sinto 0.2

sinto: tools for single-cell data processing

sinto

Tools for single-cell data processing

Installation

Install from PyPI:

pip install sinto

Install from source:

git clone https://github.com/timoast/sinto.git
cd sinto
python setup.py install

Features

Filter barcodes

Subsets of cells can be extracted from a BAM file using the sinto filterbarcodes command:

$ sinto filterbarcodes -h
usage: sinto filterbarcodes [-h] -b BAM -c CELLS -o OUTPUT [-t] [-s]
                            [-p NPROC] [-m MODE]

Filter reads based on input list of cell barcodes

optional arguments:
  -h, --help            show this help message and exit
  -b BAM, --bam BAM     Input bam file (must be indexed)
  -c CELLS, --cells CELLS
                        File or comma-separated list of cell barcodes. Can be
                        gzip compressed
  -o OUTPUT, --output OUTPUT
                        Name for output text file
  -t, --trim_suffix     Remove trail 2 characters from cell barcode in BAM
                        file
  -s, --sam             Output sam format (default bam output)
  -p NPROC, --nproc NPROC
                        Number of processors (default = 1)
  -m MODE, --mode MODE  Either tag (default) or readname. Some BAM file store
                        the cell barcode in the readname rather than under a
                        read tag

Add read tags per cell

Different read tags can be added to each cell with the sinto addtags command.

$ sinto addtags -h
usage: sinto addtags [-h] -b BAM -f TAGFILE -o OUTPUT [-t] [-s] [-p NPROC]
                     [-m MODE]

Add read tags to reads from individual cells

optional arguments:
  -h, --help            show this help message and exit
  -b BAM, --bam BAM     Input bam file (must be indexed)
  -f TAGFILE, --tagfile TAGFILE
                        Tab-delimited file containing cell barcode, tag to be
                        added, and tag identity. Can be gzip compressed
  -o OUTPUT, --output OUTPUT
                        Name for output text file
  -t, --trim_suffix     Remove trail 2 characters from cell barcode in BAM
                        file
  -s, --sam             Output sam format (default bam output)
  -p NPROC, --nproc NPROC
                        Number of processors (default = 1)
  -m MODE, --mode MODE  Either tag (default) or readname. Some BAM file store
                        the cell barcode in the readname rather than under a
                        read tag

This requires a file specifying the tags to be added to each cell, for example:

TGGCAATGTTGAAGCG-1	CI	A
GACCAATCACCATTCC-1	CI	A
CAGGATTCAGAACTTC-1	CI	B
GAACCTAAGAGAGGTA-1	CI	B
ACATGGTGTAGACGCA-1	CI	C
CCCTGATTCGGATAGG-1	CI	C

This will add a CI tag, with the tag set to A, B, or C depending on the cell barcode sequence.