If you are interested in the detailed methodology, please refer to our manuscript, A comparison of experimental assays and analytical methods for genome-wide identification of active enhancers, for more information.

Summary

Peak Identifier for Nascent Transcript Starts (PINTS) is a software that helps locate potential regulatory elements (promoters and enhancers) genome-wide from nascent transcript sequencing data, like GRO/PRO-cap libraries, which are specifically enriched for signals from transcription start sites (TSSs).

PINTS web portal is a comprehensive catalog of promoters and enhancers, and all have support from transcriptional evidence. Besides the catalog database, the portal also allows users to upload their genomic loci of interest and analyze the loci with state-of-the-art annotations. The portal is a containerized web service powered by Django, celery, and other open-source packages.

Availability

PINTS executable files are packed and distributed on both PyPI and bioconda. You can install PINTS like any other standard Python package with pip (pip install pyPINTS) or conda (conda install -c bioconda pypints). The source code is available on GitHub.

PINTS web portal is freely accessible at pints.yulab.org.

Changelog

PINTS

1.1.10

Release date: 2023-11-07

  • [Changed]: Removed warning filters in extension_engine as warnings from other packages may break downstream analysis.
  • [Changed]: years in comments

1.1.9

Release date: 2023-05-11

  • [Added]: A new QC script for evaluating TSS enrichment (over gene body regions)
  • [Changed]: Report scale factors when using pints_visualizer
  • [Changed]: Switched formatter_class for all executable scripts’ argument parsers from HelpFormatter to ArgumentDefaultsHelpFormatter, so that default values will be printed when running commands like pints_caller --help
  • [Fixed]: Added boundary caps to avoid ValueError when calling pysam.TabixFile.fetch (Corresponding to GitHub issue #6)

1.1.8

Release date: 2022-10-08

  • [Fixed]: When no divergent/bidirectional peaks are detected, PINTS may throw exceptions. In this version, empty predictions will be skipped, so errors like ERROR: Requested column 12, but database file stdin only has fields 1 - 0. will be avoided (related GitHub issue #12).
  • [Changed]: Since PINTS will automatically adjust the value of --min-mu-percent, now it prints info instead of a warning message when --min-mu-percent related issues are detected.
  • [Changed]: Reduce redundancy in the function peak_calling by abstracting statements about parsing input files.
  • [Added]: Added a new QC metric on the number of significant calls. If the number of significant calls is too large, PINTS will throw a warning message and suggest users switch to a more strict FDR cutoff.

1.1.7

Release date: 2022-09-16

  • [Added]: unit test cases
  • [Added]: Github issue templates
  • [Changed]: Improved the logic of on-the-fly QC. If QC is enabled, now PINTS tries to directly adjust corresponding parameter (for now only --min-mu-percent) and log the changes. This behavior can be repressed by using --disable-qc.

1.1.6

Release date: 2022-07-05

  • [Added]: Added chromosome length check when using BAM files as inputs
  • [Changed]: Simplified on-the-fly QC messages. So warning messages of the same type only show up once at the end of the log file.
  • [Changed]: Dropped peak length limits for empirical LER.
  • [Fixed]: Fixed inappropriate usage of str.find in annotate_tre_with_epig_info.

1.1.5

Release date: 2022-06-16

  • [Fixed]: Add explicit type conversion to avoid AttributeError: Can only use str accessor with string values

1.1.4

Release date: 2022-06-13

  • [Fixed]: fixed typos in readme;
  • [Removed]: Removed scaffold codes;
  • [Changed]: changed default output from pints_boundary_extender to standard bed format
  • [Changed]: moved codes from scripts to PINTS lib for more accurate test coverage analysis;

1.1.0 (1.1.3)

Release date: 2022-03-16 (for 1.1.0) and 2022-03-21 (for 1.1.3)

  • [Added]: Source distribution to CI/CD for creating conda packages
  • [Added]: Added MANIFEST.in file to include versioneer.py in the source distribution
  • [Added]: empirical LER
  • [Added]: On the fly QC
  • [Changed]: Switched versioning schema from PEP 440 to major_ver.middle_ver.minor_ver. The first two vers will be defined by tags; the minor_ver will be inferred automatically from commit distance.
  • [Changed]: Changed the default value for --alpha (for combining nearby peaks) to 0.3.
  • [Changed]: Renamed README.md.
  • [Changed]: Improved the implementation of independent filtering
  • [Changed]: Improved code readability with Pylint
  • [Removed]: Scaffolding parameters and simplified naming schema.

0.0.1.post0.dev8

Release date: 2022-01-07

  • [Changed]: Add requests to install_requires.

0.0.1.post0.dev7

Release date: 2022-01-07

  • [Changed]: Updated readme and help message

0.0.1.post0.dev6

Release date: 2022-01-05

  • [Fixed]: Fixed timestamp issue when creating log file

0.0.1.post0.dev5

Release date: 2022-01-04

  • [Added]: Introduced version check, which prints update hints if current version of PINTS is out-dated.

0.0.1.post0.dev3

Release date: 2021-10-30

  • [Changed]: Added pyBigWig, biopython, and matplotlib into setup.install_requires.
  • [Added]: Introduced a new module for refining peak calls with epigenomic evidence from PINTS webserver. This feature can be activated by using --epig-annotation <biosample_name>.
  • [Added]: error check for lowly sequenced libraries.

0.0.1.post0.dev2

Release date: 2021-08-04

  • [Added]: Configured CI/CD for uploading PINTS to PyPI.
  • [Added]: Added CI/CD badge in README.

0.0.1.post0.dev1

Release date: 2021-06-03

Initial implementation.

PINTS web portal

2022v1

Release date: 2022-07-17

  • [Added]: Increased biosample coverage by adding PRO-cap libraries for:
    • GM18507, GM19238 from Kristjánsdóttir et al. 2020 (DOI: 10.1038/s41467-020-19829-z)
    • MCF7 from Hou et al. 2022 (DOI: 10.1016/j.celrep.2022.110944)
    • A673, Caco-2, and MCF 10A from the ENCODE portal ( using DOI: 10.1038/s41587-022-01211-7 as a placeholder for now, will update the study link after the manuscript is published)
  • [Changed]: Updated epigenomic annotation to cCRE v3
  • [Changed]: Updated TF binding site annotation to JASPAR 2022
  • [Changed]: Updated functional characterization info for HepG2 by including consistent enhancer calls from Klein et al. 2020.
  • [Changed]: Switched to PINTS 1.1.6.
  • [Deprecated]: Removed bidirectional elements identified from RAMPAGE/CAGE libraries that overlap with protein-coding exons (except $5^\prime$ UTR).

2021v1

Release date: 2021-10-23

Initial release.