff 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -15,12 +15,21 @@ build-job: # First stage deployment and installation of dependencies.
- pip install -e .
- echo "Dependencies successfully deployed."
+unit-test-job: # This job runs in the test stage.
+ stage: test # It only starts when the job in the build stage completes successfully.
+ script:
+ - pip install -r requirements.txt
+ - pip install -r requirements_dev.txt
+ - pip install -e .
+ - coverage run --source sequence_extractor -m pytest
+ - coverage report -m
+
lint-test-job: # Test Stage
stage: test # Deploys and runs all 3 linters.
script:
- pip install -r requirements.txt
- pip install -r requirements_dev.txt
- pip install -e .
- - flake8 --docstring-convention google sequence_extractor/ gtf_processing/ --ignore=D104,F821
- - pylint sequence_extractor/ gtf_processing/
- - mypy sequence_extractor/ gtf_processing/
+ - flake8 --docstring-convention google sequence_extractor/
+ - pylint sequence_extractor/
+ - mypy sequence_extractor/
diff --git a/gtf_processing/pre_bedtools.py b/gtf_processing/pre_bedtools.py
deleted file mode 100644
index b5ccc5d2b27228d18700fc631c4fb6bcfaeb7fd6..0000000000000000000000000000000000000000
--- a/gtf_processing/pre_bedtools.py
+++ /dev/null
@@ -1,47 +0,0 @@
-"""This script defines a BED from exon annotation in a GTF, to get exon coordinates for use in bedtools. It also ensures that the concatenation happens in the correct order, regardless of the strandedness of the transcript.
-
-Args:
- GTF file
-
-Returns:
- BED file with the format: chr, start, end, transcript_id, score, strand, gene_id
-"""
-
-import argparse
-import pandas as pd
-from gtfparse import read_gtf
-
-parser = argparse.ArgumentParser(
- prog="pre_bedtools",
- description="extracts ordered information from gtf file and for transcripts in the negative strand, flips the order in which exons are ordered.",
-)
-parser.add_argument("--input_gtf_file", help="ordered and processed gtf file")
-parser.add_argument(
- "--output_bed_file",
- help="bed file with only exons with strandedness taken into account",
-)
-args = parser.parse_args()
-
-gtf = read_gtf(args.input_gtf_file)
-gtf_exons = gtf[gtf["feature"] == "exon"]
-gtf_exons = gtf_exons[
- ["seqname", "start", "end", "transcript_id", "score", "strand", "gene_id"]
-]
-
-gtf_df_neg = gtf_exons[gtf_exons["strand"] == "-"]
-gtf_df_neg = (
- gtf_df_neg.sort_values(["transcript_id", "start"], ascending=False)
- .groupby("transcript_id")
- .head(len(gtf_df_neg.transcript_id))
-)
-
-gtf_df_pos = gtf_exons[gtf_exons["strand"] == "+"]
-gtf_df_pos = (
- gtf_df_pos.sort_values(["transcript_id", "start"], ascending=True)
- .groupby("transcript_id")
- .head(len(gtf_df_pos.transcript_id))
-)
-
-pd.concat([gtf_df_pos, gtf_df_neg]).to_csv(
- args.output_bed_file, sep="\t", index=False
-) # gtf_df_pos and gtf_df_neg must be dataframes
diff --git a/images/Ahmed_mahmoud_git_tutorial.PNG b/images/Ahmed_mahmoud_git_tutorial.PNG
deleted file mode 100644
index de3936f17494e54ec1e2899e0cd1f2a7b557619b..0000000000000000000000000000000000000000
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diff --git a/images/Gina_Homework2Image.png b/images/Gina_Homework2Image.png
deleted file mode 100644
index 44b9a978228bcb08415ad42ec69320f578cbdefd..0000000000000000000000000000000000000000
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diff --git a/images/Markdown_Homework_GinaBoot.png b/images/Markdown_Homework_GinaBoot.png
deleted file mode 100644
index 0fd7e57c9add525dfab1de345f8bcbfe127cad6c..0000000000000000000000000000000000000000
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diff --git a/images/Samuel_Mondal_Markdown_tutorial_completion_page.png b/images/Samuel_Mondal_Markdown_tutorial_completion_page.png
deleted file mode 100644
index 58d025d997164ae4c7e04af178e1413fe9c1232d..0000000000000000000000000000000000000000
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diff --git a/images/Samuel_Mondal_git_tutorial_completion_page.png b/images/Samuel_Mondal_git_tutorial_completion_page.png
deleted file mode 100644
index af33f4a586aeefff0071ca592f5831a139d0effc..0000000000000000000000000000000000000000
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diff --git a/images/markdown-tutorial-AM.PNG b/images/markdown-tutorial-AM.PNG
deleted file mode 100644
index f23c78a1c79d99e264298cb4fdf6850781fbd63e..0000000000000000000000000000000000000000
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diff --git a/requirements.txt b/requirements.txt
index 1e4ef6d4d11827251de76f3b5bbada4240ecb8bd..c3cba872576efe22404bdd67a4dfc6da9ff47aeb 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,3 +1,4 @@
- pandas~=1.5
- numpy~=1.23
- gtfparse~=1.2
+numpy>=1.23.3
+pandas>=1.4.4
+gtfparse
+polars==0.16.17
diff --git a/requirements_dev.txt b/requirements_dev.txt
index ab4c4964f11ad764a889bccac4d6a17fdf1cd12e..4588ded2ab2d4143c8d8088dbccdfdc7146570d0 100644
--- a/requirements_dev.txt
+++ b/requirements_dev.txt
@@ -1,7 +1,7 @@
-pytest~=7.2
-coverage~=6.5
-black~=22.10
-flake8~=6.0
-flake8-docstrings~=1.6
-mypy~=0.991
-pylint~=2.15
+pytest
+coverage
+black>=22.10
+flake8
+flake8-docstrings
+mypy
+pylint
diff --git a/sequence_extractor/__init__.py b/sequence_extractor/__init__.py
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..d0d8d56bdb15401f4ebe8c00041039d15c0ffec3 100644
--- a/sequence_extractor/__init__.py
+++ b/sequence_extractor/__init__.py
@@ -0,0 +1 @@
+"""Initalise package."""
diff --git a/sequence_extractor/cli.py b/sequence_extractor/cli.py
index 1fc4949133d15189bd19335e85b134aecd5bf897..1b2a12051962fb895f9491bf6c82f274de45d419 100644
--- a/sequence_extractor/cli.py
+++ b/sequence_extractor/cli.py
@@ -1,40 +1,106 @@
-"""command line script to be run on output fasta file from bedtools getfasta."""
