diff --git a/.gitignore b/.gitignore
index 5cbcf089038bd06f821a4b73ce759865a540d5bb..767b8027a746e5a425b110f06756efdd492f8338 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,5 +1,7 @@
.ipynb*
+Untitled.ipynb
+
# Byte-compiled / optimized / DLL files
__pycache__/
*.py[cod]
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 09a567743e7adf10b6145e15feb7de0d343e5031..397b934540596614faec566083079aa6e9f17cd9 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -4,7 +4,8 @@ default:
image: python:3.10-slim-buster
my_tests:
- # Good to put a small description here of what this job does
+ # run tests
script:
- - echo "Command 1"
- - echo "Command 2"
+ - pip install .
+ - pip install -r requirements-dev.txt
+ - pytest
\ No newline at end of file
diff --git a/Dockerfile b/Dockerfile
new file mode 100644
index 0000000000000000000000000000000000000000..1e8f2cb74c9fa1b47400f268a13cb53ebf244fda
--- /dev/null
+++ b/Dockerfile
@@ -0,0 +1,46 @@
+FROM python:3.11.1-slim-bullseye
+
+# set maintainer
+MAINTAINER zavolab-biozentrum@unibas.ch
+
+# set names for user, group and user home
+ARG USER="bioc"
+ARG GROUP="bioc"
+ARG WORKDIR="/home/${USER}"
+
+# create user, group, user home & makes the user and group
+# the owner of the user home
+RUN mkdir -p $WORKDIR \
+ && groupadd -r $GROUP \
+ && useradd --no-log-init -r -g $GROUP $USER \
+ && chown -R ${USER}:${GROUP} $WORKDIR \
+ && chmod 700 $WORKDIR
+
+# set the user, make sure the location where pip
+# installs binaries/executables is part of the $PATH
+# and set the working directory to the user's home
+USER $USER
+ENV PATH="${WORKDIR}/.local/bin:${PATH}"
+WORKDIR $WORKDIR
+
+# copy entire content of the current directory to the
+# working directory; ensure that this does not contain any
+# files that you don't want to have end up in the Docker
+# image, especially not any secrets!
+# use `.dockerignore` to set files that you do NOT want
+# Docker to copy
+COPY --chown=${USER}:${GROUP} . $WORKDIR
+
+# install app and development dependencies
+# assumes that dependencies in `requirements.txt` are
+# automatically installed when installing the app; if
+# that is not the case, they need to be installed
+# _before_ installing the app
+RUN pip install -e . \
+ && pip install --no-cache-dir -r requirements-dev.txt
+
+# set default command; optional
+CMD ["bash exampleInput.sh"]
+
+
+
diff --git a/README.md b/README.md
index 1a489873685e74c3d4a69594b442075c2f4e8086..19582f0bd06cde7466ca4802ddf6740d798816ac 100644
--- a/README.md
+++ b/README.md
@@ -1,9 +1,33 @@
# cDNA Generator module
+Generate cDNA based on mRNA transcript sequences and the coresponding priming probabilities.
-Description of the module:
-The function of this module is to generate cdDNA based on mRNA transcript seuqences and the coresponding priming probabilities.
+## Example usage
+A simple example can be run from the test_files directory:
+ python ../cdna/cli.py -ifa yeast_example.fa -icpn copy_number_input.csv -igt Example_GTF_Input.GTF -ofa cDNA.fasta -ocsv cDNA.csv
+## Installation
+
+ pip install .
+
+## Docker
+A docker image is available, to fetch this image:
+
+ docker pull ericdb/my-image
+
+To run a simple example using this image:
+
+ docker run my-image python cdna/cli.py -ifa test_files/yeast_example.fa -icpn test_files/copy_number_input.csv -igt test_files/Example_GTF_Input.GTF -ofa test_files/cDNA.fasta -ocsv test_files/cDNA.csv
+
+## License
+
+[MIT](https://choosealicense.com/licenses/mit/) license, Copyright (c) 2022 Zavolan Lab, Biozentrum, University of Basel
+
+
+## Contributers
+Eric Boittier, Bastian Wagner, Quentin Badolle
+
+## More info:
**Input files**
@@ -17,7 +41,7 @@ transcript_copies (csv-formatted) containing:
transcript_sequences (fasta-formatted) containing:
- ID of transcript
-
+- transcript-sequence
priming_sites (gtf-formatted) containing:
diff --git a/cdna/cdna.py b/cdna/cdna.py
index c4b1ae3fd7eaa756e3b3b2cff40e5407f17081f3..d8acd5f05c684854327b61db125edc9b168c3d9a 100644
--- a/cdna/cdna.py
+++ b/cdna/cdna.py
@@ -1,94 +1,235 @@
-import sys
+import warnings
+import pandas as pd
+from Bio import SeqIO
+from Bio.Seq import Seq
+from Bio.SeqRecord import SeqRecord
+from gtfparse import read_gtf
-def translate(res):
- translate_dict = {"A": "T", "U": "A", "G": "C", "C": "G"}
+# ignore warnings from read_gtf
+warnings.filterwarnings(action="ignore", category=FutureWarning)
+
+
+def complement(res: str) -> str:
+ """
+ Returns the cDNA complement of a given base pair
+ Args:
+ res: residue code.
