g2gtools creates custom genomes by incorporating SNPs and indels into reference genome, extracts regions of interest, e.g., exons or transcripts, , and converts coordinates of files (bam, gtf, bed) between two genomes. Unlike other liftover tools, g2gtools does not throw away alignments that land on indel regions. Release Version 0.2 can now create personal diploid genomes. The new version still lifts over diploid alignments on personal genome coordinates back to that of reference so we can compare alignments from among samples in a population.
Free software: MIT License
Documentation for Release Ver. 0.2.XX: http://churchill-lab.github.io/g2gtools/.
Documentation for Release Ver. 0.1.XX: https://g2gtools.readthedocs.org.
Reference
Manuscript in preparation (expected in 2018)
History
0.2.5 (06/06/2018)
Fixed error of always generating index file
0.2.4 (06/05/2018)
Automtically generates file index if not found
0.2.3 (06/05/2018)
Fixed end of contig tree mapping
0.2.2 (06/04/2018)
Fixed extract transcripts
0.2.1 (05/30/2018)
Hotfix to solve gtf parsing problem in python 3
0.2.0 (05/09/2018)
Support for diploid VCF
Reimplemented to support G2G VCI (Variant Call Information)
Support python3
0.1.31 (02/17/2017)
Final release for custom haploid reconstruction
0.1.29 (05/17/2016)
Fixed parsing issue with GATK-generated VCF files
0.1.27 (05/04/2016)
Uploaded the package to Anaconda Cloud
Fixed Travis CI fail
0.1.23 (02/15/2016)
Setup Travis CI for automated building
0.1.22 (02/15/2016)
Updated documentation
0.1.20 (02/03/2016)
Released to public with documentation at g2gtools.readthedocs.org
0.1.0 (02/09/2015)
Started github repository
1 maintainer
Metadata
1 maintainer
Release files for g2gtools 0.2.7
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | Provenance | |
|---|---|---|---|---|
| g2gtools-0.2.7.tar.gz | 69.1 kB | Without provenance | Details |
Release files / g2gtools-0.2.7.tar.gz
| Download URL | g2gtools-0.2.7.tar.gz |
|---|---|
| Size | 69.1 kB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
b104b5afb5d0eb051cba941cdefd7f54467b92050ae5f0a294844940f5af7578
|
|
BLAKE2b-256 checksum How to use checksums |
f1f9d28af4c85786e3339c50fad21a0cbe171b23200212f1cc27a660c3d5e2ec
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
Python-urllib/2.7
|
Security for g2gtools 0.2.7
Provenance
Provenance describes where a file came from. On PyPI, provenance is shared via attestations, which provide a verifiable record of the build or publishing details. View details, limitations and caveats.
No provenance found
None of the files in this release were uploaded with provenance metadata.
A note on package security
PyPI is a repository for distributing packages, not a service for auditing them. While third-party security researchers and our staff do their best to detect and remove malicious packages, PyPI cannot guarantee the quality, security or suitability of any given package.
