User: zorbax

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zorbax130
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130
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Location:
Mexico
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1 month, 3 weeks ago
Joined:
6 years, 3 months ago
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Posts by zorbax

<prev • 24 results • page 1 of 3 • next >
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Comment: C: Error while running vcf2maf tool
... use the `${variable}` syntax in all your variables to avoid expansion. ...
written 10 weeks ago by zorbax130
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Comment: C: GLIBC error when trying to use sra-toolkit
... Two things about this. First, if you have conda, why don't you install sra-toolkit in an environment? Second, you should use the 'system gcc', not the gcc conda version. You have a gcc-7.3, you should be able to compile glibc-2.14 with a gcc > 2.5 List the installed compilers with `sudo dpkg --l ...
written 10 weeks ago by zorbax130
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Answer: A: GLIBC error when trying to use sra-toolkit
... Use [ENA directly][1], is faster. Anyway, if you want to use `sra-toolkit` in Debian 7 you can try install the 2.14 version. mkdir -p ~/glibc214 && cd "$_" wget http://ftp.gnu.org/gnu/glibc/glibc-2.14.tar.gz tar zxvf glibc-2.14.tar.gz && rm glibc-2.14.tar.gz cd glib ...
written 10 weeks ago by zorbax130
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Comment: C: GLIBC error when trying to use sra-toolkit
... Which version of GLIBC are you using in Debian 7? Use `ldd --version` ...
written 10 weeks ago by zorbax130
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Comment: C: How can I run a Biopython qblast search targeting a specific set of organisms?
... You can use boolean search, something like `"all [filter] NOT(environmental samples[organism] OR metagenomes[orgn]) AND txid3702[ORGN] AND txid9606[ORGN]"` This example exclude environmental/metagenomic sampels and include human in the search. ...
written 12 weeks ago by zorbax130
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Answer: A: Drop values in expression dataset python
... Cross-posted here https://stackoverflow.com/questions/61890315/merge-probes-and-gene-ids-with-geoparse Answered here: https://stackoverflow.com/questions/61907186/drop-values-in-expression-dataset-python ...
written 12 weeks ago by zorbax130
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Answer: A: How can I run a Biopython qblast search targeting a specific set of organisms?
... You need to use `txid3702[ORGN]`, I tested this with the Calvin cycle protein CP12-2: import urllib.request from Bio import SeqIO from Bio.Blast import NCBIWWW url = 'https://www.uniprot.org/uniprot/Q9LZP9.fasta' urllib.request.urlretrieve(url, "chain_N.faa") record = ...
written 12 weeks ago by zorbax130
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Comment: C: Python & orthomcl parsing output
... try with python3 instead. ...
written 3 months ago by zorbax130
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Answer: A: Error when converting/translating .tsv ORFs to .faa
... If you want to save the sequence in fasta format and the translation using the function `translate()` of the method `Seq` #!/usr/bin/env python3 import sys import pandas as pd from Bio import SeqIO from Bio.Seq import Seq from Bio.SeqRecord import SeqRecord inpu ...
written 4 months ago by zorbax130
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Comment: C: Error when converting/translating .tsv ORFs to .faa
... In `from Bio import SeqRecord` you should use `Bio.SeqRecord import SeqRecord` instead. Have you considered the six frame translations? you can use `from Bio.SeqUtils import six_frame_translations` ...
written 4 months ago by zorbax130

Latest awards to zorbax

Scholar 4 months ago, created an answer that has been accepted. For A: Error when converting/translating .tsv ORFs to .faa

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