+"""CLI to be run on output fasta file from bedtools getfasta."""
import argparse
import logging
-from exon_concatenation import exon_concatenation
-from poly_a import poly_a_addition_to_fasta_list
+from sequence_extractor.pre_bedtools import pre_bedtools_mode
+from sequence_extractor.exon_concatenation import exon_concatenation
+from sequence_extractor.poly_a import poly_a_addition_to_fasta_list
-parser = argparse.ArgumentParser(
- prog="transcript_sequence_extractor",
- description="extracts transcript sequences from genome sequence and ouputs transcripts with PolyA tail added to them",
-)
-parser.add_argument("--input_fasta_file", help="fasta file obtained from bedtools")
-parser.add_argument("--output_file_name", help="Name of the output fasta file")
-
-args = parser.parse_args()
+LOG = logging.getLogger(__name__)
def main():
- """Runs on the output from bedtools and concatenates the exons together and adds a polyA tail and outputs a fasta file.
+ """Use CLI arguments to extract sequences.
+
+ Runs on the output from bedtools and concatenates the exons together
+ and adds a polyA tail and outputs a fasta file.
Args:
None: this will run on its own by taking the information from argparse
Returns:
- A fasta file with a single entry for each transcript ID with polyA tail being added onto the sequence at 3'end
+ A fasta file with a single entry for each transcript ID with
+ polyA tail being added onto the sequence at 3'end
"""
- LOG.info("sequence_extractor begins")
- fasta_list = exon_concatenation(args.input_fasta_file)
- final_list = poly_a_addition_to_fasta_list(fasta_list)
- with open(args.output_file_name, "w", encoding="utf-8") as fasta_out:
- fasta_out.write("\n".join("%s\n%s" % x for x in final_list))
- LOG.info("sequence_extractor ends")
+ args = parse_args()
+ setup_logging()
+
+ if args.mode == "pre_bedtools":
+ pre_bedtools_mode(args)
+ elif args.mode == "post_bedtools":
+ post_bedtools_mode(args)
+ else:
+ LOG.error(
+ "Invalid mode specified."
+ "Please choose 'pre_bedtools' or 'post_bedtools'.")
-if ___name__ == "main":
+def setup_logging() -> None:
+ """Configure logging."""
logging.basicConfig(
- format='[%(asctime)s: %(levelname)s] %(message)s (module "%(module)s")',
+ format='[%(asctime)s: %(levelname)s] %(message)s '
+ '(module "%(module)s")',
level=logging.INFO,
)
- LOG = logging.getLogger(__name__)
+
+
+def parse_args():
+ """Parse arguments for CLI."""
+ parser = argparse.ArgumentParser(
+ description="extracts transcript sequences from genome sequence and"
+ "ouputs transcripts with PolyA tail added to them",
+ )
+ parser.add_argument(
+ "--mode",
+ choices=["pre_bedtools", "post_bedtools"],
+ required=True,
+ help="Select the mode of operation"
+ "('pre_bedtools' or 'post_bedtools')."
+ )
+ parser.add_argument(
+ "-i", "--input-fasta-file",
+ dest="input_fasta_file",
+ help="Fasta-formatted file obtained from bedtools"
+ )
+ parser.add_argument(
+ "-o", "--output-file-name",
+ dest="output_file_name",
+ help="Name of the output fasta file"
+ )
+ parser.add_argument(
+ "-p", "--polyA-length",
+ dest="poly_a_length",
+ type=int,
+ help="Length of the polyA tail to be added (def: 250)",
+ default=250
+ )
+ parser.add_argument(
+ "--input-gtf-file",
+ dest="input_gtf_file",
+ help="Ordered and processed gtf file for 'pre_bedtools' mode.")
+ parser.add_argument(
+ "--output-bed-file",
+ dest="output_bed_file",
+ help="Bed file with only exons with strandedness"
+ "taken into account for 'pre_bedtools' mode.")
+
+ args = parser.parse_args()
+ return args
+
+
+def post_bedtools_mode(args):
+ """Execute the 'post_bedtools' mode."""
+ LOG.info("Starting 'post_bedtools' mode...")
+
+ fasta_list = exon_concatenation(args.input_fasta_file)
+ final_list = poly_a_addition_to_fasta_list(fasta_list, args.poly_a_length)
+
+ if args.output_file_name is None:
+ args.output_file_name = "default_output.fasta"
+
+ with open(args.output_file_name, "w", encoding="utf-8") as fasta_out:
+ fasta_out.write("\n".join(f"{x[0]}\n{x[1]}" for x in final_list))
+ LOG.info("Transcript sequence extractor finished in 'post_bedtools' mode.")
+
+
+if __name__ == '__main__':
main()
diff --git a/sequence_extractor/exon_concatenation.py b/sequence_extractor/exon_concatenation.py
index 194e693c9603deb0195bc0db2bc80bf257c73ba7..c909878e55e874ee39c7cca9415001639c3bcb73 100644
--- a/sequence_extractor/exon_concatenation.py
+++ b/sequence_extractor/exon_concatenation.py
@@ -1,19 +1,24 @@
-"""Script containing the function to concatenate exons and output the results in a list of tuples."""
