jerrythafast / fdstools Goto Github PK

When running TSSV with verbose output (--dir option), it performs the task but fails upon closing the verbose output files. Commenting out line 635 in tssv.py gets rid of the error.

Example command:
fdstools tssv --dir results/example-2800M/ --indel-score 2 --mismatches 0.1 --num-threads 2 data/library.txt data/input.fastq > /dev/null

Terminal output:

marker  unique_seqs     tPaired fPaired rPaired tLeft   fLeft   rLeft   tRight  fRight  rRight                          
[7 lines retracted]

total reads     554718                                                                                                  
unrecognised reads      25306                                                                                           
usage: fdstools tssv [-h] [-v] [-d] [-F FORMAT] [-R FILE] [-L N] [-D DIR]                                                                    
					 [-T THREADS] [-X] [-m MISMATCHES] [-n N] [-a N] [-B]                                                                    
					 [-M ACTION]                                                                                                             
					 LIBRARY [IN] [OUT]                                                                                 
fdstools tssv: error: too many values to unpack (expected 2)

All output files are created and have the expected content.

Cheers,
Arvid

Hi,

I have encountered this issue:

FDSTools failed to load 'allelefinder': 'FileFinder' object has no attribute 'find_module'
FDSTools failed to load 'bganalyse': 'FileFinder' object has no attribute 'find_module'
FDSTools failed to load 'bgcorrect': 'FileFinder' object has no attribute 'find_module'
FDSTools failed to load 'bgestimate': 'FileFinder' object has no attribute 'find_module'
FDSTools failed to load 'bghomraw': 'FileFinder' object has no attribute 'find_module'
FDSTools failed to load 'bghomstats': 'FileFinder' object has no attribute 'find_module'
FDSTools failed to load 'bgmerge': 'FileFinder' object has no attribute 'find_module'
FDSTools failed to load 'bgpredict': 'FileFinder' object has no attribute 'find_module'
FDSTools failed to load 'findnewalleles': 'FileFinder' object has no attribute 'find_module'
FDSTools failed to load 'libconvert': 'FileFinder' object has no attribute 'find_module'
FDSTools failed to load 'library': 'FileFinder' object has no attribute 'find_module'
FDSTools failed to load 'pipeline': 'FileFinder' object has no attribute 'find_module'
FDSTools failed to load 'samplestats': 'FileFinder' object has no attribute 'find_module'
FDSTools failed to load 'seqconvert': 'FileFinder' object has no attribute 'find_module'
FDSTools failed to load 'stuttermark': 'FileFinder' object has no attribute 'find_module'
FDSTools failed to load 'stuttermodel': 'FileFinder' object has no attribute 'find_module'
FDSTools failed to load 'tssv': 'FileFinder' object has no attribute 'find_module'
FDSTools failed to load 'vis': 'FileFinder' object has no attribute 'find_module'

Can you please suggest a solution? I have tried reinstalling FDStools and installing it again but the same issue exists. I am running the most updated version of python

Hi Jerry，

I am using fdstools v2.1.0, and while analyzing the DYS389II locus, I set up flank and repeat parameters. However, the analysis results are mixed up with DYS389I, making it impossible to identify the true genotyping results. Additionally, the N48 in the DYS389 sequence structure [TAGA]a [CAGA]b N48[TAGA]c[CAGA]d was not recognized. Below are my library file, input.ini and the result files.
file.zip

I am using the command fdstools pipeline input.ini.

Could you offer some advice on how to best configure the settings for the DYS389II locus? Thank you.

Siyao