sctools provides utilities for manipulating sequence data formats suitable for use in distributed systems analyzing large biological datasets.
git clone https://github.com/humancellatlas/sctools.git
cd sctools
pip3 install .
pytest # verify installation; run tests
The sctools package provides both command line utilities and classes designed for use in python programs.
- Attach10XBarcodes: given an unaligned bam file, attach barcodes from an identically ordered forward and forward index fastq file
- Platform: an abstract class that defines a common data structure for different 3' sequencing formats. All algorithms and methods in this package that are designed to work on 3' sequencing data speak to this common data structure. Currently 10X_v2 is defined.
- Reader: a general iterator over arbitrarily zipped file(s) that is extended to work with common sequence formats like fastq (fastq.Reader) and gtf (gtf.Reader). We recommend using the pysam package for reading sam and bam files.
- TwoBit & ThreeBit DNA encoders that store DNA in 2- and 3-bit form. 2-bit is smaller but randomizes "N" nucleotides. Both classes support fastq operations over common sequence tasks such as the calculation of GC content.
- ObservedBarcodeSet & PriorBarcodeSet: classes for analysis and comparison of sets of barcodes such as the cell barcodes used by 10X genomics. Supports operations like summarizing hamming distances and comparing observed sequence diversity to expected (normally uniform) diversity.
- gtf.Reader & gtf.Record GTF iterator and GTF record class that exposes the gtf fields as a lightweight, lazy-parsed python object.
- fastq.Reader & fastq.Record fastq reader and fastq record class that exposes the fastq fields as a lightweight, lazy-parsed python object.
to calculate and view test coverage cd to the sctools directory and
type the following two commands to generate the report and open it in your web browser:
pytest --cov-report html:cov_html --cov=sctools
open cov_html/index.html