+"""Concatenate exons and output the results in a list of tuples."""
def exon_concatenation(
post_bedtools_fasta: str,
) -> list:
- """Concatenate all sequences starting with identical transcripit ID and outputs it as a list with sequence header (Transcript ID) and concatenated sequences as tuples.
+ """Concatenate exons.
+
+ Concatenate all sequences starting with identical transcript ID and
+ output it as a list with sequence header (Transcript ID) and
+ concatenated sequences as tuples.
Args:
- post_bedtools_fasta: The name of the fasta file obtained after bedtools has been run
+ post_bedtools_fasta: The name of the fasta file obtained after
+ bedtools has been run
Returns:
A list containing transcript ID and concatenated exons in tuples.
"""
with open(post_bedtools_fasta, "r", encoding="utf-8") as fasta:
- annotation = []
+ annotation: list = []
fasta_format_list = []
for line1, line2 in zip(fasta, fasta):
if len(annotation) == 0:
diff --git a/sequence_extractor/poly_a.py b/sequence_extractor/poly_a.py
index 73913713a0298e4a292120f7afc7bab41039bddd..f2cdf51a93a2c2910c36d260904fd54503543192 100644
--- a/sequence_extractor/poly_a.py
+++ b/sequence_extractor/poly_a.py
@@ -1,39 +1,47 @@
-"""This script contains two functions and the first function is called by the second function and used to add poly A tail to the concatenated exon."""
-
-
+"""Add poly A tail to the concatenated exon."""
import numpy as np
-# To do: Taking probabilities of nucleotides from user and raising error if sum != 1
+# To do: Taking probabilities of nucleotides from user
+# and raising errorif sum != 1
def poly_a_generator(
exon: str,
+ poly_a_length: int = 250,
) -> str:
- """Adds a PolyA tail to an exon sequence input into the function.
+ """Add a PolyA tail to an exon sequence input into the function.
Args:
- exon: RNA sequence, obtained from concatenation of exons, that needs polyA to be added to its 3' end.
+ exon: RNA sequence, obtained from concatenation of exons,
+ that needs polyA to be added to its 3' end.
Returns:
- RNA with polyA tail added to its 3' end.
+ RNA with polyA tail added to its 3' end.
"""
list_of_nucleotides = ["A", "T", "G", "C"]
poly_a_string = "".join(
- np.random.choice(list_of_nucleotides, 250, p=[0.914, 0.028, 0.025, 0.033])
+ np.random.choice(
+ list_of_nucleotides, poly_a_length, p=[0.914, 0.028, 0.025, 0.033]
+ )
)
return exon + poly_a_string
def poly_a_addition_to_fasta_list(
fasta_list: list,
+ poly_a_length: int = 250,
) -> list:
- """Takes in a list of tuples with annotations and exons and outputs a list where polyA tail has been added to all the exon 3' ends.
+ """Add polyA tail to all the exon 3' ends.
+
+ Takes in a list of tuples with annotations and exons and outputs a list.
Args:
- fasta_list: List contaning tuples of annotations and exons
+ fasta_list: List contaning tuples of annotations and exons
Returns:
- A list like the initial list, this time with polyA tail added onto it.
+ A list like the initial list, this time with polyA tail added onto it.
"""
- mature_rna_list = [(i[0], poly_a_generator(i[1])) for i in fasta_list]
+ mature_rna_list = [
+ (i[0], poly_a_generator(i[1], poly_a_length)) for i in fasta_list
+ ]
return mature_rna_list
diff --git a/sequence_extractor/pre_bedtools.py b/sequence_extractor/pre_bedtools.py
new file mode 100644
index 0000000000000000000000000000000000000000..98142f94b7670576d7efe866dcf9a5ee3a3833d9
--- /dev/null
+++ b/sequence_extractor/pre_bedtools.py
@@ -0,0 +1,47 @@
+"""Prepare gtf file for bedtools.
+
+This script defines a BED from exon annotation in a GTF, to get exon
+coordinates for use in bedtools. It also ensures that the concatenation happens
+in the correct order, regardless of the strandedness of the transcript.
+
+Args:
+ GTF file
+
+Returns:
+ BED file with the format:
+ chr, start, end, transcript_id, score, strand, gene_id
+"""
+import pandas as pd # type: ignore
+from gtfparse import read_gtf # type: ignore
+
+
+def pre_bedtools_mode(args):
+ """Execute the 'pre_bedtools' mode."""
+ gtf = read_gtf(args.input_gtf_file, result_type="pandas")
+ gtf_exons = gtf[gtf["feature"] == "exon"]
+ gtf_exons = gtf_exons[
+ ["seqname", "start", "end",
+ "transcript_id", "score",
+ "strand", "gene_id"]
+ ]
+
+ gtf_df_neg = gtf_exons[gtf_exons["strand"] == "-"]
+ gtf_df_neg = (
+ gtf_df_neg.sort_values(["transcript_id", "start"], ascending=False)
+ .groupby("transcript_id")
+ .head(len(gtf_df_neg.transcript_id))
+ )
+
+ gtf_df_pos = gtf_exons[gtf_exons["strand"] == "+"]
+ gtf_df_pos = (
+ gtf_df_pos.sort_values(["transcript_id", "start"], ascending=True)
+ .groupby("transcript_id")
+ .head(len(gtf_df_pos.transcript_id))
+ )
+
+ if args.output_bed_file is None:
+ args.output_bed_file = "default_output.bed"
+
+ pd.concat([gtf_df_pos, gtf_df_neg]).to_csv(
+ args.output_bed_file, sep="\t", index=False
+ ) # gtf_df_pos and gtf_df_neg must be dataframes
diff --git a/setup.py b/setup.py
index e6b45b580ea92a073bba154ec8ad7365ece02f1c..900b047e7b1602ad39d253eafb94cd85c31eaf69 100644
--- a/setup.py
+++ b/setup.py
@@ -1,22 +1,29 @@
-from setuptools import setup, find_packages
+"""Set up project."""