+
+ Returns: corresponding cDNA residue.
+ Raises: Value error
+
+ """
+ translate_dict = {"A": "T", "T": "A", "U": "A", "G": "C", "C": "G"}
if res not in translate_dict.keys():
- print("cDNA residue not A,T,U or G ")
- sys.exit(1)
+ print(f"Unknown character, {res}")
+ raise ValueError
return translate_dict[res]
-class cDNA_Gen:
- def __init__(
- self, fasta, gtf, cpn, output_fasta="cDNA.fasta", output_csv="cDNA.csv"
- ):
+def seq_complement(sequence: str) -> str or None:
+ """
+ Returns the corresponding cDNA sequence by finding the complementary
+ base pairs and returning the reversed sequence.
+
+ Args:
+ sequence: sequence to be converted into cDNA.
+
+ Returns: corresponding cDNA sequence.
+
+ """
+ if sequence is None:
+ return None
+ _ = "".join([complement(char) for char in str(sequence)])[::-1] # reverse string
+ return _
+
+
+class CDNAGen:
+ """
+ Module that performs the cDNA synthesis.
+ """
+
+ def __init__(self, ifasta: str, igtf: str, icpn: str, ofasta: str, ocsv: str):
# inputs
- self.fasta = fasta
- self.gtf = gtf
- self.cpn = cpn
- self.output_fasta = output_fasta
- self.output_csv = output_csv
- # variables
- self.prime_sites = []
- self.fasta_seq = ""
- self.fasta_id = ""
- self.copy_numbers = {}
+ self.fasta = ifasta
+ self.gtf = igtf
+ self.cpn = icpn
+ self.output_fasta = ofasta
+ self.output_csv = ocsv
+ # variables
+ self.csv_df = None
+ self.fasta_dict = None
+ self.fasta_records = None
+ self.gtf_df = None
self.run()
- def run(self):
+ def run(self) -> None:
+ """
+ Executes the cDNA workflow.
+ Returns: None
+
+ """
+ self.read_csv()
self.read_fasta()
self.read_gtf()
-
- def order_priming_sites(self):
- pass
-
- def generate_cdna(self):
- pass
-
- def read_fasta(self):
- fasta = open(self.fasta).readlines()
- self.fasta_id = fasta[0]
- print(fasta[0])
- self.fasta_seq = "".join([_.rstrip() for _ in fasta[1:]])
-
- def read_gtf(self):
- with open(self.gtf) as gtf_file:
- gtf_lines = gtf_file.readlines()
- for line in gtf_lines[:1000]:
- if not line.startswith("#"):
- temp_gtf = GTF_entry(line)
- temp_gtf.set_sequence(self.fasta_seq)
- self.prime_sites.append(temp_gtf)
-
- def write_fasta(self):
- pass
-
- def read_copy_numbers(self):
- with open(self.cpn) as cpn_file:
- cpn_lines = cpn_file.readlines()
- for line in cpn_lines:
- csv = line.split(",")
- trans_id = csv[0]
- if trans_id:
- gene_id = csv[1]
- count = csv[2]
- self.copy_numbers[gene_id] = count
-
- def return_output(self):
- return self.output_fasta, self.output_csv
-
-
-class GTF_entry:
- def __init__(self, string):
- self.string = string
- self.values = self.string.split("\t")
- self.id = self.values[0]
- self.start = int(self.values[3])
- self.end = int(self.values[4])
- self.score = float(0.5) # self.values[5]
- self.sequence = "no sequence set"
- self.length = self.end - self.start
-
- def __repr__(self):
- return self.sequence[:10] + "..." + f" len={self.length} score={self.score}"
-
- def set_sequence(self, full_sequence):
- self.sequence = full_sequence[self.start : self.end]
-
-
-if __name__ == "__main__":
- import argparse
-
- pass
+ self.add_sequences()
+ self.add_complement()
+ self.add_records()
+ self.write_fasta()
+ self.write_csv()
+
+ def add_records(self) -> None:
+ """Adds data records to fasta file.
+
+ Adds the copy number information to the fasta records.
+
+ Returns: None
+
+ """
+ self.fasta_records = []
+ for index, row in self.gtf_df.iterrows():
+ if row["complement"] is not None:
+ copy_number = row["Transcript_Copy_Number"]
+ for _ in range(int(copy_number)):
+ record = SeqRecord(
+ Seq(row["complement"]),
+ row["cdna_ID"],
+ f"Transcript copy number: {copy_number}",
+ "",
+ )
+ self.fasta_records.append(record)
+
+ def add_sequences(self) -> None:
+ """
+ Adds the sequence for a given priming site.
+ Returns: None
+
+ """
+ self.gtf_df["priming_site"] = self.gtf_df.apply(
+ lambda row: self.read_primingsite(row["seqname"], row["start"]),
+ axis=1,
+ )
+
+ def add_complement(self) -> None:
+ """
+ Adds the complementary cDNA sequence.
