edgardomortiz / fineradstructure-tools Goto Github PK

Hi,

I'm trying to convert the alleles.loci file from ipyrad 0.7.22 [edit: it's actually 0.7.23], and running finerad_input.py I get this error:

Traceback (most recent call last): File "../fineRADstructure-tools/finerad_input.py", line 181, in <module> main() File "../fineRADstructure-tools/finerad_input.py", line 174, in main pyrad_to_finerad(filename, outfile, minsample) File "../fineRADstructure-tools/finerad_input.py", line 67, in pyrad_to_finerad sample = line.split()[0].strip(">")[:-2] # Sample name does not include last two characters IndexError: list index out of range

Any ideas for a fix? Thanks

Hi dear people,

I have a few questions regarding the input file from STACKS. My data is from ddRAD, pair-end reads, aligned to a draft genome. I noticed that in the input file made by Stacks there is no info of chrom, I am wondering if the alignment information is still there. I used ordered-export but not sure it is totally fine also because of the paired reads. I asked in the Stacks group but no one answered.

I tried hapsFromVCF to make the input but the result is rather creepy. So far now I can not use the python script because of the working environment. However it is mentioned that we can specify the maximum number of SNPs allowed at a locus, is it possible to do it using the Stacks output? Or I have to convert the data and do it through the script?

Thank you very much and look forward to your ideas!

Cheers,
Han Xiao

Hi Edgardo,

Getting a syntax error when trying to use your script:

tom$ python finerad_input.py --input sosorum-min5.alleles.loci
File "/finerad_input.py", line 57
print str(locus_num)+" loci for "+str(len(genotypes))+" samples written to "+outfile
^
SyntaxError: invalid syntax

Thanks,
Tom

Hi all. I am having trouble converting one of the output files in ipyrad to the finerad format. The alleles file for iPyrad v.0.9 is slightly different then previous version when using a reference genome, and I keep running into the following error when using the finerad_input.py script:

Traceback (most recent call last):
File "./fineRADstructure-tools/finerad_input.py", line 183, in
main()
File "./fineRADstructure-tools/finerad_input.py", line 176, in main
pyrad_to_finerad(filename, outfile, minsample)
File "./fineRADstructure-tools/finerad_input.py", line 101, in pyrad_to_finerad
snp += allele[pos]
IndexError: string index out of range

I noticed with a few changes that changing the way that the loci are identified helped a little. In this version, with reference genome, by the end of each loci you have an identifier like |0:Contig name:Position of locus in the contig|, instead of the simpler |0| with denovo assemblies. I think these colons are messing up the script a little bit, so I dropped all this extra info in the identifiers using sed, but the script still doesn't work. Funny thing is that if I subset my alleles file for the first locus only, it works, but when I try to use the script for the complete alleles file, it doesn't. Does anyone know how to address this issue?

Thank you.