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  • Committer: Package Import Robot
  • Author(s): Andreas Tille
  • Date: 2013-06-17 18:28:26 UTC
  • mfrom: (9.1.2 sid)
  • Revision ID: package-import@ubuntu.com-20130617182826-376az5ad080a0sfe
Tags: 1.7.0+dfsg-1
Upload preparations done for BioLinux to Debian

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doc/scripts/filter_distance_matrix.rst
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**Description:**
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Remove samples from a distance matrix based on a mapping file or an otu table or a list of sample ids.
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**Usage:** :file:`filter_distance_matrix.py [options]`
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        -m, `-`-mapping_fp
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                Path to the mapping file
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        -s, `-`-valid_states
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                String containing valid states, e.g. 'STUDY_NAME:DOG'
 
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                String containing valid states, e.g. 'STUDY_NAME:DOB'
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        `-`-negate
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                Discard specified samples (instead of keeping them) [default: False]
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::
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        filter_distance_matrix.py -i dm.txt -o dm_out.txt --sample_id_fp sample_id_list.txt
 
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        filter_distance_matrix.py -i dm.txt -o dm_out_sample_list.txt --sample_id_fp sample_id_list.txt
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Filter samples ids in otu_table.biom from dm.txt
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::
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        filter_distance_matrix.py -i dm.txt -o dm_out.txt -t otu_table.biom
 
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        filter_distance_matrix.py -i dm.txt -o dm_out_otu_table.txt -t otu_table.biom
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Filter samples ids where DOB is 20061218 in Fasting_Map.txt. (Run "`filter_samples_from_otu_table.py <./filter_samples_from_otu_table.html>`_ -h" for additional information on how metadata filtering can be specified.)
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::
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        filter_distance_matrix.py -i dm.txt -o dm_out4.txt -m Fasting_Map.txt -s "DOB:20061218"
 
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        filter_distance_matrix.py -i dm.txt -o dm_out_mapping_file.txt -m Fasting_Map.txt -s "DOB:20061218"
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