+ Returns: None
+
+ """
+ self.gtf_df["complement"] = self.gtf_df["priming_site"].apply(
+ lambda x: seq_complement(x)
+ )
+
+ def read_primingsite(self, sequence: str, end: int) -> None:
+ """Read a fasta file from a given start character
+
+ Reads a fasta sequence with ID (sequence) and returns the
+ sequence starting from the index start.
+
+ Args:
+ sequence: sequence ID to be read.
+ end: end index of the priming site.
+
+ Returns: None
+
+ """
+ if sequence not in self.fasta_dict.keys():
+ return None
+ return self.fasta_dict[sequence].seq[:end]
+
+ def read_fasta(self) -> None:
+ """Read a given fasta file.
+
+ Wrapper for SeqIO.parse.
+
+ Returns: None
+
+ """
+ record = SeqIO.parse(self.fasta, "fasta")
+ records = list(record)
+ self.fasta_dict = {x.name: x for x in records}
+
+ def read_csv(self) -> None:
+ """Reads a given copy number csv file
+
+ Wrapper for Pandas read_csv.
+
+ Returns: None
+
+ """
+ df_csv = pd.read_csv(self.cpn, index_col=False)
+ df_csv = df_csv.reset_index() # make sure indexes pair with number of rows
+ self.csv_df = df_csv
+
+ def read_gtf(self) -> None:
+ """Read and process the GTF file.
+
+ Reads a GTF file and determines copy numbers from normalized probabilities.
+
+ Returns: None
+
+ """
+ # returns GTF with essential columns such as "feature", "seqname", "start", "end"
+ # alongside the names of any optional keys which appeared in the attribute column
+ gtf_df = read_gtf(self.gtf)
+ gtf_df["Binding_Probability"] = pd.to_numeric(
+ gtf_df["Binding_Probability"]
+ ) # convert to numeric
+ df_normalization_bind_probablility = gtf_df.groupby("seqname")[
+ "Binding_Probability"
+ ].sum() # extract binding probability
+ count = 0
+ prev_id = None
+ # Adds Normalized_Binding_Probability and Transcript_Copy_Number
+ # to each transcript in the dataframe
+ for index, row in gtf_df.iterrows():
+ # GTF transcript ID
+ id_ = str(row["seqname"])
+ if id_ == prev_id:
+ count += 1
+ else:
+ count = 0 # reset count
+ # CVS transcript ID
+ id_csv = str(row["seqname"]).split("_")[1]
+ # Calculate Normalized_Binding_Probability and add to GTF dataframe
+ gtf_df.loc[index, "Normalized_Binding_Probability"] = (
+ row["Binding_Probability"] / df_normalization_bind_probablility[id_]
+ )
+ # Calculate Normalized_Binding_Probability and add to GTF dataframe
+ csv_transcript_copy_number = self.csv_df.loc[
+ self.csv_df["ID of transcript"] == int(id_csv),
+ "Transcript copy number",
+ ].iloc[0] # pop the first value in the frame
+ gtf_df.loc[index, "Transcript_Copy_Number"] = round(
+ csv_transcript_copy_number
+ * gtf_df.loc[index, "Normalized_Binding_Probability"]
+ )
+ gtf_df.loc[index, "cdna_ID"] = f"{id_}_{count}"
+ prev_id = id_
+
+ self.gtf_df = gtf_df
+
+ def write_fasta(self) -> None:
+ """Writes cDNA fasta records to file.
+
+ Wrapper for SeqIO.write.
+
+ Returns: None
+
+ """
+ SeqIO.write(self.fasta_records, self.output_fasta, "fasta")
+ print(f"Fasta file successfully written to: {self.output_fasta}")
+
+ def write_csv(self) -> None:
+ """Writes the copy number information to a csv file.
+
+ Wrapper for Pandas to_csv.
+
+ Returns: None
+
+ """
+ self.gtf_df[["cdna_ID", "Transcript_Copy_Number"]].to_csv(
+ self.output_csv, index=False
+ )
+ print(f"Copy number csv file successfully written to: {self.output_csv}")
diff --git a/cdna/cli.py b/cdna/cli.py
index 8a623693ef8b7df6bfea53c8825d65639ba81a6a..86f1babf669c3aeadb136922d036ca442eeef8a1 100644
--- a/cdna/cli.py
+++ b/cdna/cli.py
@@ -1 +1,58 @@
-import cdna
+import argparse
+import logging
+
+from cdna import CDNAGen
+
+
+def cdna_parser() -> None:
+ """Parser for cDNA generator
+
+ Parses command line arguments for cDNA generation.
