SRA-Importer

An easy and convenient way to import data from the sra database and creating OTU and Taxonomy tables.

Requirements

The package's use requires:

• qiime2 conda environment: The package must run from qiime2 conda environment. If one do not have a qiime2 conda environment installed, follow the instructions from here to install it.
• SRA Toolkit: The package also depends on SRA Toolkit. If one do not have a SRA Toolkit installed, follow the instructions from here to install it. 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.

In order to decide the trim and trunc values for the next stage, drag and drop the visualization output (.qzv) to QIIME2-VIEW

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 be txt/tsv.
• taxonomy_output_file: An output path for the taxonomy table. The directory must exist, and the file's format must be tsv.
• 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 is 12. (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")