TorkamaniLab/bhuvan-s_utilities

Name: bhuvan-s_utilities

Owner: The Scripps Research Institute - Torkamani Lab

Description: null

Created: 2015-10-27 22:18:14.0

Updated: 2016-02-10 02:28:04.0

Pushed: 2017-10-04 22:33:54.0

Homepage: null

Size: 39

Language: Python

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README

Utility scripts

GTF Parser

Either performs proper sorting of GTF for PrimerSeq or checks if GTF is sorted. Note - The “score” field is parsed as a float and if it fails the str to float conversion then a value of 0.0 is assigned to it.

For Sorting GTF:

checking if GTF is sorted:  

Arguments:

-h, --help    show the help message and exit
-i GTF/GFF    Path to gtf file to sort
-f FileType   Valid options are 'gff' or 'gtf', default 'gtf'
-o OUTPUT     Path name of properly sorted gtf
-c IS_SORTED  Path to gtf file to check if sorted correctly
-v SORT_VARS  Comma separated list of vaiables to sort by, in the order that
              is desired. Attributes to be used should be mentioned after
              the key word attributes separated by a ":" and separated by a
              semicolon. For example -

              start,source,attributes:gene_id;transcript_id

Job Handler

Has a useful Jobs object which can be initialized using a python list object containing the commands for submitting a job.

Static Methods -

• get_job_status - Takes a job ID as input and returns the job status (R,H,C)
• multiple_jobs_completed - Takes a list of job IDs and returns True if all of them are completed/cancelled and False if even one is running.
• isRunning - Takes a job ID as input and returns True if the job is running else returns False

Bound Methods

submit_job - Submits the initialized job object to the cluster and returns the job ID