mrparse.mr_jpred module

Created on 14 Nov 2018

@author: jmht

class JPred(seq_info=None)

Bases: object

cleanup(results_directory)

static create_annotation(annotation)

find_results_file(jpred_rundir)

get_prediction(download_tgz=None, jpred_output=None, cleanup=False)

Calculate SS using the online JPRED server

Parameters

• download_tgz (str) – A results tar.gz file from the JPRED server - FOR RUNNING UNIT TESTS

• jpred_output (str) – A results file from the JPRED server - FOR RUNNING UNIT TESTS

• cleanup (bool) – Delete the downloaded/unpacked results

get_results(jobid)

Check results and download from the server

static parse_jpred_output(out_concise)

static parse_results_output(output)

Parse directory path of JPRED

Your job status will be checked with the following parameters: JobId: jp_H_5vG49 getResults: yes checkEvery: 10 [sec] Thu Nov 29 15:02:01 2018 —> Job jp_H_5vG49 finished. Results available at the following URL: http://www.compbio.dundee.ac.uk/jpred4/results/jp_H_5vG49/jp_H_5vG49.results.html

Will attempt to download results now (using ‘wget’) from: http://www.compbio.dundee.ac.uk/jpred4/results/jp_H_5vG49/jp_H_5vG49.tar.gz

Job results archive is now available at: jp_H_5vG49/jp_H_5vG49.tar.gz

static parse_status_url(output)

Parse jobid and status url for JPRED

Your job will be submitted with the following parameters: file: ../data/Q13586.fasta format: seq skipPDB: on email: jens.thomas@liverpool.ac.uk name: jens_test_job

Created JPred job with jobid: jp_H_5vG49 You can check the status of the job using the following URL: http://www.compbio.dundee.ac.uk/jpred4/cgi-bin/chklog?jp_H_5vG49 …or using ‘perl jpredapi status jobid=jp_H_5vG49 getResults=yes checkEvery=60 silent’ command (Check documentation for more details.)

run_jpred(seqin)

submit_job(seqin)

unpack_results(download_tgz)

exception OutOfTimeException

Bases: Exception