Commit 16b04cd5 authored by Martin Larralde's avatar Martin Larralde
Browse files

Fix rendering of main `pyrodigal` docstring in terminal

parent e6ad2466
......@@ -11,12 +11,13 @@ Example:
>>> import gzip
>>> import Bio.SeqIO
>>> with gzip.open("pyrodigal/tests/data/KK037166.fna.gz", "rt") as f:
>>> seq_path = "pyrodigal/tests/data/KK037166.fna.gz"
>>> with gzip.open(seq_path, "rt") as f:
... record = Bio.SeqIO.read(f, "fasta")
Then use Pyrodigal to find the genes in *metagenomic* mode (without
training first), for instance to build a map of codon frequencies for
each gene::
training first), for instance to build a map of codon frequencies
for each gene::
>>> from collections import Counter
>>> import pyrodigal
......@@ -48,10 +49,10 @@ References:
- Larralde, M.
*Pyrodigal: Python bindings and interface to Prodigal, an efficient
method for gene prediction in prokaryotes*. Journal of Open Source
Software 7, no. 72 (25 April 2022): 4296. :doi:`10.21105/joss.04296`.
Software 7, no. 72 (25 April 2022). :doi:`10.21105/joss.04296`.
- Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW, Hauser LJ.
*Prodigal: prokaryotic gene recognition and translation initiation site
identification. BMC Bioinformatics 11, no. 1 (December 2010): 119.
*Prodigal: prokaryotic gene recognition and translation initiation
site identification*. BMC Bioinformatics 11, no. 1 (December 2010).
:doi:`10.1186/1471-2105-11-119`. :pmid:`20211023`. :pmc:`2848648`.
"""
......
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