/PCRTilerRubyClient

Primary LanguageRuby

Several convenient functions to interact with the PCRTiler servlet.

Create job

require 'pcr_tiler_client'

PCRTiler_BASE_URL = 'http://pcrtiler.alaingervais.org:8080/PCRTiler'

params = {
  'sequence' => 'ACCAATGGTGGCGCGATGTAACACGAGAAAGCACATACCAAGGCCACCACACACCACCTGTCCAAAAAGGCCTTCGATACGGGATAATCCTATTTATTACCTCAGAAGTTTTTTTCTTCGCAGGATTTTTCTGAGCCTTTTACCACTCCAGCCTAGCCCCTACCCCCCAACTAGGAGGGCACTGGCCCCCAACAGGCATCAACCAATGGTGGCGCGATGTAACACGAGAAAGCACATACCAAGGCCACCACACACCACCTGTCCAAAAAGGCCTTCGATACGGGATAATCCTATTTATTACCTCAGAAGTTTTTTTCTTCGCAGGATTTTTCTGAGCCTTTTACCACTCCAGCCTAGCCCCTACCCCCCAACTAGGAGGGCACTGGCCCCCAACAGGCATCAACCAATGGTGGCGCGATGTAACACGAGAAAGCACATACCAAGGCCACCACACACCACCTGTCCAAAAAGGCCTTCGATACGGGATAATCCTATTTATTACCTCAGAAGTTTTTTTCTTCGCAGGATTTTTCTGAGCCTTTTACCACTCCAGCCTAGCCCCTACCCCCCAACTAGGAGGGCACTGGCCCCCAACAGGCATCA',
  'organism' => 'Homo_sapiens'
}
id = PCRTiler.post_job(PCRTiler_BASE_URL, params)

If you don't specify other params, they will take default values:

job_name=PCRTilerRubyClient

minimum_tm=60
maximum_tm=63
minimum_length=100
maximum_length=150

segmentation_type=primer_pair_count
primer_pair_count=20
primer_target_length=200

filter=

total_mismatches=4
three_prime_mismatches=2
number_of_candidates=1000
distance_threshold=3000

program=blastn

email=

Check job result

result = PCRTiler.check_job(PCRTiler_BASE_URL, id)

result examples:

  • {:status => 'queued'}
  • {:status => 'doing', :done => 10, :total => 16}
  • {:status => 'done', :txt => 'Oligos for job No name...'}