mgkit.workflow.sampling_utils module¶
New in version 0.3.1.
Resampling Utilities¶
sample command¶
This command samples from a Fasta or FastQ file, based on a probability defined by the user (0.001 or 1 / 1000 by default, -r parameter), for a maximum number of sequences (100,000 by default, -x parameter). By default 1 sample is extracted, but as many as desired can be taken, by using the -n parameter.
The sequence file in input can be either be passed to the standard input or as last parameter on the command line. By defult a Fasta is expected, unless the -q parameter is passed.
The -p parameter specifies the prefix to be used, and if the output files can be gzipped using the -z parameter.
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mgkit.workflow.sampling_utils.
main
()¶ Main function
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mgkit.workflow.sampling_utils.
sample_command
(options)¶
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mgkit.workflow.sampling_utils.
set_parser
()¶ Sets command line arguments parser
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mgkit.workflow.sampling_utils.
set_sample_parser
(parser)¶