+
+ Returns: None
+
+ """
+ parser = argparse.ArgumentParser(
+ prog="cDNA generator",
+ description="Generate cDNA sequences based on primer probabilities.",
+ )
+ parser.add_argument(
+ "-ifa", "--input_fasta", help="genome fasta file", required=True
+ )
+ parser.add_argument("-igtf", "--input_gtf", help="gtf file", required=True)
+ parser.add_argument(
+ "-ofa", "--output_fasta", help="output fasta file", required=True
+ )
+ parser.add_argument(
+ "-icpn",
+ "--input_copy_number",
+ help="input copy number (csv) file",
+ required=True,
+ )
+ parser.add_argument(
+ "-ocsv", "--output_csv", help="output fasta file", required=True
+ )
+ args = parser.parse_args()
+ # Print parser arguments
+ print(" \n".join(f"{k}={v}" for k, v in vars(args).items()))
+ print()
+ cdna_inst = CDNAGen(
+ ifasta=args.input_fasta,
+ igtf=args.input_gtf,
+ icpn=args.input_copy_number,
+ ocsv=args.output_csv,
+ ofasta=args.output_fasta,
+ )
+ return cdna_inst
+
+
+if __name__ == "__main__":
+ logging.basicConfig(
+ format='[%(asctime)s: %(levelname)s] %(message)s (module "%(module)s")',
+ level=logging.INFO,
+ )
+ LOG = logging.getLogger(__name__)
+ print("**********************")
+ print("Running cDNA generator")
+ print("**********************")
+ cdna_parser()
diff --git a/exampleInput.sh b/exampleInput.sh
new file mode 100644
index 0000000000000000000000000000000000000000..547236c18a023c23a7d9fb68a80ce9c3f847f921
--- /dev/null
+++ b/exampleInput.sh
@@ -0,0 +1,4 @@
+python cdna/cli.py -ifa test_files/yeast_example.fa \
+ -icpn test_files/copy_number_input.csv \
+ -igt test_files/Example_GTF_Input.GTF \
+ -ofa test_files/cDNA.fasta -ocsv test_files/cDNA.csv
\ No newline at end of file
diff --git a/requirements_dev.txt b/requirements-dev.txt
similarity index 62%
rename from requirements_dev.txt
rename to requirements-dev.txt
index 074eda1a7a8500264266efe852248e12a7161c8a..a511aad9d7b7d9ab2e6d885ba48915c49d907b28 100644
--- a/requirements_dev.txt
+++ b/requirements-dev.txt
@@ -1,3 +1,6 @@
+gtfparse
+biopython
+pytest
black
flake8
flake8-docstrings
diff --git a/requirements.txt b/requirements.txt
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..d9abb6b59de6846eaa50eaefc737f65f3b674c31 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -0,0 +1,3 @@
+gtfparse
+biopython
+pandas
diff --git a/setup.py b/setup.py
index 96ecc09a8223aebbcef30db4096998562b1f0976..73e2bfd1cb029c83a18f4d43ff8309ff8d1ff6eb 100644
--- a/setup.py
+++ b/setup.py
@@ -1,5 +1,8 @@
from setuptools import setup, find_packages
+with open('requirements.txt') as f:
+ required = f.read().splitlines()
+
setup(
name='cdna',
url='https://gitlab.com/my_user_name/my_package.git',
@@ -9,5 +12,5 @@ setup(
license='MIT',
version='1.0.0',
packages=find_packages(), # this will autodetect Python packages from the directory tree, e.g., in `code/`
- install_requires=[], # add here packages that are required for your package to run, including version or range of versions