from pathlib import Path
+from setuptools import setup, find_packages
project_root_dir = Path(__file__).parent.resolve()
+with open(project_root_dir / "requirements.txt",
+ "r", encoding="utf-8") as file:
+ INSTALL_REQUIRES = file.read().splitlines()
-with open(project_root_dir / "requirements.txt", "r", encoding="utf-8") as _file:
- INSTALL_REQUIRES = _file.read().splitlines()
+URL = ('https://git.scicore.unibas.ch/zavolan_group/'
+ 'tools/transcript-sequence-extractor')
setup(
- name='sequence_extractor',
+ name='transcript-sequence-extractor',
+ version='0.1.0',
+ url=URL,
+ license='MIT',
author='Samuel Mondal',
author_email='samuel.mondal@unibas.ch',
- url='https://git.scicore.unibas.ch/zavolan_group/tools/transcript-sequence-extractor',
- license='MIT',
- version='0.0.1',
- description='Extracts transcript sequences from gtf file and adds polyA tail to the output sequence',
+ description=('Extracts transcript sequences from gtf file'
+ 'and adds polyA tail to the output sequence'),
packages=find_packages(),
install_requires=INSTALL_REQUIRES,
- entrypoints={
- 'console_scripts': ['sequence_extractor=sequence_extractor.cli:main']
+ entry_points={
+ 'console_scripts': [
+ 'sequence-extractor=sequence_extractor.cli:main'
+ ]
}
)
diff --git a/tests/test_exon_concatenation.py b/tests/test_exon_concatenation.py
index 01cbd49eeb0c0ee5acd4e07bef6a4a75bd13e7af..9c8c44b77b1a2996548f3cf24ae6b25428e06c57 100644
--- a/tests/test_exon_concatenation.py
+++ b/tests/test_exon_concatenation.py
@@ -1,9 +1,28 @@
-import pytest
-import exon_concatenation from exon_concatenation
+"""Test exon_concatenation.py."""
+from pathlib import Path
+from sequence_extractor.exon_concatenation import exon_concatenation
+
+test_dir = Path(__file__).parent.resolve()
+
+test_fasta_1 = test_dir / "test_files" / "test_1.fa"
+test_fasta_2 = test_dir / "test_files" / "test_2.fa"
-test_fasta_1 = "test_files/test_1.fa"
-test_fasta_2 = "test_files/test_2.fa"
def test_exon_concatenation():
- assert exon_concatenation(test_fasta_1) == expected_list_of_tuples
- assert exon_concatenation(test_fasta_2) == expected
+ """Test exon_concatenation function."""
+ # Test for test_fasta_1
+ expected_fasta_1 = [
+ (">ENST00000673477", "TTTCGCCTGCGCAGTGGTCCTGGCCACCGGCTCGCGGCGCGTGGAGGCTGCTCCCAGCCGCGCCCGAGTCAGACTCGGGTGGGGGTCCCGGTTACGCCAAGGAGGCCCTGAATCTGGCGCAGATGCAGGAGCAGACGCTGCAGTTGGAGCAACAGTCCAAGCTCAAA"),
+ (">ENST00000378391", "AAATACTGACGGACGTGGAAGTGTCGCCCCAGGAAGGCTGCATCACAAAGTCTCCGAAGACCTGGGCAGTGAGAAGTTCTGCGTGGATGCAAATCAGGCGGGGG"),
+ ]
+
+ result_fasta_1 = exon_concatenation(test_fasta_1)
+ assert result_fasta_1 == expected_fasta_1
+
+ # Test for test_fasta_2
+ expected_fasta_2 = [
+ (">ENST00000673477", "ACGGCTGGCACCTTGTTTGGGGAAGGATTCCGTGCCTTTGTGACAGACCGGGACAAAGTGACTGGCTGGGCTGACGCTGCTGGCTGTCGGGGTCTACTCAGCCAAGAATGCGATCAGCCGGCGGCTCCTCAGTCGACCCCAGGACGTGCTGGAGGGTGTTGTGCTTAGT"),
+ ]
+
+ result_fasta_2 = exon_concatenation(test_fasta_2)
+ assert result_fasta_2 == expected_fasta_2
diff --git a/tests/test_files/test.gtf b/tests/test_files/test.gtf
new file mode 100644
index 0000000000000000000000000000000000000000..7342b86ed26a4ce8e0f657faf49c5f7080ecf16f
--- /dev/null
+++ b/tests/test_files/test.gtf
@@ -0,0 +1,144 @@
+seqname source feature start end score strand frame free_text
+1 havana exon 1980 2000 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_0"; exon_number "1"; exon_id "ENSE00001890219"; transcript_support_level "1";
+1 havana exon 1900 1950 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_0"; exon_number "2"; exon_id "ENSE00003507205"; transcript_support_level "1";
+1 havana exon 1800 1850 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_0"; exon_number "3"; exon_id "ENSE00003477500"; transcript_support_level "1";
+1 havana exon 1700 1750 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_0"; exon_number "4"; exon_id "ENSE00003565697"; transcript_support_level "1";
+1 havana exon 1551 1650 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_0"; exon_number "5"; exon_id "ENSE00003475637_4"; transcript_support_level "1";
+1 havana exon 1500 1550 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_0"; exon_number "6"; exon_id "ENSE00003502542"; transcript_support_level "1";
+1 havana exon 1351 1450 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_0"; exon_number "7"; exon_id "ENSE00003553898_6"; transcript_support_level "1";
+1 havana exon 1251 1350 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_0"; exon_number "8"; exon_id "ENSE00003621279_7"; transcript_support_level "1";
+1 havana exon 1200 1250 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_0"; exon_number "9"; exon_id "ENSE00002030414"; transcript_support_level "1";
+1 havana exon 1051 1150 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_0"; exon_number "10"; exon_id "ENSE00001935574_9"; transcript_support_level "1";
+1 havana exon 1000 1050 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_0"; exon_number "11"; exon_id "ENSE00001843071"; transcript_support_level "1";
+1 havana exon 1980 2000 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_1"; exon_number "1"; exon_id "ENSE00001890219"; transcript_support_level "1";
+1 havana exon 1900 1950 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_1"; exon_number "2"; exon_id "ENSE00003507205"; transcript_support_level "1";
+1 havana exon 1800 1850 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_1"; exon_number "3"; exon_id "ENSE00003477500"; transcript_support_level "1";
+1 havana exon 1700 1750 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_1"; exon_number "4"; exon_id "ENSE00003565697"; transcript_support_level "1";
+1 havana exon 1551 1650 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_1"; exon_number "5"; exon_id "ENSE00003475637_4"; transcript_support_level "1";
