WSDL API

You can submit your jobs and fetching results in command line by the WSDL API scripts below

Usage: prodres_wsdl.py -m submit|get [-seq SEQFILE] [-jobname NAME] [-email EMAIL]
                                     [-jobid JOBID] [-outpath DIR]


Description:
    Access the PRODRES web-server (http://prodres.bioinfo.se) through WSDL service

OPTIONS:
  -m submit|get  Set the mode
                 submit - submit a job to WSDL
                 get    - retrieve the result from the server

  -seq    FILE   Supply input sequence in FASTA format

  -jobname STR   Give the job a name

  -email   STR   Send a notification to the email when the result is ready

  -jobid   STR   Retrieve the result by supplying a valid jobid

  -outpath DIR   Save the retrieved data to outpath, (default: ./)

  -h, --help     Print this help message and exit

Advanced options:
  -second-search STR             Choose method for second round search,
                                 psiblast or jackhmmer (default: psiblast)
  -pfamscan_bitscore FLOAT       Set bit-score threshold for PfamScan, (default: 2)

  -pfamscan_e-val    FLOAT       Set e-value threshold for PfamScan, (default: None)

  -pfamscan_clan-overlap yes|no  Whether use PfamScan clan overlapping, (default: yes)

  -jackhmmer-threshold-type  e-value|bit-score
                                 Set the threshold type for jackhmmer, (default: bit-score)

  -jackhmmer_bitscore FLOAT      Set bit-score threshold for jackhmmer, (default: 25)

  -jackhmmer_e-val    FLOAT      Set e-value threshold for jackhmmer, (default: None)

  -jackhmmer_max_iter INT        Set maximum iterations for jackhmmer, (default: 3)

  -psiblast_e-val     FLOAT      Set e-value threshold for psiblast, (default: 0.1)

  -psiblast_iter      INT        Set maximum iterations for psiblast, (default: 3)

  -psiblast_outfmt    STR        Set output format for psiblast, (default: 0)

  Note that for the option sets {-jackhmmer_e-val, -jackhmmer_bitscore} and 
  {-pfamscan_e-val, -pfamscan_bitscore}, only one of them can be set.

Created 2017-02-06, updated 2017-02-07, Nanjiang Shu


Examples:
    # submit test.fa with jobname 'test' to the server 
    prodres_wsdl.py -m submit -seq test.fa -jobname test

    # try to retrieve the result for jobid 'rst_TTT' and save it to the current
    # directory
    prodres_wsdl.py -m get -jobid rst_TTT