+ install_requires=required, # add here packages that are required for your package to run, including version or range of versions
)
diff --git a/test_files/priming_sites.gtf b/test_files/Example_GTF_Input.GTF
similarity index 50%
rename from test_files/priming_sites.gtf
rename to test_files/Example_GTF_Input.GTF
index df3aafd0f3266cd3f912c116a10821d36a371e8e..3b7a10689330b4b92b02f423c329a79c83b06c37 100644
--- a/test_files/priming_sites.gtf
+++ b/test_files/Example_GTF_Input.GTF
@@ -1,3 +1,6 @@
Transcript_1 RIBlast Priming_site 10 25 . + . Accessibility_Energy "1.49"; Hybridization_Energy "-9.76"; Interaction_Energy "-8.74"; Number_of_binding_sites "2"; Binding_Probability "0.12"
Transcript_1 RIBlast Priming_site 640 655 . + . Accessibility_Energy "1.71"; Hybridization_Energy "-9.12"; Interaction_Energy "-8.34"; Number_of_binding_sites "2"; Binding_Probability "0.05"
Transcript_2 RIBlast Priming_site 3 18 . + . Accessibility_Energy "1.21"; Hybridization_Energy "-5.12"; Interaction_Energy "-2.34"; Number_of_binding_sites "1"; Binding_Probability "0.15"
+Transcript_3 RIBlast Priming_site 5 35 . + . Accessibility_Energy "1.21"; Hybridization_Energy "-5.12"; Interaction_Energy "-2.34"; Number_of_binding_sites "1"; Binding_Probability "0.25"
+Transcript_4 RIBlast Priming_site 5 35 . + . Accessibility_Energy "1.21"; Hybridization_Energy "-5.12"; Interaction_Energy "-2.34"; Number_of_binding_sites "1"; Binding_Probability "0.15"
+Transcript_5 RIBlast Priming_site 5 35 . + . Accessibility_Energy "1.21"; Hybridization_Energy "-5.12"; Interaction_Energy "-2.34"; Number_of_binding_sites "1"; Binding_Probability "0.15"
\ No newline at end of file
diff --git a/test_files/cDNA.csv b/test_files/cDNA.csv
new file mode 100644
index 0000000000000000000000000000000000000000..d88da423c611025b828e53eb4de0409f8f7d4cbe
--- /dev/null
+++ b/test_files/cDNA.csv
@@ -0,0 +1,7 @@
+cdna_ID,Transcript_Copy_Number
+Transcript_1_0,8.0
+Transcript_1_1,4.0
+Transcript_2_0,11.0
+Transcript_3_0,33.0
+Transcript_4_0,11.0
+Transcript_5_0,55.0
diff --git a/test_files/cDNA.fasta b/test_files/cDNA.fasta
new file mode 100644
index 0000000000000000000000000000000000000000..2a8d9b5f817d8e06453d71fa464237be6c77d1bf
--- /dev/null
+++ b/test_files/cDNA.fasta
@@ -0,0 +1,86 @@
+>Transcript_1_0
+AAAAAAAAAA
+>Transcript_1_0
+AAAAAAAAAA
+>Transcript_1_0
+AAAAAAAAAA
+>Transcript_1_0
+AAAAAAAAAA
+>Transcript_1_0
+AAAAAAAAAA
+>Transcript_1_0
+AAAAAAAAAA
+>Transcript_1_0
+AAAAAAAAAA
+>Transcript_1_0
+AAAAAAAAAA
+>Transcript_1_1
+ACATATGTGTGGATGATATAAGATTTGTCCCAAGGACGCTTCTCGAATAGTTCTTTTGTC
+CCTAGATATTTCCTTCTCTAATTTCTTCTGTCTCTCCAAAACATCTTGTTCATTTTTGGG
+TGGTGGCAGCATTTGTTCTTTATGTAGGAAAGCCTTTGTAGCACGGTTTACAATTTTTAC
+TGCACAAACCTCATTAGTGTAACGATGTTTTGCCAGCTTCACTTTACCCATAGAACCTGC
+ACCAACTGTTTCAACAAACTCCCAATCTCCTAACGATTTTCGATGAAACTGCTTAGGCAT
+GCCCTGAGAAGACGAAACTCGACTCTGGCTGGTAGTATTTGGCTTTGGTGCATTCTCTCT
+CGATTTACCTTCAAGTTCTACTTGTCTCTCCTTTTGCTCTGCTTGATGTGAGTTACCATT
+ATTGGCGTATTTGATATCCGCCGGGGGCATTAGCGGTGTGTTCTGCTGCTGCTGCTGCTG
