Moderator: Medhat

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Medhat8.2k
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Location:
Texas
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http://combio.pl/
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6 years, 3 months ago
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m*************@gmail.com

 Computational biology PhD, Software engineer. love programming using Java, Python and R. Thrive on challenges and live for breakthroughs (and coffee). working on  data analysis,genome assembly and comparative analysis.  also interested in evolution and mutations and phylogenetics.  Where others say “that’s impossible”,I say “when do I start?” (usually after a cup of coffee).

Posts by Medhat

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News: Workshop for Comparative genomics with a focus on structural variation
... **OVERVIEW** This course will introduce biologists and bioinformaticians into the field of comparative genomics. We will cover a broad range of software and analysis workflows that extend over the spectrum from assembling and annotating small eukaryotic genomes, via the identification of single nuc ...
genome news structural variant written 4 hours ago by Medhat8.2k
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Comment: C: VOR BIOPHARMA - Job Posting - Scientist / Sr. Scientist Bioinformatics
... I assume this is the company website http://www.vorbiopharma.com/ (correct me If I am wrong). I put it here in case someone want to know more about the company. ...
written 27 days ago by Medhat8.2k
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Comment: C: Reading vcf file using python gives UnicodeDecodeError
... I do not have access now But what you are suggesting is really interesting, I will try and keep you updates (when using bcftools there were no errors) ...
written 6 weeks ago by Medhat8.2k
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Comment: C: Reading vcf file using python gives UnicodeDecodeError
... The old file was data as I mentioned in a comment on your answer. https://www.biostars.org/p/362177/#362321 ...
written 6 weeks ago by Medhat8.2k
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Comment: C: Reading vcf file using python gives UnicodeDecodeError
... Yes I will just stay with file from vcftools ...
written 6 weeks ago by Medhat8.2k
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Comment: C: Reading vcf file using python gives UnicodeDecodeError
... I tryied your suggestion using: `-O z -o result.vcf.gz` But still have `(result, consumed) = self._buffer_decode(data, self.errors, final) UnicodeDecodeError: 'utf-8' codec can't decode byte 0x9d in position 8116: invalid start byte` ...
written 6 weeks ago by Medhat8.2k
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Answer: A: Reading vcf file using python gives UnicodeDecodeError
... So I manage to work around , but did not fix the issue. The original file was a result of using `bcftools merge A.vcf B.vcf C.vcf > someresult.vcf` and that gave me the error above. But when using `vcf-merge A.vcf B.vcf C.vcf > someresult.vcf` The issue was fixed. This does not clearly an ...
written 6 weeks ago by Medhat8.2k
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Comment: C: Reading vcf file using python gives UnicodeDecodeError
... when using: `with open(myfile, 'r', encoding="ascii") as datain:` It changes the error to : `UnicodeDecodeError: 'ascii' codec can't decode byte 0x9d in position 8077: ordinal not in range(128)` ...
written 6 weeks ago by Medhat8.2k
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Comment: C: Reading vcf file using python gives UnicodeDecodeError
... @ https://www.biostars.org/u/41557/ If I used the code like: `myline = myline.encode('utf-8').strip()` It will give this error: `TypeError: startswith first arg must be bytes or a tuple of bytes, not str` Then I could use `str()` but this will not help in fixing the main issue. ...
written 6 weeks ago by Medhat8.2k
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Comment: C: Reading vcf file using python gives UnicodeDecodeError
... The file is `data` also the loop does not fail in the first line it reads couple of hundreds of line then raise that error. ...
written 6 weeks ago by Medhat8.2k

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