Problem with codon #8
Comments
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Hi, Thank you for reporting the issue! Have you been running IgDetective on Mac OS? I was able to reproduce the problem on my laptop. It looks like the "Alignment" class from BioPython package has a different structure as compared to what we expect from it. It is either caused by differences between BioPython versions or the way it works on Linux and Mac OS systems. I will work on unifying the versions, in the meantime please feel free to send me genomes you'd like to process. Best regards, |
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Yes. this was on a Mac. A fix would be wonderful! |
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I installed it in Linux and got the same error: (igdetective) c305-005.ls6(198)$ python run_iterative_igdetective.py /work/06127/pdoris/BN_HiFi_curated.fa /work/06127/pdoris/BN |
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Thank you for checking how it works on linux! I am now confident that this issue can be explained by the differences between Biopython versions. It looks like we used an older version than you do. I will add a fix next week. |
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Hi Yana.... any progress with the fix? Peter |
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Hi Yana and Peter, Using BioPython v1.81 I encountered the same error as you described here, Peter. As Yana mentioned, the issue seems to be related to the version of BioPython and how the data is being processed. Using an older version of BioPython solved it: I created a python venv where I installed BioPython version 1.77. That resolved this issue for me. In more detail: Debugging using BioPython v1 .81 shows that the 
Stefan |
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Similar bug within Biopython It looks like a biopython translate issue. I down degraded to Biopython 1.77 and it fixed the issue. Thank you!! |
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However, I got a new one today. Again this is with Biopython 1.77 |
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Hello everyone, I deeply apologize for the long response (tool support and job transitions are not easy to combine) and appreciate your patience. The issue with a "GET" codon was related to a change in the biopython interface for alignment representation. I made a fix that seems to be working fine with BioPython 1.82. @raw937 Richard, I anticipate that the issue you described should also go away. Could you please update the repository and rerun your analyses? Thank you! Best regards, |
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Oh hi Yana! We will give it a try. I will give this a try. And, let you know. Also, will send a follow up email. many thanks, |
Much of the pipeline proceeds until seq is translating presumably detected Ig sequences. It repeatedly terminates with the "Codon 'GET' is invalid" error
pdoris$ python run_iterative_igdetective.py /Volumes/ms_imm_doris/Rat_references/BN-HiFi/Final_curated_BN-HiFi_assembly/BN_final.curated_primary.no_mt.unscrubbed.fa /Users/pdoris/IgDetective-1.1.0/BN
/usr/local/bin/minimap2
==== Aligning human IG genes...
Aligning IGLV genes (datafiles/human_reference_genes/IGLV.fa)...
Aligning IGLJ genes (datafiles/human_reference_genes/IGLJ.fa)...
Aligning IGKV genes (datafiles/human_reference_genes/IGKV.fa)...
Aligning IGHJ genes (datafiles/human_reference_genes/IGHJ.fa)...
Aligning IGHV genes (datafiles/human_reference_genes/IGHV.fa)...
Aligning IGKJ genes (datafiles/human_reference_genes/IGKJ.fa)...
Aligning IGHC genes (datafiles/human_reference_genes/IGHC.fa)...
Aligning IGKC genes (datafiles/human_reference_genes/IGKC.fa)...
Aligning IGLC genes (datafiles/human_reference_genes/IGLC.fa)...
==== Identifying IG contigs...
==== Running RSS-based IgDetective for IGH...
Contig: CHR_6, contig range: (137515617, 147156653), approx locus length: 9641036
Running: python py/IGDetective.py -i /Users/pdoris/IgDetective-1.1.0/BN/denovo_search/combined_contigs_IGH.fasta -o /Users/pdoris/IgDetective-1.1.0/BN/denovo_search/predicted_genes_IGH -m 1 -l IGH
==== Running RSS-based IgDetective for IGK...
Contig: CHR_4, contig range: (97247562, 104902484), approx locus length: 7654922
Running: python py/IGDetective.py -i /Users/pdoris/IgDetective-1.1.0/BN/denovo_search/combined_contigs_IGK.fasta -o /Users/pdoris/IgDetective-1.1.0/BN/denovo_search/predicted_genes_IGK -m 1 -l IGK
==== Running RSS-based IgDetective for IGL...
==== Iterative processing IGHV genes...
Running minimap...
Alignment of IG genes datafiles/combined_reference_genes/IGHV.fa to /Volumes/ms_imm_doris/Rat_references/BN-HiFi/Final_curated_BN-HiFi_assembly/BN_final.curated_primary.no_mt.unscrubbed.fa
Processing SAM file...
/Users/pdoris/opt/anaconda3/envs/igdetective/lib/python3.11/site-packages/Bio/Seq.py:2804: BiopythonWarning: Partial codon, len(sequence) not a multiple of three. Explicitly trim the sequence or add trailing N before translation. This may become an error in future.
warnings.warn(
Traceback (most recent call last):
File "/Users/pdoris/IgDetective-1.1.0/run_iterative_igdetective.py", line 290, in
main(genome_fasta, output_dir, ig_gene_dir)
File "/Users/pdoris/IgDetective-1.1.0/run_iterative_igdetective.py", line 259, in main
AlignGenesIteratively(ref_gene_fasta, igdetective_tsv, genome_fasta, iter_dir, gene)
File "/Users/pdoris/IgDetective-1.1.0/run_iterative_igdetective.py", line 134, in AlignGenesIteratively
gene_finding_tools.main(genome_fasta, ref_gene_fasta, iter0_dir)
File "/Users/pdoris/IgDetective-1.1.0/py/extract_aligned_genes.py", line 147, in main
aa_seq = str(Seq(alignment.gene_seq).translate())
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/pdoris/opt/anaconda3/envs/igdetective/lib/python3.11/site-packages/Bio/Seq.py", line 1448, in translate
_translate_str(str(self), table, stop_symbol, to_stop, cds, gap=gap)
File "/Users/pdoris/opt/anaconda3/envs/igdetective/lib/python3.11/site-packages/Bio/Seq.py", line 2836, in _translate_str
raise CodonTable.TranslationError(
Bio.Data.CodonTable.TranslationError: Codon 'GET' is invalid
(igdetective) IMM-MAC-184391:IgDetective-1.1.0 pdoris$
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