+TGGACTTTTTCCCATCATTCTCAGCGTAGCGGGCGCCATAGTGCTTGGTTGTGTATGCAT
+GCTGTTGCTTTCACTATTGCCATCATCCTGCTGGTTACCTCTGCCCATTGAGAAGGCAGT
+ATTTACGTGATAATCATCCATAAAAAAAAAAAAAAAAAAA
+>Transcript_1_1
+ACATATGTGTGGATGATATAAGATTTGTCCCAAGGACGCTTCTCGAATAGTTCTTTTGTC
+CCTAGATATTTCCTTCTCTAATTTCTTCTGTCTCTCCAAAACATCTTGTTCATTTTTGGG
+TGGTGGCAGCATTTGTTCTTTATGTAGGAAAGCCTTTGTAGCACGGTTTACAATTTTTAC
+TGCACAAACCTCATTAGTGTAACGATGTTTTGCCAGCTTCACTTTACCCATAGAACCTGC
+ACCAACTGTTTCAACAAACTCCCAATCTCCTAACGATTTTCGATGAAACTGCTTAGGCAT
+GCCCTGAGAAGACGAAACTCGACTCTGGCTGGTAGTATTTGGCTTTGGTGCATTCTCTCT
+CGATTTACCTTCAAGTTCTACTTGTCTCTCCTTTTGCTCTGCTTGATGTGAGTTACCATT
+ATTGGCGTATTTGATATCCGCCGGGGGCATTAGCGGTGTGTTCTGCTGCTGCTGCTGCTG
+TGGACTTTTTCCCATCATTCTCAGCGTAGCGGGCGCCATAGTGCTTGGTTGTGTATGCAT
+GCTGTTGCTTTCACTATTGCCATCATCCTGCTGGTTACCTCTGCCCATTGAGAAGGCAGT
+ATTTACGTGATAATCATCCATAAAAAAAAAAAAAAAAAAA
+>Transcript_1_1
+ACATATGTGTGGATGATATAAGATTTGTCCCAAGGACGCTTCTCGAATAGTTCTTTTGTC
+CCTAGATATTTCCTTCTCTAATTTCTTCTGTCTCTCCAAAACATCTTGTTCATTTTTGGG
+TGGTGGCAGCATTTGTTCTTTATGTAGGAAAGCCTTTGTAGCACGGTTTACAATTTTTAC
+TGCACAAACCTCATTAGTGTAACGATGTTTTGCCAGCTTCACTTTACCCATAGAACCTGC
+ACCAACTGTTTCAACAAACTCCCAATCTCCTAACGATTTTCGATGAAACTGCTTAGGCAT
+GCCCTGAGAAGACGAAACTCGACTCTGGCTGGTAGTATTTGGCTTTGGTGCATTCTCTCT
+CGATTTACCTTCAAGTTCTACTTGTCTCTCCTTTTGCTCTGCTTGATGTGAGTTACCATT
+ATTGGCGTATTTGATATCCGCCGGGGGCATTAGCGGTGTGTTCTGCTGCTGCTGCTGCTG
+TGGACTTTTTCCCATCATTCTCAGCGTAGCGGGCGCCATAGTGCTTGGTTGTGTATGCAT
+GCTGTTGCTTTCACTATTGCCATCATCCTGCTGGTTACCTCTGCCCATTGAGAAGGCAGT
+ATTTACGTGATAATCATCCATAAAAAAAAAAAAAAAAAAA
+>Transcript_1_1
+ACATATGTGTGGATGATATAAGATTTGTCCCAAGGACGCTTCTCGAATAGTTCTTTTGTC
+CCTAGATATTTCCTTCTCTAATTTCTTCTGTCTCTCCAAAACATCTTGTTCATTTTTGGG
+TGGTGGCAGCATTTGTTCTTTATGTAGGAAAGCCTTTGTAGCACGGTTTACAATTTTTAC
+TGCACAAACCTCATTAGTGTAACGATGTTTTGCCAGCTTCACTTTACCCATAGAACCTGC
+ACCAACTGTTTCAACAAACTCCCAATCTCCTAACGATTTTCGATGAAACTGCTTAGGCAT
+GCCCTGAGAAGACGAAACTCGACTCTGGCTGGTAGTATTTGGCTTTGGTGCATTCTCTCT
+CGATTTACCTTCAAGTTCTACTTGTCTCTCCTTTTGCTCTGCTTGATGTGAGTTACCATT
+ATTGGCGTATTTGATATCCGCCGGGGGCATTAGCGGTGTGTTCTGCTGCTGCTGCTGCTG
+TGGACTTTTTCCCATCATTCTCAGCGTAGCGGGCGCCATAGTGCTTGGTTGTGTATGCAT
+GCTGTTGCTTTCACTATTGCCATCATCCTGCTGGTTACCTCTGCCCATTGAGAAGGCAGT
+ATTTACGTGATAATCATCCATAAAAAAAAAAAAAAAAAAA
+>Transcript_2_0
+AAA
+>Transcript_2_0
+AAA
+>Transcript_2_0
+AAA
+>Transcript_2_0
+AAA
+>Transcript_2_0
+AAA
+>Transcript_2_0
+AAA
+>Transcript_2_0
+AAA
+>Transcript_2_0
+AAA
+>Transcript_2_0
+AAA
+>Transcript_2_0
+AAA
+>Transcript_2_0
+AAA
diff --git a/test_files/copy_number_input.csv b/test_files/copy_number_input.csv
new file mode 100644
index 0000000000000000000000000000000000000000..d3bfaaa6e44d0ae7b52ee8f60f6ec61060c4b636
--- /dev/null
+++ b/test_files/copy_number_input.csv
@@ -0,0 +1,6 @@
+ID of transcript,ID of parent transcript,Transcript copy number
+1,1,12
+2,1,11
+3,2,33
+4,3,11
+5,4,55
\ No newline at end of file
diff --git a/test_files/yeast_example.fa b/test_files/yeast_example.fa
new file mode 100644
index 0000000000000000000000000000000000000000..8af0a80debe4d1c24cd8a5ca73900891450e6a93
