cDNA Generator module

Generate cDNA based on mRNA transcript sequences 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 license, Copyright (c) 2022 Zavolan Lab, Biozentrum, University of Basel

Contributers

Eric Boittier, Bastian Wagner, Quentin Badolle

More info:

Input files

transcript_copies (csv-formatted) containing:

• ID of transcript
• ID of parent transcript
• transcript copy number

transcript_sequences (fasta-formatted) containing:

• ID of transcript
• transcript-sequence

priming_sites (gtf-formatted) containing:

• ID of transcript
• Position of priming site
• Binding likelihood of priming site

Output files

cDNA_sequences (fasta-formatted) containing:

• cDNA sequence ID
• cDNA-sequence

cDNA_counts (csv-formatted) containing:

• cDNA sequence ID
• cDNA-counts