srst2

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… in the name, instead just pass sample_name along to functions requiring it. This addresses #99

ericenns

Cannot parse strain name when '.' in file path

3

So the following [line](https://github.com/katholt/srst2/blob/master/scripts/srst2.py#L453) keeps failing when one or more '.' are found on the path to pileup file. Example failing file path is /Storage/galaxy-17.05/working/dapE_11.out__Strain1.dataset_357596.pileup

Takadonet

Hi there, I added a bit of code to the getmlst.py script to add an option for an output folder. It should take all the downloaded files, and the log...

alegione

read depth calculation

2

Hi, how each allele read depth is calculated? The read depth that I find in the output (column "depth") is the average of each one of the seven loci read...

abrozzi

creating srst2 executable

2

I've tried both the pip install and python setup.py ways of installing srst2, and I can't seem to get the "srst2" executable to generate. I get the "slurm_srst2.py" and "getmlst.py"...

najoshi

ValueError("Inputs must not be empty") when running srst2 invoking --input_pe

1

Hi, I encounter the following error "ValueError("Inputs must not be empty.")" when I run the following command: srst2 --output output_845354 --input_pe strain845354_1.fastq.gz strain845354_2.fastq.gz -mlst_db Staphylococcus_aureus.fasta --mlst_definitions saureus.txt --mlst_delimiter '_' --threads...

lilipeng

Different MLST result when re-running SRST2 after adding in new alleles

3

Howdy all, So running into an odd issue. I am running a few K. pneumoniae samples against an MLST database using 0.2.0, and on first run, it generated the following...

swlong

Difference in log files for negatives when using gene_db

2

Hi Kat, this is in reply to your email, but I have included the original query below also. The files that are created are: 3__3-paired.gene_db.sam 3__3-paired.gene_db.sam.mod 3__3-paired.gene_db.unsorted.bam 3__genes__gene_db__results.txt However the...

kajcox