Metadata-Version: 2.1
Name: sinto
Version: 0.2
Summary: sinto: tools for single-cell data processing
Home-page: https://github.com/timoast/sinto
Author: Tim Stuart
Author-email: tstuart@nygenome.org
License: UNKNOWN
Description: # sinto
        Tools for single-cell data processing
        
        ## Installation
        
        Install from PyPI:
        
        ```bash
        pip install sinto
        ```
        
        Install from source:
        
        ```bash
        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.
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Classifier: Intended Audience :: Science/Research
Description-Content-Type: text/markdown
