"parallel edges are forbidden" error in v1.6.4 but not in v1.5.1

[mtisza1]

Hi,

On certain sequences (perhaps because they have large gaps between ORFs), phanotate v1.6.4 throws an error. This is not observed with phanotate v1.5.1, which returns ORF predictions.

(phanotate_164) mjt % phanotate.py --version
1.6.4
(phanotate_164) mjt % phanotate.py -f tabular uParvo3481.fasta -o uParvo3481.phan_v1.6.4.tsv
Traceback (most recent call last):
  File "/Users/michaeltisza/miniconda3/envs/phanotate_164/bin/phanotate.py", line 49, in <module>
    graph = functions.get_graph(orfs)
  File "/Users/michaeltisza/miniconda3/envs/phanotate_164/lib/python3.10/site-packages/phanotate_modules/functions.py", line 429, in get_graph
    G.add_edge(Edge(left_node, right_node, score ))	
  File "/Users/michaeltisza/miniconda3/envs/phanotate_164/lib/python3.10/site-packages/phanotate_modules/graphs.py", line 74, in add_edge
    raise ValueError("parallel edges are forbidden")
ValueError: parallel edges are forbidden

The sequence below was used as the input. Notably, this contig is not predicted to belong to a phage genome, and therefore this may be the intended behavior of phanotate.

