aimap is a Python3 module that provides support for finding the modification from Adenosine to inosine (A to I). This is a one-step automated A to I modification analysis pipeline (AIMAP) for bacteria that works on illumine RNA-seq raw reads. The pipeline integrates reads quality control, adaptor removal, reference genome mapping, coverage pileup and synonymous-nonsynonymous annotation.

aimap installs one scripts into the $PATH:

• Adenosine_to_inosine.py that enables command-line A to I analysis.

The easiest way to install aimap is to use pip3:

pip3 install aimap

Note that Python package dependencies should automatically be installed

• Biopython https://biopython.org/
• pandas https://pandas.pydata.org/
• gffutils https://github.com/daler/gffutils

• trim_galore http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/
• BWA https://github.com/lh3/bwa
• Samtools http://www.htslib.org/
• Bcfools http://www.htslib.org/

Note that you can find the full install instruction in install file.

The Adenosine_to_inosine.py script - installed as part of this package - enables straightforward ANI analysis at the command-line, and uses the aimap module behind the scenes.

You can get a summary of available command-line options with Adenosine_to_inosine.py -h

$ Adenosine_to_inosine.py -h
usage: Adenosine_to_inosine.py [-h] [--version] -o OUTDIRNAME -g GENOMENAME -a ANNOTATION
                --outfile_name OUTFILE_NAME [-l LENGTH] [-f FILENAME]
                [-f1 FILENAME1] [-f2 FILENAME2] [-m {single,paired}]
                [-t THREADS] [--logfile LOGFILE]
                

[…]

For example you may type:

Adenosine_to_inosine.py -o /path/to/result -g /path/to/genome/file -a /path/to/annotation/file --outfile_name sample_name -f1 /path/to/r1.fastq -f2 /path/to/r2.fastq -m paired -t 4

At last, you will get a result file, it will be separated by “\t”. You can see the test_result for more information.

Unless otherwise indicated, all code is subject to the following agreement:

(c) Agriculture and Biology 2018, 2019
Author: Sai Wang

Contact: skyws@outlook.com

Address: 
Sai Wang,
Agriculture and Biology,
Shanghai Jiao Tong University,
ShangHai,
CN

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