User: Tariq Daouda

gravatar for Tariq Daouda
Tariq Daouda190
Reputation:
190
Status:
Trusted
Location:
IRIC | Institute for Research in Immunology and Cancer
Website:
http://www.tariqdaouda...
Twitter:
tariqdaouda
Last seen:
6 days, 20 hours ago
Joined:
2 years, 8 months ago
Email:
t***********@umontreal.ca

Posts by Tariq Daouda

<prev • 28 results • page 1 of 3 • next >
0
votes
4
answers
900
views
4
answers
Answer: A: pyGeno 1.2: Python package for Personalized Genomics and Proteomics
... 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 8 days ago by Tariq Daouda190
0
votes
2
answers
814
views
2
answers
Answer: A: querying 5'UTR, first exon, and flanking sequences
... 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: print tr ...
written 2.0 years ago by Tariq Daouda190
2
votes
1
answer
3.5k
views
1
answers
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 2.2 years ago by Tariq Daouda190
1
vote
2
answers
911
views
2
answers
Answer: A: Ensembl & biomaRt: extracting in-frame codons near specified position
... 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 2.2 years ago by Tariq Daouda190
0
votes
2
answers
794
views
2
answers
Answer: A: Ensembl REST requests for CDS sequences returning AA sequences
... If you have many sequences to fetch and don't mind a little python, pyGeno could also be good alternative. ...
written 2.3 years ago by Tariq Daouda190
0
votes
2
answers
1.6k
views
2
answers
Answer: A: Ensembl REST: How to retrieve CDS from a protein id?
... 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 2.3 years ago by Tariq Daouda190
0
votes
5
answers
4.4k
views
5
answers
Answer: A: extract only geneID and gene symbol from GTF file
... 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 2.3 years ago by Tariq Daouda190
1
vote
3
answers
1.1k
views
3
answers
Answer: A: From Ensembl protein ID to sequence
... 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 2.4 years ago by Tariq Daouda190
0
votes
4
answers
900
views
4
answers
Comment: C: pyGeno 1.2: Python package for Personalized Genomics and Proteomics
... Thank you, your feedback is greatly appreciated. ...
written 2.4 years ago by Tariq Daouda190
0
votes
4
answers
900
views
4
answers
Comment: C: pyGeno 1.2: Python package for Personalized Genomics and Proteomics
... 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 2.4 years ago by Tariq Daouda190

Latest awards to Tariq Daouda

Appreciated 2.4 years ago, created a post with more than 5 votes. For pyGeno 1.2: Python package for Personalized Genomics and Proteomics
Scholar 2.5 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 2.5 years ago, created an answer with at least 3 up-votes. For A: How to get gene name from coordinates using python.
Scholar 2.7 years ago, created an answer that has been accepted. For A: How to extract DNA sequences for individual genes from GenBank complete genome f

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1444 users visited in the last hour