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
acc_list
: Accession list file. This file must be stored locally.output_vis_path
: An output path for the visualisation. (Optional)
Return
The name of the directory created for all the files.
Usage
from SRA_Importer import visualization
output_dir = visualization(acc_list="AccList.txt", output_vis_path="vis.qzv")
print(output_dir) # .../SRA-Importer-[creation_time]
Note: This stage creates a directory. DO NOT DELETE IT! Its name is an input to the next stage.
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
.classifier_file
: A path to the classifier file. If one needs to download it, it is recommended to download from https://data.qiime2.org/< qiime2-version >/common/gg-13-8-99-nb-classifier.qza
DADA2 parameters
trim
: a non-negative integer of the right edge of the trimming range. If the reads are both forward and reverse a tuple of 2 values is expected.trunc
: a non-negative integer of the left edge of the truncating range. If the reads are both forward and reverse a tuple of 2 values is expected.threads
: Number of threads to run on. Default is12
. (Optional)
Note: All the parameters except threads
must be given.
Usage
from SRA_Importer import export
export(output_dir="SRA-Importer...", trim=20, trunc=200,
classifier_file="gg-13-8-99-nb-classifier.qza",
otu_output_file="otu.txt", taxonomy_output_file="taxonomy.tsv")
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