+1 havana exon 1451 1550 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_1"; exon_number "6"; exon_id "ENSE00003502542_5"; transcript_support_level "1";
+1 havana exon 1400 1450 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_1"; exon_number "7"; exon_id "ENSE00003553898"; transcript_support_level "1";
+1 havana exon 1251 1350 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_1"; exon_number "8"; exon_id "ENSE00003621279_7"; transcript_support_level "1";
+1 havana exon 1151 1250 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_1"; exon_number "9"; exon_id "ENSE00002030414_8"; transcript_support_level "1";
+1 havana exon 1051 1150 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_1"; exon_number "10"; exon_id "ENSE00001935574_9"; transcript_support_level "1";
+1 havana exon 1000 1050 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_1"; exon_number "11"; exon_id "ENSE00001843071"; transcript_support_level "1";
+1 havana exon 1980 2000 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_2"; exon_number "1"; exon_id "ENSE00001890219"; transcript_support_level "1";
+1 havana exon 1900 1950 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_2"; exon_number "2"; exon_id "ENSE00003507205"; transcript_support_level "1";
+1 havana exon 1751 1850 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_2"; exon_number "3"; exon_id "ENSE00003477500_2"; transcript_support_level "1";
+1 havana exon 1700 1750 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_2"; exon_number "4"; exon_id "ENSE00003565697"; transcript_support_level "1";
+1 havana exon 1600 1650 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_2"; exon_number "5"; exon_id "ENSE00003475637"; transcript_support_level "1";
+1 havana exon 1500 1550 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_2"; exon_number "6"; exon_id "ENSE00003502542"; transcript_support_level "1";
+1 havana exon 1400 1450 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_2"; exon_number "7"; exon_id "ENSE00003553898"; transcript_support_level "1";
+1 havana exon 1300 1350 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_2"; exon_number "8"; exon_id "ENSE00003621279"; transcript_support_level "1";
+1 havana exon 1200 1250 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_2"; exon_number "9"; exon_id "ENSE00002030414"; transcript_support_level "1";
+1 havana exon 1051 1150 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_2"; exon_number "10"; exon_id "ENSE00001935574_9"; transcript_support_level "1";
+1 havana exon 1000 1050 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_2"; exon_number "11"; exon_id "ENSE00001843071"; transcript_support_level "1";
+1 havana exon 1980 2000 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_3"; exon_number "1"; exon_id "ENSE00001890219"; transcript_support_level "1";
+1 havana exon 1900 1950 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_3"; exon_number "2"; exon_id "ENSE00003507205"; transcript_support_level "1";
+1 havana exon 1751 1850 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_3"; exon_number "3"; exon_id "ENSE00003477500_2"; transcript_support_level "1";
+1 havana exon 1651 1750 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_3"; exon_number "4"; exon_id "ENSE00003565697_3"; transcript_support_level "1";
+1 havana exon 1551 1650 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_3"; exon_number "5"; exon_id "ENSE00003475637_4"; transcript_support_level "1";
+1 havana exon 1451 1550 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_3"; exon_number "6"; exon_id "ENSE00003502542_5"; transcript_support_level "1";
+1 havana exon 1351 1450 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_3"; exon_number "7"; exon_id "ENSE00003553898_6"; transcript_support_level "1";
+1 havana exon 1251 1350 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_3"; exon_number "8"; exon_id "ENSE00003621279_7"; transcript_support_level "1";
+1 havana exon 1200 1250 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_3"; exon_number "9"; exon_id "ENSE00002030414"; transcript_support_level "1";
+1 havana exon 1051 1150 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_3"; exon_number "10"; exon_id "ENSE00001935574_9"; transcript_support_level "1";
+1 havana exon 1000 1050 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_3"; exon_number "11"; exon_id "ENSE00001843071"; transcript_support_level "1";
+1 havana exon 1980 2000 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_4"; exon_number "1"; exon_id "ENSE00001890219"; transcript_support_level "1";
+1 havana exon 1851 1950 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_4"; exon_number "2"; exon_id "ENSE00003507205_1"; transcript_support_level "1";
+1 havana exon 1800 1850 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_4"; exon_number "3"; exon_id "ENSE00003477500"; transcript_support_level "1";
+1 havana exon 1651 1750 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_4"; exon_number "4"; exon_id "ENSE00003565697_3"; transcript_support_level "1";
+1 havana exon 1600 1650 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_4"; exon_number "5"; exon_id "ENSE00003475637"; transcript_support_level "1";
+1 havana exon 1451 1550 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_4"; exon_number "6"; exon_id "ENSE00003502542_5"; transcript_support_level "1";
+1 havana exon 1351 1450 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_4"; exon_number "7"; exon_id "ENSE00003553898_6"; transcript_support_level "1";
+1 havana exon 1300 1350 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_4"; exon_number "8"; exon_id "ENSE00003621279"; transcript_support_level "1";
+1 havana exon 1151 1250 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_4"; exon_number "9"; exon_id "ENSE00002030414_8"; transcript_support_level "1";