--- /dev/null
+++ b/test_files/yeast_example.fa
@@ -0,0 +1,76 @@
+>Transcript_1
+TTTTTTTTTTTTTTTTTTTATGGATGATTATCACGTAAATACTGCCTTCTCAATGGGCAGAGGTAACCAGCAGGATGAT
+GGCAATAGTGAAAGCAACAGCATGCATACACAACCAAGCACTATGGCGCCCGCTACGCTG
+AGAATGATGGGAAAAAGTCCACAGCAGCAGCAGCAGCAGAACACACCGCTAATGCCCCCG
+GCGGATATCAAATACGCCAATAATGGTAACTCACATCAAGCAGAGCAAAAGGAGAGACAA
+GTAGAACTTGAAGGTAAATCGAGAGAGAATGCACCAAAGCCAAATACTACCAGCCAGAGT
+CGAGTTTCGTCTTCTCAGGGCATGCCTAAGCAGTTTCATCGAAAATCGTTAGGAGATTGG
+GAGTTTGTTGAAACAGTTGGTGCAGGTTCTATGGGTAAAGTGAAGCTGGCAAAACATCGT
+TACACTAATGAGGTTTGTGCAGTAAAAATTGTAAACCGTGCTACAAAGGCTTTCCTACAT
+AAAGAACAAATGCTGCCACCACCCAAAAATGAACAAGATGTTTTGGAGAGACAGAAGAAA
+TTAGAGAAGGAAATATCTAGGGACAAAAGAACTATTCGAGAAGCGTCCTTGGGACAAATC
+TTATATCATCCACACATATGTAGACTTTTTGAGATGTGCACGTTGTCAAATCATTTCTAT
+ATGTTGTTTGAATATGTTTCAGGTGGTCAGCTGTTAGACTATATCATCCAACATGGGTCA
+ATACGAGAACACCAAGCGAGAAAGTTTGCTAGGGGTATCGCGAGCGCCTTAATATATTTG
+CATGCTAACAACATCGTCCATAGAGATTTGAAGATAGAAAATATAATGATTTCAGATTCC
+AGTGAAATCAAGATAATTGATTTTGGACTTTCAAATATTTATGATTCTAGGAAGCAGCTT
+CATACATTCTGTGGCTCTCTGTATTTTGCCGCTCCCGAGCTGTTAAAAGCGAATCCTTAT
+ACAGGACCTGAAGTAGATGTCTGGTCATTTGGTGTAGTTTTATTTGTTTTGGTATGCGGT
+AAAGTGCCATTTGACGACGAAAATTCGAGCGTTTTACATGAAAAGATCAAGCAAGGTAAG
+GTTGAATATCCCCAACATTTATCTATCGAAGTAATATCACTGTTATCCAAAATGTTGGTA
+GTAGATCCGAAAAGAAGAGCCACACTTAAACAGGTTGTGGAGCACCACTGGATGGTAAGA
+GGGTTCAATGGTCCCCCTCCTTCTTACTTACCGAAAAGAGTTCCCCTAACTATCGAAATG
+CTTGATATAAATGTCTTAAAAGAAATGTACCGTTTAGAATTTATTGACGATGTAGAGGAA
+ACAAGAAGTGTTTTGGTCAGTATAATCACAGATCCTACTTACGTTCTTCTCTCTAGACAA
+TACTGGACTTTAGCGGCCAAAATGAACGCAGAATCCAGTGATAACGGAAACGCGCCAAAC
+ATAACAGAGAGTTTTGAAGACCCAACTCGGGCATATCATCCAATGATTTCCATATATTAC
+TTGACTTCTGAGATGCTTGATAGGAAACATGCGAAAATTCGGAATCAACAACAGCGACAG
+AGCCACGAAAATATAGAAAAGCTTTCTGAAATACCGGAAAGTGTGAAGCAAAGGGACGTA
+GAGGTCAATACAACCGCTATGAAATCAGAGCCAGAAGCCACGTTGGCGACAAAAGATACC
+TCTGTGCCATTCACTCCAAAGAATAGCGATGGCACAGAGCCCCCCTTACATGTCTTAATT
+CCACCGAGGTTAGCAATGCCAGAACAAGCGCATACGTCACCAACGAGTAGAAAAAGTTCT
+GATAATCAACGCCGTGAAATGGAATATGCTCTCTCTCCAACTCCTCAGGGAAATGACTAT
+CAACAATTTAGGGTACCTTCAACTACTGGCGATCCCTCAGAAAAGGCGAAGTTTGGGAAT
+ATATTTAGAAAATTATCACAGCGCCGTAAAAAGACCATTGAACAGACATCTGTTAATAGT
+AATAATAGTATCAATAAACCTGTGCAAAAGACGCATTCTCGCGCTGTTTCAGACTTTGTC
+CCTGGTTTTGCTAAACCGAGTTATGATTCAAATTATACCATGAATGAGCCTGTCAAGACA
+AACGATAGCAGAGGTGGCAATAAAGGTGACTTTCCAGCATTGCCTGCGGATGCAGAAAAT
+ATGGTAGAGAAGCAAAGGGAGAAGCAAATTGAAGAAGATATAATGAAATTGCATGATATT
+AATAAACAGAATAATGAAGTTGCAAAAGGAAGCGGGCGGGAAGCTTACGCTGCACAGAAG
+TTTGAAGGAAGCGACGACGACGAGAATCATCCCTTACCACCTCTCAATGTTGCAAAAGGT
+CGAAAACTACATCCAAGCGCAAGAGCTAAATCAGTTGGTCATGCTCGTCGTGAATCACTC
+AAATATATGAGACCCCCAATGCCTTCATCTGCCTATCCTCAGCAAGAGCTTATAGATACT
+GGGTTCTTAGAATCAAGTGACGATAACAAATCCGATAGTTTGGGAAATGTTACTTCACAG
+ACGAATGATAGCGTCAGCGTGCATTCTGTGAACGCACACATAAACTCGCCATCTGTGGAG
+AAGGAATTAACAGATGAAGAGATATTGCAGGAAGCTTCTAGAGCTCCAGCCGGTTCTATG
+CCATCCATCGATTTCCCCCGTTCTTTATTTTTGAAGGGTTTCTTTTCTGTTCAGACAACT
+TCATCGAAGCCTTTGCCAATTGTTAGATACAAGATTATGTTTGTTCTGAGGAAAATGAAT
