Fetch microbiome tables from Qiita using RedBiom based on a metadata file and filter:
- blooms,
- read-sum based
- duplicate hosts and preps
For the first install:
pip install git+https://github.com/FranckLejzerowicz/Xrbfetch.git
and then if there are updates...
pip install --upgrade git+https://github.com/FranckLejzerowicz/Xrbfetch.git
*Note that python and pip should be python3
-m option [required]: Must be an existing path to a metadata file containing the samples
to fetch and filter (the samples must be listed in the first column).
-o option [required]: Path to the output metadata table file.
Will contain the same info as the input but only for the samples that pass filters.
Only for samples named according to the AGP standard (i.e. <study-id>.<9-digits-sample-id>)
-b option [required]: Path to the output biom table file. Will contain only the samples that pass filters.
-
Running:
Xrbfetch \ -m ./Xrbfetch/tests/metadata/metadata.tsv \ -o ./Xrbfetch/tests/output/metadata_out.tsv \ -b ./Xrbfetch/tests/output/featuredata.biomWould return
metadata_out_<number>s.tsvandfeaturedata_<number>s.tsv -
Running:
Xrbfetch \ -m ./Xrbfetch/tests/metadata/metadata.tsv \ -o ./Xrbfetch/tests/output/metadata_out.tsv \ -b ./Xrbfetch/tests/output/featuredata.biom --no-dimWould return
metadata_out.tsvandfeaturedata.tsv
-m, --m-metadata-file TEXT Path to metadata file containing the samples
to fetch and filter (must be in the first
column). [required]
-o, --o-metadata-file TEXT Path to the output metadata table file.
[required]
-b, --o-biom-file TEXT Path to the output biom table file.
[required]
-r, --p-redbiom-context TEXT Redbiom context for fetching 16S data from
Qiita. [default: Deblur-
Illumina-16S-V4-150nt-780653]
-s, --p-bloom-sequences TEXT Fasta file containing the sequences known to
bloom in fecal samples (defaults to
'newblooms.all.fasta' file from package's
folder 'resources').
-f, --p-reads-filter INTEGER Minimum number of reads per sample. [default:
1500]
--unique / --no-unique Keep a unique sample per host (most read, or
most features). [default: True]
--update / --no-update Update the sample names to remove Qiita-prep
info. [default: True]
--dim / --no-dim Add the number of samples in the final biom
file name before extension (e.g. for '-b
out.biom' it becomes 'out_1000s.biom').
[default: True]
--verbose / --no-verbose Show missing, non-fetched samples and
duplicates. [default: True]
--version Show the version and exit.
--help Show this message and exit.
contact flejzerowicz@health.ucsd.edu