uludag

#!/usr/bin/python3

# Example script that queries UCSC DAS servers to retrieve 50 bases of sequence regions
# specified in an input file (format: chr5 + 12345)

import csv
from urllib.request import FancyURLopener

urlOpener = FancyURLopener()

uludag

#!/usr/bin/python3
"""
Example script to copy protein-lncRNA interactions from an input CSV file to a Neo4j Database

Example input file (header line expected, first 2 columns are protein identifiers):

    Source,UniprotName,Target,lncRNA_name
    NM_006428,RM28_HUMAN,ENSG00000278995,Z69720.3

"""

uludag

/*
   Example Node.js script to submit NCBI-BLAST sequence similarity searches
   on EMBL-EBI compute farms, input files can include multiple sequences.

   Before running this script install required node.js libraries:
   > npm install node-rest-client fasta-parser minimist querystring fs 

   Example command line:
   > node ebi-sss-nodejs-rest-client.js\
    --qseqsfile=your/query/sequences.fasta\

uludag

/*
   Example Node.js script to submit NCBI-BLAST sequence similarity searches
   to NCBI compute farms.

   https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=DeveloperInfo
  1.) Do not contact the server more often than once every three seconds.
  2.) Do not poll for any single RID more often than once a minute.
  3.) Use the URL parameter email, and tool, so that we can track your project
      and contact you if there is a problem.
  4.) Run scripts weekends or between 9 pm and 5 am Eastern Time weekday

uludag

#!/usr/bin/python
"""
Call genenames.org Biomart REST service to get gene names
and symbols for a given list of Ensembl gene ids.
Since this script uses the fetch API for each individual ID it is not fast
for large number of ids.
Script biomartxmlquery_gene_names_symbols.py[1] uses XML bulk queries
and is much faster when the number of ids are large.
[1] https://bitbucket.org/hspsdb/biomart-sample-clients/src
"""

uludag

#!/usr/bin/python
"""
Script to call genenames.org Biomart xml query service to get gene names
and symbols for a given list of Ensembl gene ids

Usage:
 > ./biomartxmlquery_gene_names_symbols.py --inputFile ensgeneids.txt > results.tsv

Input file: one Ensembl gene id per line
"""

uludag

#!/usr/bin/env python
# Sample UniProt sequence isoforms query
import requests

uniprotid = "P00750"

params = {"query": uniprotid, "format": "fasta", "include": "yes"}

response = requests.get("http://www.uniprot.org/uniprot/", params=params)