+ATAGAGTTCAAGGAGGTTAAGGGTGGTTTTGTTTGTATGCAAAGGTTCTCTTCCAATAAT
+GTGGCAGCGAAGAGAGAAGGGACTCCAAGATCGATCATGCCACTTTCGCACCACGAATCC
+ATTAGACGTCAAGGCTCTAATAAATACTCACCTTCTTCTCCTTTGACAACTAATTCCATT
+CACCAGAGAAAAACATTTTTTTTTTTTTTTTTTTTCTATTACCGAAACCTATGGAGATGATAAGCATTCGGGAACATCT
+TTGGAGAACATCCACCAACAAGGTGACGGTAGCGAAGGCATGACTACAACAGAAAAAGAG
+CCCATCAAATTCGAAATTCATATCGTCAAGGTTCGTATTGTTGGTTTAGCCGGTGTGCAT
+TTTAAGAAAATTTCTGGGAACACTTGGTTGTATAAAGAGCTGGCTTCTAGTATATTAAAA
+GAACTAAAGTTGTAA
+>Transcript_2
+TTTTTTTTTTTTTTTTTTTTTATGTATGTTGATCCGATGAACAACAATGAAATCAGGAAATTAAGCATTACTGCCAAGACA
+GAAACAACTCCAGATAACGTTGGACAAGACATTCCTGTAAACGCACATTCGGTGCATGAG
+GAATGTTCTTCCAACACACCCGTGGAGATAAATGGAAGAAACAGCGGAAAGTTGAAAGAA
+GAAGCGTCTGCAGGTATTTGTTTGGTTAAAAAACCAATGCTACAATATAGAGATACCTCA
+GGAAAGTATTCCCTAAGTGACTTTCAGATTTTAAGAACTTTGGGAACTGGCTCATTTGGG
+AGAGTTCACCTAATTCGTTCCAATCACAATGGGAGGTTTTACGCTTTGAAGACATTGAAA
+AAGCACACTATAGTGAAGCTGAAGCAGGTTGAACACACCAATGACGAACGCCGAATGCTT
+TCAATTGTTTCACATCCATTCATCATTCGAATGTGGGGAACGTTCCAAGATTCTCAGCAA
+GTTTTCATGGTAATGGACTACATTGAAGGTGGTGAATTATTTTCTTTACTACGTAAATCT
+CAAAGATTTCCCAACCCAGTAGCCAAATTTTATGCCGCAGAGGTATGCTTAGCGTTGGAA
+TATTTGCACAGTAAGGATATAATATATATTTTTTTTTTTTTTTTTTTTTTTTTTGAGACTTGAAACCAGAAAATATCCTTCTAGAT
+AAAAACGGCCATATCAAGATAACCGACTTTGGCTTCGCAAAATACGTTCCCGATGTCACA
+TACACATTATGTGGCACACCAGATTACATAGCGCCGGAAGTGGTCAGTACAAAACCGTAT
+AATAAATCAGTGGATTGGTGGAGTTTTGGTGTGCTAATCTATGAAATGCTTGCCGGATAC
+ACTCCATTTTACAATTCGAACACCATGAAAACTTACGAAAATATACTGAACGCCGAATTG
+AAGTTCCCACCATTTTTCCATCCAGACGCGCAGGACTTATTGAAGAAGCTAATTACCAGA
+GACTTAAGTGAAAGGTTGGGTAACTTACAAAATGGAAGTGAAGATGTCAAGAACCATCCG
+TGGTTTAACGAAGTGATATGGGAGAAATTGTTAGCAAGATACATAGAAACGCCGTACGAA
+CCACCAATCCAACAGGGCCAAGGTGACACTTCTCAATTTGACAGATACCCTGAAGAGGAA
+TTCAACTATGGAATTCAAGGGGAGGATCCATATATGGATTTAATGAAAGAATTTTAATTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
diff --git a/tests/test_cdna.py b/tests/test_cdna.py
index ae9fcb17877f4666f9d76fcf3e866520358d24c4..5ad8caa2b55d5159d1e2a90591a8d07f2ab5cdb1 100644
--- a/tests/test_cdna.py
+++ b/tests/test_cdna.py
@@ -1,2 +1,35 @@
# imports
import pytest
+from cdna.cdna import complement, seq_complement
+
+@pytest.mark.parametrize(
+ "test_input,expected",
+ [("A", "T")]
+)
+def test_complement_param(test_input, expected): # we need to pass the lists to the test function...
+ assert complement(test_input) == expected
+
+@pytest.mark.parametrize(
+ "test_input,expected",
+ [("AA", "TT")]
+)
+def test_seq_complement_param(test_input, expected): # we need to pass the lists to the test function...
+ assert seq_complement(test_input) == expected
+
+
+# we can do the same for the tests that raise an error:
+@pytest.mark.parametrize(
+ "test_input,expected",
+ [(1, ValueError)]
+)
+def test_complement_param_failing(test_input, expected):
+ with pytest.raises(expected):
+ complement(test_input)
+
+@pytest.mark.parametrize(
+ "test_input,expected",
+ [("11", ValueError)]
+)
+def test_complement_param_failing(test_input, expected):
+ with pytest.raises(expected):
+ seq_complement(test_input)