humanlongevity/tredparse

TREDPARSE: HLI Short Tandem Repeat (STR) caller

tredparse's Issues

Filter results based on FullReads, PartialReads, RepeatReads, PairedReads?

Hi,

Thanks for developing such a useful tool.

I wonder if we need to filter the calls based on such as FullReads, PartialReads, RepeatReads, PairedReads.

If the answer is YES, could you please show some filtering cretiria?

Thanks in advance.

Bests,
Yiwei

problem with reference genome (hg19_nochr)

Hi,
I'm trying to use Tredparse against some samples aligned on hg19_nochr. The calling seems to works fine (ends without errors). However, reports are outputs on hg38 coordinates and samples are always treated as females (the gender can't be inferred).

Here is my code:
tred.py samples.csv --ref hg19_nochr --workdir test
tredreport.py test/*.json --tsv test.tsv --ref hg19

And here are some output.

AX1401.tred.vcf.gz:

X 146993569 FXTAS CGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGG CGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGG . . END=146993628;MOTIF=CGG;NS=1;REF=20;CR=55;IH=XLD;RL=60;VT=STR;RPA=30 GT:GB:FR:PR:RR:DP:FDP:PDP:RDP:PEDP:CI:PP:LABEL 1/1:30/30:30|8:4|1;5|2;7|1;8|1;10|2;12|1;13|3;14|2;18|1;20|2;22|1;24|1;25|1;26|1;30|1:50|1:24.8762135922:8:21:1:19:30-30|30-65:0.1425:ok

test.tsv.cases.txt:

[FXTAS] - Fragile X-associated tremor/ataxia syndrome
rep=CGG inherit=XLD cutoff=55 n_risk=8 n_carrier=0 loc=chrX:147912051-147912110
SampleKey inferredGender FXTAS.calls FXTAS.FR FXTAS.PR FXTAS.RR FXTAS.PP
AX1401 Unknown 30|57 30|7 ...|3;26|1;29|1;30|5;32|2;33|1 50|3 0.821746

tred.py --version

tred.pyc 0.7.8

Note: in the VCF file, the coordinates are correctly mapped to FXTAS on hg19, but in the report file corresponds to hg38.

Can't run tred.py: multiple exceptions

Given Centos 6.x, Python 2.7.7 installed to custom NFS directory, tred.py, and a correctly-formatted CVS file, an end-user gets these errors:

ERROR:tredparse.tred:Exception on /<path_to_data1>/data1.bam DM1 (init() got an unexpected keyword argument 'mismatch')
ERROR:tredparse.tred:Exception on /<path_to_data1>/data2.bam HD (init() got an unexpected keyword argument 'mismatch')

We also have Python 3.6.1, but I don't believe your tredparse item works for that. Do you have any leads on this type of error?

Regards,
W. John Burns

ERROR when using tredreport.py

hi!! I am trying to use your tool for analyzing HTT sequences. I think I correctly installed the program, since I have been able to use the first script without errors (tred.py). However, when I have to run the tredreport.py (using as input the .json file generated previously), I obtained this error:

Using 1 cpus to parse 1 JSON files
/media/sequentia/visitors/visitor4/HTT/tredparse/tredparse/tredreport.py:135: FutureWarning: '.reindex_axis' is deprecated and will be removed in a future version. Use '.reindex' instead.
tf = df.reindex_axis(columns, axis='columns')
TSV output written to out.tsv (# samples=1)
Traceback (most recent call last):
File "tredreport.py", line 20, in
main(sys.argv[1:])
File "/media/sequentia/visitors/visitor4/HTT/tredparse/tredparse/tredreport.py", line 274, in main
casesfw=casesfw, detailsfw=detailsfw)
File "/media/sequentia/visitors/visitor4/HTT/tredparse/tredparse/tredreport.py", line 52, in get_tred_summary
carrier = df[(df[label] != "risk") & (df[pf2] >= cutoff_risk)]
File "/home/visitor4/.local/lib/python2.7/site-packages/pandas/core/ops.py", line 1766, in wrapper
res = na_op(values, other)
File "/home/visitor4/.local/lib/python2.7/site-packages/pandas/core/ops.py", line 1651, in na_op
return invalid_comparison(x, y, op)
File "/home/visitor4/.local/lib/python2.7/site-packages/pandas/core/ops.py", line 1058, in invalid_comparison
.format(dtype=left.dtype, typ=type(right).name))
TypeError: Invalid comparison between dtype=int64 and str

Maybe I am making some mistakes, have you any suggestions?

Thanks you,

Cannot find tredprepare.py

Hello. I'm trying to add loci to be searched for, but I don't see tredprepare.py anywhere.

tred.py not working with test data

Hi,

For my case, i created a virtual environment that has python 2.7.18 , installed tredparse in this virtual environment and git clone the tredparse repository. I have the following questions regarding the tool:

1. I understand that using the tredprepare.py, we can add additional str regions. Would your tool work with repeats that are dinucleotide repeats?

2. After running the tredprepare.py, i opened the .json file to fill in the additional details:
   
   Could i check which are optional and what is the difference between motif and repeat?

3. Lastly, i tried tred.py tests/samples.csv --workdir work but there was an error:
   

Thank you !

FMR1 Gene

Hi,

I would like to know if this tool can be used to get CGG repeats in FMR1 gene?

I found in a publication that they were able to get the repeats from this gene, but in the TRED list I could not find this gene.

Please help.

Server Installation

Is there a target environment for installing the web based application? I have tried the instructions in both Ubuntu 16.04 and Ubuntu 18.04 on AWS and have gotten errors related to compilation of node-gyp, fibers, and bcrypt. Any guidance would be appreciated.

Ken

I wonder if it is possible to use a custom genome as ref?

I wonder if it is possible to use a custom genome as ref? such as cotton?