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.pythat enables command-line A to I analysis.
The easiest way to install aimap is to use conda:
conda create -n aimap_env python=3.10
conda activate aimap_env
conda install bioconda::fastp
conda install -c bioconda bcftools=1.16
conda install -c bioconda samtools=1.16
pip install aimap
Need to give execute file permission
chmod +x /path/to/aimap_env/bin/Adenosine_to_inosine.py
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/
- fastp <OpenGene/fastp: An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...) (github.com)>
- BWA https://github.com/lh3/bwa
- Samtools 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 *_A_I_result.tsv for more information.
| Accession | Position | Old_base | New_base | Raw read depth | Coverage | Edit_level | snp_coverage | snp_f_coverage | snp_r_coverage | Gene_biotype | locus_tag | Gene_name | Gene_strand | gene_start | gene_end | Amino acid_change | codon_num |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| (Example) | (Example) | (Example) | (Example) | (Example) | (Example) | (Example) | (Example) | (Example) | (Example) | (Example) | (Example) | (Example) | (Example) | (Example) | (Example) | (Example) | (Example) |
| (Example) | (Example) | (Example) | (Example) | (Example) | (Example) | (Example) | (Example) | (Example) | (Example) | (Example) | (Example) | (Example) | (Example) | (Example) | (Example) | (Example) | (Example) |
| (Example) | (Example) | (Example) | (Example) | (Example) | (Example) | (Example) | (Example) | (Example) | (Example) | (Example) | (Example) | (Example) | (Example) | (Example) | (Example) | (Example) | (Example) |
Below are specific descriptions for each column：
| Column Name | Description |
|---|---|
| Accession | The unique identifier assigned to a genetic sequence in a public database, such as NCBI. |
| Position | The specific location of a nucleotide within the genetic sequence, often given as a numerical coordinate. |
| Old_base | The original nucleotide base at a specific position before any changes or mutations. |
| New_base | The mutated or altered nucleotide base at a specific position after a change has occurred. |
| Raw read depth | The total number of sequencing reads that cover a particular genomic position. |
| Coverage | The average number of sequencing reads that align to a specific region of the genome, indicating how well that region is covered by the sequencing data. |
| Edit_level | The percentage of reads supporting a specific edit (mutation) at a given position relative to the total read depth. |
| snp_coverage | The depth of coverage specifically at the site of a single nucleotide polymorphism (SNP). |
| snp_f_coverage | The depth of forward reads covering the SNP position. |
| snp_r_coverage | The depth of reverse reads covering the SNP position. |
| Gene_biotype | The classification of a gene based on its predicted biological function or properties. |
| locus_tag | A unique identifier assigned to a gene within a genome, often used when the gene has not been given a standard name. |
| Gene_name | The common or standard name of a gene, which may be based on its function, phenotype, or historical nomenclature. |
| Gene_strand | The DNA strand (plus or minus) on which the gene is located. |
| gene_start | The starting position of a gene on the DNA sequence. |
| gene_end | The ending position of a gene on the DNA sequence. |
| Amino acid_change | The specific change in the amino acid sequence resulting from a nucleotide mutation. |
| codon_num | The position of the codon within the gene sequence that is affected by a mutation, often used to indicate where in the protein sequence the amino acid change occurs. |
Unless otherwise indicated, all code is subject to the following agreement:
(c) Agriculture and Biology 2018, 2024
Author: Sai Wang
Contact: [email protected]
Address:
Sai Wang,
Agriculture and Biology,
Shanghai Jiao Tong University,
ShangHai,
CN
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