User: duxan

gravatar for duxan
duxan50
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50
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New User
Location:
Serbia/Novi Sad
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dooxan
Last seen:
1 year, 7 months ago
Joined:
3 years, 3 months ago
Email:
d****************@sbgenomics.com

Posts by duxan

<prev • 6 results • page 1 of 1 • next >
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Answer: A: Meaning Of N_Alleles And N_Chr In .Frq Files
... On this [thread][1] from vcftools mailing list: N_ALLELES represents number of different alt alleles + reference allele, and N_CHR is number of chromosomes that have data for that locus (usually #samples_covering_locus x 2). [1]: https://sourceforge.net/p/vcftools/mailman/message/30908984/ ...
written 23 months ago by duxan50
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Answer: A: How can I produce a fasta file from a GTF file containing my isoforms?
... Hi, I have tried [Cufflinks gffread][1] and [Tophat gtf_to_fasta][2]. Tophat returns some strange headers, but Cufflinks *gffread* works great: ``` gffread -w transcripts.fa -g /path/to/genome.fa transcripts.gtf ``` Note that genome.fa need to have contigs with same names as in transcripts.gtf &g ...
written 3.0 years ago by duxan50
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Answer: A: Reading CRAM files in pysam
... It seems that pysam doesn't recognize your file as CRAM. You can check this by: cram.is_bam and cram.is_cram. From the source you can see a way how you can hack it (since I haven't found this in documentation, it is safe to call it a hack) by setting mode to 'rc' instead of 'rb'. This same issue is ...
written 3.2 years ago by duxan50
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Comment: C: cannot import pysam. Module has no attribute error
... Good point about aliases, especially since it seems nothing else changed dramatically in pysam/samtools. As for managing packages with anaconda - another way to add a package into conda env would be to search for different versions of it into [public channels](https://anaconda.org/search?q=pysam). ...
written 3.2 years ago by duxan50 • updated 6 months ago by RamRS20k
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Answer: A: cannot import pysam. Module has no attribute error
... As @rtliu suggested, you should install latest version of *pysam*, which does have AlignmentFile in API to samtools (from [version 0.8.1](http://pysam.readthedocs.org/en/latest/release.html#release-0-8-1)). To do that inside *conda* environment, you should first activate the environment you are usin ...
written 3.2 years ago by duxan50 • updated 6 months ago by RamRS20k
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Comment: C: Python IndexError: list index out of range
... Can you show a snippet of PhenoSNPs.csv file? It seems like your script doesn-t parse it well. In script, on line 19, you use ";" as delimiter and my guess is that maybe CSV has commas. ...
written 3.3 years ago by duxan50

Latest awards to duxan

Scholar 3.2 years ago, created an answer that has been accepted. For A: cannot import pysam. Module has no attribute error

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