althonos / althonos/pyrodigal

Pyrodigal misses a valid CDS in the input FASTA file

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Description

When using Pyrodigal to predict CDS, it only returns two CDS regions with coordinates 1–1218 and 1429–2040, respectively. However, the region from 1163 to 1387 also appears to be a valid CDS.

Is there a way to configure or adjust Pyrodigal so that it detects this additional CDS as well?

My code:

```
#!/usr/bin/env python3
from Bio import SeqIO
import pyrodigal

fasta_records = {}
for record in SeqIO.parse('seq.txt', 'fasta'):
fasta_records[record.id] = record.seq

gene_finder = pyrodigal.GeneFinder(closed=True, mask=False, meta=True)

for seq_id, seq in fasta_records.items():
genes = gene_finder.find_genes(bytes(seq))
for gene in genes:
print(f'start:{gene.begin}\tend:{gene.end}')
```
Output:

```
start:1 end:1218
start:1429 end:2025
```
The sequence I used: [seq.txt](https://github.com/user-attachments/files/23926045/seq.txt)

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