yana-safonova
commented
1 year ago 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, Yana
pdoris
StefanLelieveld
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$