Variants filtering issue

[Riccardo Altea]

Hello, I'm trying to filter variants from vcf files obtained using lobSTR. I get some errors while calling lobSTR_filter_vcf.py script:

Traceback (most recent call last):
  File "/home/rich/Scrivania/Tool_Espansioni/lobSTR-bin-Linux-x86_64-4.0.6/share/lobSTR/scripts/lobSTR_filter_vcf.py", line 97, in <module>
    reader = vcf.Reader(open(args.vcf, "rb"))
  File "/home/rich/miniconda3/lib/python3.6/site-packages/vcf/parser.py", line 300, in __init__
    self._parse_metainfo()
  File "/home/rich/miniconda3/lib/python3.6/site-packages/vcf/parser.py", line 319, in _parse_metainfo
    while line.startswith('##'):
TypeError: startswith first arg must be bytes or a tuple of bytes, not str

I don't know Python language, but I found that writing the letter 'b' before '##' should solve my problem. When I do this, I get new error messages:

Traceback (most recent call last):
  File "/home/rich/Scrivania/Tool_Espansioni/lobSTR-bin-Linux-x86_64-4.0.6/share/lobSTR/scripts/lobSTR_filter_vcf.py", line 97, in <module>
    reader = vcf.Reader(open(args.vcf, "rb"))
  File "/home/rich/miniconda3/lib/python3.6/site-packages/vcf/parser.py", line 300, in __init__
    self._parse_metainfo()
  File "/home/rich/miniconda3/lib/python3.6/site-packages/vcf/parser.py", line 353, in _parse_metainfo
    fields = self._row_pattern.split(line[1:])
TypeError: cannot use a string pattern on a bytes-like object

Probably I should not edit the scripts, but I've been trying for over a week and didn't manage to solve this...Any suggestions?

[Melissa Gymrek]

Dear Ricardo,

Thanks for your message. I recommend you use the updated HipSTR tool instead:

https://github.com/tfwillems/HipSTR

There are many new features and bug fixes since the last release of lobSTR.
~M

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[RICCARDO ALTEA]

Thanks for your answer, I was using both tools!

2018-09-05 17:37 GMT+02:00 Melissa Gymrek <melissa...@gmail.com>:

Dear Ricardo,

Thanks for your message. I recommend you use the updated HipSTR tool instead:

https://github.com/tfwillems/HipSTR

There are many new features and bug fixes since the last release of lobSTR.
~M

On Tue, Sep 4, 2018 at 5:53 AM Riccardo Altea <riccardo.altea01@universitadipavia.it> wrote:

Hello, I'm trying to filter variants from vcf files obtained using lobSTR. I get some errors while calling lobSTR_filter_vcf.py script:

Traceback (most recent call last):
  File "/home/rich/Scrivania/Tool_Espansioni/lobSTR-bin-Linux-x86_64-4.0.6/share/lobSTR/scripts/lobSTR_filter_vcf.py", line 97, in <module>
    reader = vcf.Reader(open(args.vcf, "rb"))
  File "/home/rich/miniconda3/lib/python3.6/site-packages/vcf/parser.py", line 300, in __init__
    self._parse_metainfo()
  File "/home/rich/miniconda3/lib/python3.6/site-packages/vcf/parser.py", line 319, in _parse_metainfo
    while line.startswith('##'):
TypeError: startswith first arg must be bytes or a tuple of bytes, not str

I don't know Python language, but I found that writing the letter 'b' before '##' should solve my problem. When I do this, I get new error messages:

Traceback (most recent call last):
  File "/home/rich/Scrivania/Tool_Espansioni/lobSTR-bin-Linux-x86_64-4.0.6/share/lobSTR/scripts/lobSTR_filter_vcf.py", line 97, in <module>
    reader = vcf.Reader(open(args.vcf, "rb"))
  File "/home/rich/miniconda3/lib/python3.6/site-packages/vcf/parser.py", line 300, in __init__
    self._parse_metainfo()
  File "/home/rich/miniconda3/lib/python3.6/site-packages/vcf/parser.py", line 353, in _parse_metainfo
    fields = self._row_pattern.split(line[1:])
TypeError: cannot use a string pattern on a bytes-like object

Probably I should not edit the scripts, but I've been trying for over a week and didn't manage to solve this...Any suggestions?

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