SAPiN

---

Summarize Alignment Pile by Nucleotide

Table of Contents

• Foreword
• Install
• Usage
  • Usage
• Output
• Acknowledgement

Foreword

This tool aims to summarize BAM read alignment by pileup or reads at each position in a tabulated way. More convenient as a mpileup format and containing extra information.

Output

Here an example of output you would get with SAPiN

SEQID   POS     REF     QUAL    A       T       G       C       N       INS     DEL     IUPAC   COV     COV_ATGC    MUT_RAT APOBEC  ADAR    REGION  CODON   NUC     DESC
HPV42REF        118     C       38.28   0       16      0       1356    0       0       0       0       1374    1372    1.17    1.2     .       AATGTCAGGTA             CAG     1       gene:ID=gene-1;Name=E6@@mRNA:ID=nbis-rna-1;Parent=gene-1;Name=E6@@exon:ID=nbis-exon-1;Parent=nbis-rna-1;Name=E6@@CDS:ID=cds-1;Parent=nbis-rna-1;Name=E6

Here a description of the different fields

Field	Optional	Type	Description
SEQID		String	The ID of the landmark used to establish the coordinate system for the current feature.
POS		Integer	The reference position, with the 1st base having position 1
REF		Character	The reference base.
QUAL		Float	Mean Phred-scaled quality score for the sequenced position.
A		Integer	Number of Adenine nucleotide at the position
T		Integer	Number of Thymine nucleotide at the position
G		Integer	Number of Guanosine nucleotide at the position
C		Integer	Number of Cytosine nucleotide at the position
N		Integer	Number of Unknown nucleotide at the position
INS		Integer	Number of Insertion at the position
DEL		Integer	Number of Deletion at the position
IUPAC		Integer	Number of IUPAC nucleotide (minus A,T,G,C,N) at the position
COV		Integer	Coverage at the position (including INS,DEL,IUPAC)
COV_ATGC		Integer	Coverage at the position of A,T,G,C nucleotide only
MUT_RAT		Float	Mutation ration (COV_ATGC/nb mutated nuc*100)
APOBEC		Float	Mutation ration of C-to-T or G-to-A. Usefull when studying transcriptomes
ADAR		Float	Mutation ration of A-to-G or T-to-C. Usefull when studying transcriptomes
REGION		STRING	substring of 5 nucleotide on each side. Usefill to make pattern
CODON	Only if GFF provided	STRING	substring of codon in phase/frame (/!\ do not take spliced CDS in account).
NUC	Only if GFF provided	Integer	1,2 or 3. Indicate in the CODON (previous column) which nucleotide is the one studied at the position
DESC	Only if GFF provided	STRING	feature type and attributes extracted from the gff at the position

Install

Prerequisite

• python3
• pysam
• gffutils
• matplotlib

They should be automatically installed during SAPiN installation.

Installation with pip:

pip install git+https://github.com/Juke34/SAPiN.git

or if you do not have administrative rights on your machine

pip install --user git+https://github.com/Juke34/SAPiN.git

Installation with git:

Clone the repository:

git clone https://github.com/Juke34/SAPiN.git

Move into the folder:

cd SAPiN/

Install:

python setup.py install

or if you do not have administrative rights on your machine:

python setup.py install --user

Check installation

Executing:

sapin

or

sapin -h

will display some help.

Update

Update with pip:

pip install git+https://github.com/Juke34/SAPiN.git --upgrade

or if you do not have administartive rights on your machine

pip install --user git+https://github.com/Juke34/SAPiN.git --upgrade

Update with git:

Move into the repository folder and execute:

git pull
cd SAPiN/
python setup.py install

Uninstall

pip uninstall sapin

Usage

sapin -a t/reference.bam -f t/reference.fasta 

advanced:

sapin -a t/reference.bam -f t/reference.fasta -g t/reference_agat.gff3 -cf 1000 -bqf 20 -p

Parameters

Parameter	Type	Description
-a, --ali	String	Path to the BAM input file
-f, --fasta	String	Path to the reference fasta file used to align the reads against.
-g, --gff	String	Optional - Path to the reference gff
-o, --output	String	Path to the tsv output file
-p, --plot	Boolean	To plot the ratio of mutation per position (sapin_plot.svg by default. If outpout provided output.svg).
-q, --quiet	Boolean	"Decrease verbosity
-v, --verbose	Boolean	Increase verbosity
-z, --gzip	Boolean	Gzip output file
-s, --shame	Boolean	Suppress the shameless plug
-cf, --cover_filter	Integer	filter output to report only site with coverage >=
-bqf, --base_quality_filter	Integer	filter output to report only site with base quality >= (default 0)
-mqf, --base_quality_filter	Integer	filter output to report only site with mapping quality >= (default 0)
-mf, --mutation_filter	Integer	filter output to report only site where the mutation ratio >= (default 0)