An easy and convenient way to import data from the sra database and creating OTU and Taxonomy tables.
Project description
SRA-Importer
An easy and convenient way to import data from the sra database and creating OTU and Taxonomy tables.
Importing is divided to 2 stages:
Create Visualization
The first stage is in charge of taking the data from the sra database and make a visualization of the reads. The visualization purpose is to make better assessment of the range in which one should trim and truncate the reads generated by qiime2.
Parameters
--sra-study
: SRA experiment code.--acc-list
: Accession list file. This file must be stored locally.--output-vis-path
: An output path for the visualisation. (Optional)
Note: Only one of the following must be given --sra-study
/--acc-list
. If both are given, an error will be raised.
Usage:
create_visualization --sra-study <sra-study-code> --acc-list <accession-list-file-path> --output-vis-path <final-output-path-of-visualisation>
Export Data
The second stage is in charge of creating OTU and Taxonomy tables and export them into a usable file formats.
Parameters
--output-dir
: The path of the directory created by the first stage.--otu-output-file
: An output path for the OTU table. The directory must exist, and the file's format must betxt
/tsv
.--taxonomy-output-file
: An output path for the taxonomy table. The directory must exist, and the file's format must betsv
.
DADA2 parameters
--trim
: a non-negative integer of the right edge of the trimming range. If the reads are both forward and reverse 2 values should be given seperated with comma:20,28
--trunc
: a non-negative integer of the left edge of the truncating range. If the reads are both forward and reverse 2 values should be given seperated with comma:200,220
--threads
: Number of threads to run on. Default is12
. (Optional)
Note: All the parameters except --threads
must be given.
Usage:
export-data --output-dir <output-directory-path> --trim <trim-from> --trunc <trunc-to> --threads <number-of-threads-to-use> --otu-output-file <otu-output-file-path> --taxonomy-output-file <taxonomy-output-file-path>
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