Output Formats

Pyrodigal was created among other things to skip parsing the results from Prodigal while building a larger pipeline. Therefore, it’s advised to manipulate the genes predicted by Pyrodigal through the object layer instead of writing them to a file only to parse it later.

Nevertheless, Pyrodigal provides convenience methods to write the genes from a Genes collection to a variety of formats, as found in the Prodigal command line. Note that all these functions need to know the name of the sequence they were obtained from.

Note

The methods shown before are implemented using only the Python interface, so it should be possible to replicate them using the attributes of the individual Gene objects.

Genes

Use Genes.write_genes to write the nucleotide sequences of all the genes found by Pyrodigal to a file or a file-like object, similar to prodigal -d:

genes = orf_finder.find_genes(sequence)
with open("genes.fna", "w") as dst:
    genes.write_genes(dst, sequence_id="seqXYZ")

It’s also possible to change the width of the FASTA columns, if needed (use math.inf as the width to write 2-line FASTA):

genes = orf_finder.find_genes(sequence)
with open("genes.fna", "w") as dst:
    genes.write_genes(dst, sequence_id="seqXYZ", width=80)

Translations

Use Genes.write_translations to write the protein sequences of all the genes found by Pyrodigal to a file or file-object, similar to prodigal -a:

genes = orf_finder.find_genes(sequence)
with open("proteins.faa", "w") as dst:
    genes.write_translations(dst, sequence_id="seqXYZ")

It’s also possible to change the translation table and to control the width of the FASTA columns, if needed:

genes = orf_finder.find_genes(sequence)
with open("proteins.faa", "w") as dst:
    genes.write_translations(dst, sequence_id="seqXYZ", width=80, translation_table=11)

GFF

Use Genes.write_gff to write the genes to a file or file-like object in GFF format, similar to prodigal -f gff -o:

genes = orf_finder.find_genes(sequence)
with open("genes.gff", "w") as dst:
    genes.write_gff(dst, sequence_id="seqXYZ")

Use header=False to skip writing the GFF3 header. This can be useful when writing genes from different sequences to the same result file:

with open("genes.gff", "w") as dst:
    for i, record in enumerate(Bio.SeqIO.parse("contig.fna")):
        genes = orf_finder.find_genes(str(record.seq))
        genes.write_gff(dst, sequence_id=record.id, header=(i == 0))

Use include_translation_table=True to include the translation table of the genes in the GFF attributes. This may be useful for genes predicted in metagenomic mode, since they may have been predicted with non-standard genetic codes.

Genbank

Use Genes.write_genbank to write the genes to a file or file-like object in GenBank format, similar to prodigal -f gbk -o:

genes = orf_finder.find_genes(sequence)
with open("genes.gbk", "w") as dst:
    genes.write_genbank(dst, sequence_id="seqXYZ")

Note

The original Prodigal outputs incomplete GenBank files containing only the coordinates of the predicted genes inside CDS features, without including the translation or the original sequence. Since this is not the most useful output, and often requires additional post-processing, Pyrodigal outputs a complete GenBank record instead.

Scores

Use Genes.write_scores to write the scores of all potential genes in a format proprietary to Prodigal, similar to prodigal -s:

genes = orf_finder.find_genes(sequence)
with open("scores.txt", "w") as dst:
    genes.write_scores(dst, sequence_id="seqXYZ")