Seq Report

Simple reporting on a set of sequences for documentation purposes.

Install

pip install git+https://github.com/Edinburgh-Genome-Foundry/Seq_Report.git

See also build.yml or PDF Reports Installation instructions.

Usage

import seqreport

seq_fasta = "seq.fa"
seq_coll = seqreport.SeqCollection(records=seqreport.read_fasta(seq_fasta), projectname="EGF24")
seqreport.write_pdf_report("seq_report.pdf", seq_coll)

Alternatively, use a CSV file to specify parameters:

seq_coll = seqreport.seqcollection_from_csv(csv_file="tests/data/values.csv")

Header is ignored, but there must be a header. Entries must match the SeqCollection parameters (example).

Versioning

Seq Report uses the semantic versioning scheme.

License = MIT

Seq Report is free/libre and open-source software, which means the users have the freedom to run, study, change and distribute the software.

Seq Report was written at the Edinburgh Genome Foundry by Peter Vegh.

Copyright 2024 Edinburgh Genome Foundry, University of Edinburgh