+1 havana exon 1051 1150 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_4"; exon_number "10"; exon_id "ENSE00001935574_9"; transcript_support_level "1";
+1 havana exon 1000 1050 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_4"; exon_number "11"; exon_id "ENSE00001843071"; transcript_support_level "1";
+1 havana exon 1951 2000 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_5"; exon_number "1"; exon_id "ENSE00001890219_0"; transcript_support_level "1";
+1 havana exon 1900 1950 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_5"; exon_number "2"; exon_id "ENSE00003507205"; transcript_support_level "1";
+1 havana exon 1800 1850 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_5"; exon_number "3"; exon_id "ENSE00003477500"; transcript_support_level "1";
+1 havana exon 1651 1750 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_5"; exon_number "4"; exon_id "ENSE00003565697_3"; transcript_support_level "1";
+1 havana exon 1600 1650 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_5"; exon_number "5"; exon_id "ENSE00003475637"; transcript_support_level "1";
+1 havana exon 1451 1550 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_5"; exon_number "6"; exon_id "ENSE00003502542_5"; transcript_support_level "1";
+1 havana exon 1400 1450 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_5"; exon_number "7"; exon_id "ENSE00003553898"; transcript_support_level "1";
+1 havana exon 1300 1350 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_5"; exon_number "8"; exon_id "ENSE00003621279"; transcript_support_level "1";
+1 havana exon 1151 1250 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_5"; exon_number "9"; exon_id "ENSE00002030414_8"; transcript_support_level "1";
+1 havana exon 1051 1150 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_5"; exon_number "10"; exon_id "ENSE00001935574_9"; transcript_support_level "1";
+1 havana exon 1000 1050 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_5"; exon_number "11"; exon_id "ENSE00001843071"; transcript_support_level "1";
+1 havana exon 1951 2000 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_6"; exon_number "1"; exon_id "ENSE00001890219_0"; transcript_support_level "1";
+1 havana exon 1900 1950 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_6"; exon_number "2"; exon_id "ENSE00003507205"; transcript_support_level "1";
+1 havana exon 1751 1850 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_6"; exon_number "3"; exon_id "ENSE00003477500_2"; transcript_support_level "1";
+1 havana exon 1700 1750 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_6"; exon_number "4"; exon_id "ENSE00003565697"; transcript_support_level "1";
+1 havana exon 1551 1650 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_6"; exon_number "5"; exon_id "ENSE00003475637_4"; transcript_support_level "1";
+1 havana exon 1451 1550 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_6"; exon_number "6"; exon_id "ENSE00003502542_5"; transcript_support_level "1";
+1 havana exon 1400 1450 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_6"; exon_number "7"; exon_id "ENSE00003553898"; transcript_support_level "1";
+1 havana exon 1300 1350 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_6"; exon_number "8"; exon_id "ENSE00003621279"; transcript_support_level "1";
+1 havana exon 1200 1250 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_6"; exon_number "9"; exon_id "ENSE00002030414"; transcript_support_level "1";
+1 havana exon 1051 1150 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_6"; exon_number "10"; exon_id "ENSE00001935574_9"; transcript_support_level "1";
+1 havana exon 1000 1050 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_6"; exon_number "11"; exon_id "ENSE00001843071"; transcript_support_level "1";
+1 havana exon 1951 2000 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_7"; exon_number "1"; exon_id "ENSE00001890219_0"; transcript_support_level "1";
+1 havana exon 1851 1950 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_7"; exon_number "2"; exon_id "ENSE00003507205_1"; transcript_support_level "1";
+1 havana exon 1800 1850 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_7"; exon_number "3"; exon_id "ENSE00003477500"; transcript_support_level "1";
+1 havana exon 1700 1750 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_7"; exon_number "4"; exon_id "ENSE00003565697"; transcript_support_level "1";
+1 havana exon 1551 1650 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_7"; exon_number "5"; exon_id "ENSE00003475637_4"; transcript_support_level "1";
+1 havana exon 1451 1550 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_7"; exon_number "6"; exon_id "ENSE00003502542_5"; transcript_support_level "1";
+1 havana exon 1351 1450 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_7"; exon_number "7"; exon_id "ENSE00003553898_6"; transcript_support_level "1";
+1 havana exon 1251 1350 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_7"; exon_number "8"; exon_id "ENSE00003621279_7"; transcript_support_level "1";
+1 havana exon 1200 1250 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_7"; exon_number "9"; exon_id "ENSE00002030414"; transcript_support_level "1";
+1 havana exon 1100 1150 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_7"; exon_number "10"; exon_id "ENSE00001935574"; transcript_support_level "1";
+1 havana exon 1000 1050 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_7"; exon_number "11"; exon_id "ENSE00001843071"; transcript_support_level "1";
+1 havana exon 1951 2000 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_8"; exon_number "1"; exon_id "ENSE00001890219_0"; transcript_support_level "1";
+1 havana exon 1851 1950 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_8"; exon_number "2"; exon_id "ENSE00003507205_1"; transcript_support_level "1";
