User: Tariq Daouda
Tariq Daouda • 210
- Reputation:
- 210
- Status:
- Trusted
- Location:
- IRIC | Institute for Research in Immunology and Cancer
- Website:
- http://www.tariqdaouda...
- Twitter:
- tariqdaouda
- Last seen:
- 2 years, 8 months ago
- Joined:
- 5 years, 4 months ago
- Email:
- t***********@umontreal.ca
Posts by Tariq Daouda
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... Hi Hao,
It was going well until it stopped at the indexing of exons. This is by far the biggest index that is automatically created.
Unfortunately, I can't tell you what caused the error since I don't have admin access to you computer. I can however give you some tips.
You need at least 2GB of fr ...
written 2.7 years ago by
Tariq Daouda • 210
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... Hi,
If you convert your hgnc_ids to ensembl ids using biomart and don't mind a bit of python, pyGeno allows you to do that quite easily by querying genes/transcripts/exons by ids. Here are some example snipets.
To get the 5' UTR of a transcript:
print trans.UTR5
To get the first exon:
p ...
written 4.7 years ago by
Tariq Daouda • 210
• updated
5 months ago by
RamRS ♦ 26k
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Answer:
A: FASTA and FASTQ tools
... Python
There's also the the parsers module of pyGeno. It supports: FASTA, FASTQ, VCF, GTF and CSV files. With an emphasis on simple and convenient interfaces.
...
written 4.9 years ago by
Tariq Daouda • 210
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... A very similar example of what you need is on the front page of pyGeno's website.
Here's a way to get what you're asking for:
from pyGeno.Genome import *
ref = Genome(name = "GRCh37.75") #or whatever other ref genome you've chosen to import
exons = ref.get(Exon, {"chromosome.number" : "2", "star ...
written 4.9 years ago by
Tariq Daouda • 210
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... If you have many sequences to fetch and don't mind a little python, pyGeno could also be good alternative.
...
written 4.9 years ago by
Tariq Daouda • 210
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... Hi,
There's a python package called pyGeno that can do that for you. It can can retrieve anything from anything including proteins from transcripts. You simply have to do protein.transcript. The same for proteins from transcripts, proteins from genes, genes from proteins, exons from transcripts etc ...
written 4.9 years ago by
Tariq Daouda • 210
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... Hi,
I have written a GTF parser, it is part of pyGeno but you can also download it separately from github. It should make the extraction easier.
from pyGeno.tools.parsers.GTFTools import GTFFile
gtf = GTFFile(gtfFilePath)
for line in gtf :
print line["gene_id"], line["gene_name"]
Cheers,
...
written 4.9 years ago by
Tariq Daouda • 210
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... pyGeno is also you friend. It does not require access to a REST API so it is more reliable and faster if you have a lot of proteins.
from pyGeno.Genome import *
ref = Genome(name = 'GRCh37.75')
prot = ref.get(Protein, id = 'ENSMUSP00000137272')[0]
And you also get all the information supplied b ...
written 5.0 years ago by
Tariq Daouda • 210
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... Thank you, your feedback is greatly appreciated.
...
written 5.0 years ago by
Tariq Daouda • 210
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... Thank you for bringing that up, the pip version was lagging behind. It is fixed now but I recommend the git version.
I had a look at the issue, the problem was that the folders containing the datawraps were not included in the pip version. But the rest of the installation went fine and you can impo ...
written 5.0 years ago by
Tariq Daouda • 210
Latest awards to Tariq Daouda
Appreciated
5.0 years ago,
created a post with more than 5 votes.
For pyGeno 1.2: Python package for Personalized Genomics and Proteomics
Scholar
5.1 years ago,
created an answer that has been accepted.
For A: How to extract DNA sequences for individual genes from GenBank complete genome f
Teacher
5.1 years ago,
created an answer with at least 3 up-votes.
For A: How to get gene name from coordinates using python.
Scholar
5.3 years ago,
created an answer that has been accepted.
For A: How to extract DNA sequences for individual genes from GenBank complete genome f
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