issues Search Results · repo:gyorilab/protmapper language:Python

Filter by

• • Code... (...)results
  • Issues7 (7)results
  • Pull requests40 (40)results
  • Discussions0 (0)results
  • Commits0 (0)results
  • Packages0 (0)results
  • Wikis0 (0)results

• State

  • Open
  • Closed

• Advanced

  • Owner
  • State
  • Close reason
  • Has linked pull request
  • Author
  • Assignee
  • Mentioned user
  • Mentioned team
  • Commenter
  • Involved user
  • Label
  • Milestone
  • Number of comments
  • Number of interactions
• Advanced search

Issues7 (7)

7 results

 (87 ms)

7 results

ingyorilab/protmapper (press backspace or delete to remove)

Sort by: Best match

Filter

gyorilab/protmapper

Migrate UniProt resources to new web service

The UniProt legacy web service was recently permanently shut down so we need to follow up https://github.com/indralab/protmapper/pull/43 with a full migration to the new data standards.

• bgyori
·
• Opened 
  on Jun 12, 2023
·
• #44

gyorilab/protmapper

Rdflib issue on Github actions

A new issue just appeared related to rdflib: ====================================================================== ERROR: test_uniprot_client.test_get_modifications ---------------------------------------------------------------------- ...

• bgyori
·
• 1
·
• Opened 
  on Oct 25, 2021
·
• #40

gyorilab/protmapper

Problematic Entrez ID

The GNAS gene (https://www.ncbi.nlm.nih.gov/gene/2778) seems to make protmapper upset. Try the following code: from protmapper.uniprot_client import get_gene_name, get_id_from_entrez entrez_id = 2778 ...

• cthoyt
·
• 5
·
• Opened 
  on Aug 10, 2020
·
• #30

gyorilab/protmapper

Add entrez identifier conversions

I think it would be very helpful to have functions to get the UniProt identifier for a given entrez identifier, and get the entrez identifier for a given UniProt identifier

• cthoyt
·
• 3
·
• Opened 
  on May 26, 2020
·
• #28

gyorilab/protmapper

Issue when mapping peptides to uniprot non-base isoforms

from protmapper import ProtMapper pm = ProtMapper() pm.map_peptide( Q8N3V7-2 , LPAGPSSCTSPRS , 7) correctly returns the site position 834, but pm.map_peptide_to_human_ref( Q8N3V7-2 , uniprot , LPAGPSSCTSPRS ...

• FFroehlich
·
• 6
·
• Opened 
  on Jul 2, 2019
·
• #18

gyorilab/protmapper

Issues when mapping non-unique HGNC ids

The code from protmapper import ProtMapper pm = ProtMapper() pm.map_peptide_to_human_ref( TMPO , hgnc , RKVPRLSEKSVEE , 7) fails with the following error message: --------------------------------------------------------------------------- ...

• FFroehlich
·
• 3
·
• Opened 
  on Jul 2, 2019
·
• #16

gyorilab/protmapper

Error in refseq download

====================================================================== ERROR: test_uniprot_client.test_get_ids_from_refseq ---------------------------------------------------------------------- Traceback ...

• bgyori
·
• 1
·
• Opened 
  on Mar 6, 2019
·
• #9

Learn how you can use GitHub Issues to plan and track your work.

Save views for sprints, backlogs, teams, or releases. Rank, sort, and filter issues to suit the occasion. The possibilities are endless.Learn more about GitHub Issues

ProTip! 

Restrict your search to the title by using the in:title qualifier.

Learn how you can use GitHub Issues to plan and track your work.

Save views for sprints, backlogs, teams, or releases. Rank, sort, and filter issues to suit the occasion. The possibilities are endless.Learn more about GitHub Issues

ProTip! 

Press the

/

key to activate the search input again and adjust your query.