+1 havana exon 1800 1850 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_8"; exon_number "3"; exon_id "ENSE00003477500"; transcript_support_level "1";
+1 havana exon 1700 1750 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_8"; exon_number "4"; exon_id "ENSE00003565697"; transcript_support_level "1";
+1 havana exon 1551 1650 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_8"; exon_number "5"; exon_id "ENSE00003475637_4"; transcript_support_level "1";
+1 havana exon 1451 1550 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_8"; exon_number "6"; exon_id "ENSE00003502542_5"; transcript_support_level "1";
+1 havana exon 1351 1450 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_8"; exon_number "7"; exon_id "ENSE00003553898_6"; transcript_support_level "1";
+1 havana exon 1251 1350 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_8"; exon_number "8"; exon_id "ENSE00003621279_7"; transcript_support_level "1";
+1 havana exon 1151 1250 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_8"; exon_number "9"; exon_id "ENSE00002030414_8"; transcript_support_level "1";
+1 havana exon 1051 1150 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_8"; exon_number "10"; exon_id "ENSE00001935574_9"; transcript_support_level "1";
+1 havana exon 1000 1050 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_8"; exon_number "11"; exon_id "ENSE00001843071"; transcript_support_level "1";
+1 havana exon 1951 2000 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_9"; exon_number "1"; exon_id "ENSE00001890219_0"; transcript_support_level "1";
+1 havana exon 1851 1950 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_9"; exon_number "2"; exon_id "ENSE00003507205_1"; transcript_support_level "1";
+1 havana exon 1751 1850 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_9"; exon_number "3"; exon_id "ENSE00003477500_2"; transcript_support_level "1";
+1 havana exon 1651 1750 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_9"; exon_number "4"; exon_id "ENSE00003565697_3"; transcript_support_level "1";
+1 havana exon 1600 1650 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_9"; exon_number "5"; exon_id "ENSE00003475637"; transcript_support_level "1";
+1 havana exon 1500 1550 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_9"; exon_number "6"; exon_id "ENSE00003502542"; transcript_support_level "1";
+1 havana exon 1351 1450 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_9"; exon_number "7"; exon_id "ENSE00003553898_6"; transcript_support_level "1";
+1 havana exon 1251 1350 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_9"; exon_number "8"; exon_id "ENSE00003621279_7"; transcript_support_level "1";
+1 havana exon 1151 1250 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_9"; exon_number "9"; exon_id "ENSE00002030414_8"; transcript_support_level "1";
+1 havana exon 1100 1150 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_9"; exon_number "10"; exon_id "ENSE00001935574"; transcript_support_level "1";
+1 havana exon 1000 1050 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_9"; exon_number "11"; exon_id "ENSE00001843071"; transcript_support_level "1";
+1 havana exon 1951 2000 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_10"; exon_number "1"; exon_id "ENSE00001890219_0"; transcript_support_level "1";
+1 havana exon 1851 1950 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_10"; exon_number "2"; exon_id "ENSE00003507205_1"; transcript_support_level "1";
+1 havana exon 1751 1850 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_10"; exon_number "3"; exon_id "ENSE00003477500_2"; transcript_support_level "1";
+1 havana exon 1651 1750 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_10"; exon_number "4"; exon_id "ENSE00003565697_3"; transcript_support_level "1";
+1 havana exon 1600 1650 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_10"; exon_number "5"; exon_id "ENSE00003475637"; transcript_support_level "1";
+1 havana exon 1451 1550 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_10"; exon_number "6"; exon_id "ENSE00003502542_5"; transcript_support_level "1";
+1 havana exon 1351 1450 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_10"; exon_number "7"; exon_id "ENSE00003553898_6"; transcript_support_level "1";
+1 havana exon 1251 1350 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_10"; exon_number "8"; exon_id "ENSE00003621279_7"; transcript_support_level "1";
+1 havana exon 1151 1250 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_10"; exon_number "9"; exon_id "ENSE00002030414_8"; transcript_support_level "1";
+1 havana exon 1051 1150 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_10"; exon_number "10"; exon_id "ENSE00001935574_9"; transcript_support_level "1";
+1 havana exon 1000 1050 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_10"; exon_number "11"; exon_id "ENSE00001843071"; transcript_support_level "1";
+1 havana exon 1951 2000 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_11"; exon_number "1"; exon_id "ENSE00001890219_0"; transcript_support_level "1";
+1 havana exon 1851 1950 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_11"; exon_number "2"; exon_id "ENSE00003507205_1"; transcript_support_level "1";
+1 havana exon 1751 1850 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_11"; exon_number "3"; exon_id "ENSE00003477500_2"; transcript_support_level "1";
+1 havana exon 1651 1750 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_11"; exon_number "4"; exon_id "ENSE00003565697_3"; transcript_support_level "1";
+1 havana exon 1551 1650 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_11"; exon_number "5"; exon_id "ENSE00003475637_4"; transcript_support_level "1";
+1 havana exon 1500 1550 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_11"; exon_number "6"; exon_id "ENSE00003502542"; transcript_support_level "1";