Best,

Mike

uParvo_sus_pigfeces_SRR11413591_3481
CTGATGAAGATAATAATTTATCAGATCTTGTAAAAATATCTCCAAAATATTTCAAGATTTCTACTGGTGGTGAAAC
TACTATTAATCCTGCATTTAGTACTGACAGTACAAATGCTGATCCTGATTATCGTTTATGGAGTATGACAAAACAA
GGACTTGATCAAAATAACTCTCCTTGTTTAAATTATAACATTTGGAAGAATGCTAGTAGATTTTATATATTCAGTT
TTGCTGAGAATTTCAGCTTACTTGATAATAATAACTATATTAATTATGAATTAAGATTTTCTGACGACGATACTGT
TGATATTCCTGAAAAGGTCAATATTCATAGAATTTATTTGAAGGATTATCTAACTATTTTTGAAAGTCAAACTGAA
TAATTGAGAAGAATTTATTCGTTGAAACAACTTTTTTACTTTGTTTCTAACAGTGACGTAAGTGACGATAGTGACG
ATACTTTATAAACTTTTAAAATAGAACAGATTTTCAGTTTTTCTTAAAATCTTAAAAATAAAAATCTTTTATTAAA
TTATCGTCACTATTGTCACTGTAAATTATAAAATCAAGCAAATTAAACAAAATATAGTAAAATCATCTGTATGACA
TTCCCTTAAACGTTAAAAAGTAGGGAGTGACGTTAAATATAAATTATCGTCACTAGTGTCGATAATTAACGTCACT
GTTAAAGATTTCTAGAAAAATTTAGACTAACTGTTAAAATTATTATCGTCACTGTTTAAATTATTATCGTCACTGT
TAAATATTAAGTGACGTTAAACAAAGTGAAACGCTGAATTGCTTATTCAAAGTAAAAGAATTAATTTAAGATTTTT
AATCTTCTTCAAATTCACAAGCATCAATACGATCTTCTGGTAAAATATTATATTTTTCCTCAATAAGATCTCTTAC
ATAGTGTAAATCAATTAAACGAATACCATTAGAGCGTCTATATACATTATTTCCAAATAATTTGGTCATTTCTTTA
CTAATATTACGTATACTAAGATCTTTAATATCCTCATCAGCACAAATTCTAATTTGATTTACAAGTTCAGATGGAG
TATATGTATCAAATAACTTATTATAATATATAACTTCCACAATCCATGGCATATTACATCTTTGCATAGTATCTTT
TGAAGGAGTATATATATTTCTATGGAAATCATATGAAGAATCATACCATTCACAAGCTTTATGATAACAACTTGAT
AAGAAATCAGGATTATTTTCCCATTTTGTTCTAAATTCTTTTGCAAATGATTTTTTAACAGGAACCCCTTGTAAAT
TATAAAATAATCCACGACGTTCACCAGTTTCCCATTCAAGAGGTATACCTTGAGTAGTATTACTAAATAAGAATAA
TGTTGATTTATTATCTTTTGTTTCAATATGACCATATTTATGATTTACTGTAACTTCAGATGCTGTAATATAATCT
TTAATCTTATTAACAGTATCAGTGGATCTATCATGACATTCATTAATCATAACAACACATTTACCTGCATTTACAT
TAAATTGTCCAACAACTTTATCTAGTGTTGATTTTGCAGTTTCAATAGGATCATACCACTTACTTACTATATCAAA
AAGAGTATCTTTACCATATCCTTGATTTGATGCTATACAAACAGCAATTTCAGTACGATATCCAGGTTTCATAGCA
AGTGATCCTAATAGTTTCTTAAGAGGTTCAATATATTGTAATTGTAATTCGACACAATTTGATTCACCATATGCAA
AAGTGTTAACAAATTTTTCAAAATCATCACCAATTTCTTTATTGTAATGTCCATTAATAATTTCAGGTTTTATGCC
CATAAACATACTGTAATATAAATCCCCATTTTGTGTTTTTATTAACCATTTACGAGGATTATCAATATCATCTTTT
CTATATGCAGTTTCAATATAAGAGTATAAGTGTTCACATCCGTTTTGAGCTAAAATTGCTTTAAAATCACTAGGTT
TATACATTGTCATATTATTAATAGTATATCTGCACATTACAGTATTTGTCATAATATCAATAACAACATACTGTCT
AATATAATTAATTTGTCTGTCAATACGATCTCCTTGTTTTAATGACTTTAATTTTCCAAAACTGAATGGTTCATTT
GGATATTCAATACATTCTGGTTTTGCTGATAAATATTCAGCATATGTGTTATATTTACATGGCTGATATTCCATAG
GATCAAAATCATTTTGTTCGAAATCTTTTGATATAAATTTGATATTATCAAGAGGAATATAGAAATCAATATTATG
TATATATTCATTAATAGCATCTGTTAATTGATTAGGTGTTAATTTAATTTTTTCTAGTTGATCCTTTCTTATCATG
CATCCATCAAAACAATATATGCATGTACTAATATCAATACCAAGATCACTTAATTTCTTATAAACTTGACGAATTA
TATTAACTTCTAAGAATTGCATATATCTACTAATACATGAATTATCAAGTTCATATTGTGATAATTTTCCTGTTGA
TTTACTGTCTGCAATAAGAATATTCTTTAATTTACAACAATGTTGTTTACCATCAGGATTTTGATACTTATTATTT
TTAATAGTACAGTTTGTTTTAATAGTAATTTTATTAGCATGATCAATAATAATTTTTCTTGAATTTTGCATTTCAT
TATAATAATTAATAACAAATTCTGTTGGTTGTACATTTTTAGCATTATTATTATACCAAGTTCTATAATTACCACC
AAATCCAATCATTAAAAATAATCTTTTTGCTAAATCACGTGAAACTTTACATGATTCCATTATTTCTTTAAGATAT
TTATCTCTATTATTTATGTATTCACCCAAATACTTACCATTTGTTATTGAATACATAAAATTAGGATATGCATTAA
CAATATCAATATCGATATAATTATCTTTATATAATGCAGCTCTTATTTCTCTCATAAAATGACAGGCACCACAAGC
ATTACAATTATTTACAGTTGCATATTTTCTATATAATCCGAATTTGTCACCACCACCTGATGAATATAGAATATCT
ATTGATTTATCTGCTGATAAAACATTTTTATTAATAGAATTTTCTAAATAACATAAATAAACTGATGGATTTACAC
CTTGACTGATTTCAACATTATTTCTTAATATTTTTTCTTTTTCTATTAAAAAAGAAATACATCTTCTTAAAGTGTC
TTCATTGTATACTTCATAGTAAGGTTGGCATAAAATATCAGATTCCATTTTACTTTGTATTTATTTAATAAATAAA
AAAAATTTTTAAAATAGAAAATAAAAATTAGTTAGAATTAATTTAGATAAAATTTATGATTACTAAGAAAAAACTT
GCAGTGACGATAATAGTTTAAACAGTTAGTCTAAATTTTTCTAGAAATCTTTAACAGTGCCGATATTTATCGTCAC
TAGTGACGTTAAACACCAAATTATCGTCACTGTCAATTACTATCAATTTGTTACTATTTAA

[deprekate]

Ah, a week ago or so ago I increased the distance threshold during the ORF connection step from 300bp to 500bp to fix a situation where gaps in the ORFs of the genome broke the path through the genome, but I forgot to also increase the distance in the code that should have found those gaps above the threshold and connected ORFs across the gap (not sure why it didn't to catch the gaps, probably an off-by-one error on my part)

Just fixed both distance thresholds to match and pushed the new version to pypi and here : )

$ phanotate.py -V
1.6.5

$ phanotate.py input.fasta | head
#id:	uParvo_sus_pigfeces_SRR11413591_3481
#START	STOP	FRAME	CONTIG	SCORE
3	383	+	uParvo_sus_pigfeces_SRR11413591_3481	-5.187465E+01
3240	835	-	uParvo_sus_pigfeces_SRR11413591_3481	-2.416964E+27

[mtisza1]

Wow thanks for the quick fix! I'll close this.