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katholt / sonneityping

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bam mode not working #4

Open RJBeng opened 4 years ago

RJBeng commented 4 years ago

Hello,

I am running into issues when using the --bam mode. This is my command:

python sonnei_genotype.py --mode bam --bam *.bam --ref ref.fa --ref_id HE616528 --allele_table alleles.txt --samtools_location ~/SOFTWARE/samtools-1.2/ --bcftools_location ~/SOFTWARE/bcftools-1.2/ --output genotypes.txt

I get the following errors

  File "sonnei_genotype.py", line 658, in <module>
    main()
  File "sonnei_genotype.py", line 501, in main
    ordered_loci = list(loci + qrdr_loci)
TypeError: can only concatenate list (not "dict") to list

The code is working for --vcf mode.

Many thanks Rebecca

jhawkey commented 4 years ago

Hi Rebecca,

I suspect both of these issues are due to me playing around with the development branch working on future updates. The code in the dev branch currently isn’t stable.

However all the issues you raised before, as well as updating the code to find all mutations in the known gyrA and parC codons, have now been fixed in the master branch.

Could you please try your commands on the master branch instead?

Thanks!

Jane On 7 Feb 2020, 11:22 PM +1100, RJBeng notifications@github.com, wrote:

Hello, I am running into issues when using the --bam mode. This is my command: python sonnei_genotype.py --mode bam --bam *.bam --ref ref.fa --ref_id HE616528 --allele_table alleles.txt --samtools_location ~/SOFTWARE/samtools-1.2/ --bcftools_location ~/SOFTWARE/bcftools-1.2/ --output genotypes.txt I get the following errors File "sonnei_genotype.py", line 658, in main() File "sonnei_genotype.py", line 501, in main ordered_loci = list(loci + qrdr_loci) TypeError: can only concatenate list (not "dict") to list The code is working for --vcf mode. Many thanks Rebecca — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or unsubscribe.

RJBeng commented 4 years ago

Hi Jane,

I just cloned the repository from the Github page and ran the code on my data. I am still getting the same errors for the bam and parsnp mode, the vcf mode is working though.

Best Rebecca