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WansonChoi / CookHLA

An accurate and efficient HLA imputation method.
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[5] Converting out imputation result(s) with TypeError: expected string or bytes-like object #12

Open masen1991 opened 2 years ago

masen1991 commented 2 years ago

@WansonChoi
Thanks for making this tools. When i use Pan-Asian reference panel to do imputation ,on final step Converting out imputation result(s),it will report TypeError: expected string or bytes-like object. Pan_Asina_REF_log.txt

I would be grateful if you could shed some light on this.

WansonChoi commented 2 years ago

@masen0407

Hi, masen0407.

It seems the 9 imputations were successful, but the HLA type calling step failed.

Could you attach these 9 VCF files of the imputation results? (or email them to me)?

masen1991 commented 2 years ago

@WansonChoi i try to send you tar.gz filr by email,but mymail is returned for Connection to the remote recipient's server was denied for unknown reason.

WansonChoi commented 2 years ago

@masen0407

I received the file well and replied by e-mail today.

Xuling-SC commented 2 years ago

@WansonChoi Thanks for making this tools. When i use Pan-Asian reference panel to do imputation ,on final step Converting out imputation result(s),it will report TypeError: expected string or bytes-like object. Pan_Asina_REF_log.txt

I would be grateful if you could shed some light on this.

Hi，@masen0407，I have encountered the same problem as you. I wonder if you have solved it now? If so, could you provide a solution please?

PoojaMiddha commented 1 year ago

Hi @masen0407 and @WansonChoi I am encountering the same problem while using the T1GDC reference panel. Were you able to solve this issue and if yes, how? Thank you.

Xuling-SC commented 1 year ago

Replace line 21 of the ALLELES2HPED.py file drop with the following：  f_4digit = df_alleles.applymap(lambda x : (bool(p_4digit_pair.match(str(x))) and (not bool(re.match(r'^,$', str(x)))))).apply(lambda x : x.any(), axis=0)

------------------ 原始邮件 ------------------ 发件人: "WansonChoi/CookHLA" @.>; 发送时间: 2023年2月7日(星期二) 凌晨3:19 @.>; 抄送: "Say @.**@.>; 主题: Re: [WansonChoi/CookHLA] [5] Converting out imputation result(s) with TypeError: expected string or bytes-like object (Issue #12)

Hi @masen0407 and @WansonChoi I am encountering the same problem while using the T1GDC reference panel. Were you able to solve this issue and if yes, how? Thank you.

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PoojaMiddha commented 1 year ago

Thank you @Xuling-SC. It worked :)