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Description:
this script outputs a new otu table and mapping file with some samples removed and replaced with one pooled sample. the new pooled sample will have fields in the mapping file the same as its constituent samples, if all are idential. Else it will just say ‘multipleValues’.
Usage: pool_by_metadata.py [options]
Input Arguments:
Note
[REQUIRED]
[OPTIONAL]
Output:
The result is a pooled OTU table and mapping file.
Examples:
The following command pools all the Control samples into one sample named ‘pooledControl’. The resulting data is written to seqs_otus.txt.filtered.xls and Fasting_Map.txt.filtered.xls:
pool_by_metadata.py -i seqs_otus.txt -m Fasting_Map.txt -s 'Treatment:Control' -l pooledControl
Some variations are:
Pooling all samples in both Control and Fast in the Treatment field (i.e. pooling everything):
pool_by_metadata.py -i seqs_otus.txt -m Fasting_Map.txt -s 'Treatment:Control,Fast' -l pooledSamples
Excluding Fast in the Treatment field - the syntax here is “*” to keep everything, then !Fast to eliminate the Fast group:
pool_by_metadata.py -i seqs_otus.txt -m Fasting_Map.txt -s 'Treatment:*,!Fast' -l pooledNonFast