Script cd_hit_para_CCRT_py

source code

Launch cd-hit program in a parallel mode compatible with the CCRT architecture.

Requires:

python (tested with 2.7.5)
cd-hit (tested with v4.5.8-2012-03-24)
Input : a FASTA file Output : a clustering FASTA

Functions

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get_parser()

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string

launchJobCCRT(filename, jobDependency=None)
launch the ccc_msub commande with a bash script as arguments and optionnally a job ID for the job dependency.

source code

writeJobScript(filename, cores, task, queue, projid)
Create the job parser script header

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main()

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Variables

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__doc__ = ...

__package__ = None

Function Details

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launchJobCCRT(filename, jobDependency=None)

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launch the ccc_msub commande with a bash script as arguments and optionnally a job ID for the job dependency. Then this function recovers and return the job ID generated.

Parameters:

filename (string) - bash script file name
jobDependency (string) - put an "after" dependency on the set of jobs defined as the argument.\ The submitted job will only be started when the jobs corresponding to the provided ids are terminated.

Returns: string

job ID

writeJobScript(filename, cores, task, queue, projid)

source code

Create the job parser script header

Parameters:

filename (string) - bash script file name
cores (integer) - cores number reserved
task (integer) - max task number
queue (string) - requested queue

Variables Details

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doc

Value:

"""
Launch cd-hit program in a parallel mode compatible with the CCRT arch
itecture.

@requires: U{python<https://github.com/lh3/seqtk>} (tested with 2.7.5)
@requires: U{cd-hit<https://code.google.com/p/cdhit/downloads/list>} (
tested with v4.5.8-2012-03-24)

...