+1 havana exon 1351 1450 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_11"; exon_number "7"; exon_id "ENSE00003553898_6"; transcript_support_level "1";
+1 havana exon 1251 1350 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_11"; exon_number "8"; exon_id "ENSE00003621279_7"; transcript_support_level "1";
+1 havana exon 1151 1250 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_11"; exon_number "9"; exon_id "ENSE00002030414_8"; transcript_support_level "1";
+1 havana exon 1100 1150 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_11"; exon_number "10"; exon_id "ENSE00001935574"; transcript_support_level "1";
+1 havana exon 1000 1050 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_11"; exon_number "11"; exon_id "ENSE00001843071"; transcript_support_level "1";
+1 havana exon 1951 2000 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_12"; exon_number "1"; exon_id "ENSE00001890219_0"; transcript_support_level "1";
+1 havana exon 1851 1950 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_12"; exon_number "2"; exon_id "ENSE00003507205_1"; transcript_support_level "1";
+1 havana exon 1751 1850 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_12"; exon_number "3"; exon_id "ENSE00003477500_2"; transcript_support_level "1";
+1 havana exon 1651 1750 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_12"; exon_number "4"; exon_id "ENSE00003565697_3"; transcript_support_level "1";
+1 havana exon 1551 1650 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_12"; exon_number "5"; exon_id "ENSE00003475637_4"; transcript_support_level "1";
+1 havana exon 1451 1550 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_12"; exon_number "6"; exon_id "ENSE00003502542_5"; transcript_support_level "1";
+1 havana exon 1351 1450 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_12"; exon_number "7"; exon_id "ENSE00003553898_6"; transcript_support_level "1";
+1 havana exon 1251 1350 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_12"; exon_number "8"; exon_id "ENSE00003621279_7"; transcript_support_level "1";
+1 havana exon 1151 1250 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_12"; exon_number "9"; exon_id "ENSE00002030414_8"; transcript_support_level "1";
+1 havana exon 1100 1150 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_12"; exon_number "10"; exon_id "ENSE00001935574"; transcript_support_level "1";
+1 havana exon 1000 1050 . - . gene_id "GENE2"; transcript_id "TRANSCRIPT2_12"; exon_number "11"; exon_id "ENSE00001843071"; transcript_support_level "1";
diff --git a/tests/test_files/test_1.fa b/tests/test_files/test_1.fa
index f92bb2b84f79e445dcda17c45ae0e6f34aa64c82..e8a3b1eb26ed5ca5cc9a0ea92272b03c04c9aac9 100644
--- a/tests/test_files/test_1.fa
+++ b/tests/test_files/test_1.fa
@@ -1,8 +1,8 @@
>ENST00000673477::1:1471765-1472089
-TTTCGCCTGCGCAGTGGTCCTGGCCACCGGCTCGCGGCGCGTGGAGGCTGCTCCCAGCCGCGCCCGAGTCAGACTCGGGTGGGGGTCCCGGCGGCGGTAGCGGCGGCGGCGGTGCGAGCATGTCGTGGCTCTTCGGCGTTAACAAGGGCCCCAAGGGTGAAGGCGCGGGGCCGCCGCCGCCTTTGCCGCCCGCGCAGCCCGGGGCCGAGGGCGGCGGGGACCGCGGTTTGGGAGACCGGCCGGCGCCCAAGGACAAATGGAGCAACTTCGACCCCACCGGCCTGGAGCGCGCCGCCAAGGCGGCGCGCGAGCTGGAGCACTCGC
+TTTCGCCTGCGCAGTGGTCCTGGCCACCGGCTCGCGGCGCGTGGAGGCTGCTCCCAGCCGCGCCCGAGTCAGACTCGGGTGGGGGTCCCGG
>ENST00000673477::1:1477274-1477350
TTACGCCAAGGAGGCCCTGAATCTGGCGCAGATGCAGGAGCAGACGCTGCAGTTGGAGCAACAGTCCAAGCTCAAA
>ENST00000378391::1:3244087-3244137
AAATACTGACGGACGTGGAAGTGTCGCCCCAGGAAGGCTGCATCACAAAG
>ENST00000378391::1:3385152-3385286
-TCTCCGAAGACCTGGGCAGTGAGAAGTTCTGCGTGGATGCAAATCAGGCGGGGGCTGGCAGCTGGCTCAAGTACATCCGTGTGGCGTGCTCCTGCGATGACCAGAACCTCACCATGTGTCAGATCAGTGAGCAG
+TCTCCGAAGACCTGGGCAGTGAGAAGTTCTGCGTGGATGCAAATCAGGCGGGGG
diff --git a/tests/test_files/test_2.fa b/tests/test_files/test_2.fa
index 7b8ebb26c52072dc4431535d5a0eae56fee268ee..6acd1f1bf50641b3eb5bddc4ce164edaae77ca05 100644
--- a/tests/test_files/test_2.fa
+++ b/tests/test_files/test_2.fa
@@ -1,7 +1,7 @@
>ENST00000673477::1:1482545-1482614
-ACGGCTGGCACCTTGTTTGGGGAAGGATTCCGTGCCTTTGTGACAGACCGGGACAAAGTGACAGCCACG
+ACGGCTGGCACCTTGTTTGGGGAAGGATTCCGTGCCTTTGTGACAGACCGGGACAAAGTGAC
>ENST00000673477::1:1485016-1485171
-TGGCTGGGCTGACGCTGCTGGCTGTCGGGGTCTACTCAGCCAAGAATGCGACAGCCGTCACTGGCCGCTTCATCGAGGCTCGGCTGGGGAAGCCGTCCCTAGTGAGGGAGACGTCCCGCATCACGGTGCTGGAGGCGCTGCGGCACCCCATCCAG
+TGGCTGGGCTGACGCTGCTGGCTGTCGGGGTCTACTCAGCCAAGAATGCGA
>ENST00000673477::1:1485782-1485838
TCAGCCGGCGGCTCCTCAGTCGACCCCAGGACGTGCTGGAGGGTGTTGTGCTTAGT
>ENST00000673477::1:1486110-1486235
diff --git a/tests/test_poly_a.py b/tests/test_poly_a.py
index 91f90c19937d45778c56b8b3fdeafecd31fe9ea5..c22e83322afaa3b551d1aa0e10512b0d81622211 100644
--- a/tests/test_poly_a.py
+++ b/tests/test_poly_a.py
@@ -1,12 +1,26 @@
-import pytest
-from poly_a import poly_a_generator, poly_a_addition_to_fasta_list
-
+"""Test poly_a.py script."""
+import numpy as np
+from sequence_extractor.poly_a import (
+ poly_a_generator, poly_a_addition_to_fasta_list
+)
def test_poly_a_generator():
- assert poly_a_generator(exon_string) == exon_and_polya
+ """Test poly_a_generator function."""
+ exon_string = 'ACGGCTGGCACCTTGTTTGGGGAAGGATTCCGTGCCTTTG'
+ poly_a_length = np.random.randint(100, 250)
+ test_string = poly_a_generator(exon_string, poly_a_length)
+
+ assert len(test_string) == sum([len(exon_string), poly_a_length])
def test_poly_a_addition_to_fasta_list():
- assert poly_a_addition_to_fasta_list(list_of_tuples) == manipulated_list_of_tuples
+ """Test poly_a_addition_to_fasta_list function."""
+ exon_list = [('>ENST00000673477', 'ACGGCTGGCACCTTGTTTGGGGAAG'),
+ ('>ENST00000378391', 'AAATACTGACGGACGTGG')]
+ poly_a_length = np.random.randint(100, 250)
+ test_list = poly_a_addition_to_fasta_list(exon_list, poly_a_length)
+
+ assert len(test_list[0][1]) == sum([len(exon_list[0][1]), poly_a_length])
+ assert len(test_list[1][1]) == sum([len(exon_list[1][1]), poly_a_length])