airpg
Accessing the inverted repeats of archived plastid genomes
Science Score: 36.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
○.zenodo.json file
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✓DOI references
Found 2 DOI reference(s) in README -
✓Academic publication links
Links to: zenodo.org -
○Committers with academic emails
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○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (10.6%) to scientific vocabulary
Repository
Accessing the inverted repeats of archived plastid genomes
Basic Info
- Host: GitHub
- Owner: michaelgruenstaeudl
- License: gpl-3.0
- Language: Python
- Default Branch: main
- Size: 165 KB
Statistics
- Stars: 4
- Watchers: 3
- Forks: 0
- Open Issues: 1
- Releases: 10
Metadata Files
README.md
airpg: Automatically accessing the inverted repeats of archived plastid genomes
A Python package for automatically accessing the inverted repeats of thousands of plastid genomes stored on NCBI Nucleotide
INSTALLATION
To get the most recent stable version of airpg, run:
pip install airpg
Or, alternatively, if you want to get the latest development version of airpg, run:
pip install git+https://github.com/michaelgruenstaeudl/airpg.git
Update May 2024 (tested on Debian)
To install airpg, clone it via git, cd into the cloned directory, open a terminal and run:
sudo pip install .
EXAMPLE USAGE
Tutorial 1: Very short survey (runtime ca. 5 min.; for the impatient)
Survey of all plastid genomes of flowering plants submitted to NCBI Nucleotide within the past 10 days.
Tutorial 2: Short survey (runtime ca. 15 min.; for testing)
Survey of all plastid genomes of flowering plants submitted to NCBI Nucleotide within the current month.
Tutorial 3: Medium survey (runtime ca. 5 hours)
Survey of all plastid genomes of flowering plants submitted to NCBI Nucleotide in 2019 only. Note: The results of this survey are available on Zenodo via DOI 10.5281/zenodo.4335906
Tutorial 4: Full survey (runtime ca. 19 hours; with explanations)
Survey of all plastid genomes of flowering plants submitted to NCBI Nucleotide from January 2000 until, and including, December 2020. Note: The results of this survey are available on Zenodo via DOI 10.5281/zenodo.4335906
TIPS & TRICKS
How to sort output_script1.tsv
sort -t$'\t' -k7.1,7.4 -k7.6,7.7 -k7.9,7.10 -n output_script1.tsv > output_script1.sorted.tsv
awk '{print $2}' output_script1.sorted.tsv > output_script1.sorted.index
How to sort output_script2.tsv and output_script3.tsv
awk 'NR==FNR{o[FNR]=$1; next} {t[$1]=$0} END{for(x=1; x<=FNR; x++){y=o[x]; print t[y]}}' output_script1.sorted.index output_script2.tsv > output_script2.sorted.tsv
awk 'NR==FNR{o[FNR]=$1; next} {t[$1]=$0} END{for(x=1; x<=FNR; x++){y=o[x]; print t[y]}}' output_script1.sorted.index output_script3.tsv > output_script3.sorted.tsv
How to measure the number of angiosperm families represented by the plastid genomes archived on GenBank
```
Using the sorted output of script1 as input
awk -F'\t' '{print $11}' output_script1.sorted.tsv | tr ";" "\n" | grep "aceae" | grep -v "incertae sedis" | sort -u | wc -l ```
CHANGELOG
See CHANGELOG.md for a list of recent changes to the software.
Owner
- Name: Michael Gruenstaeudl, PhD
- Login: michaelgruenstaeudl
- Kind: user
- Location: Hays, Kansas
- Company: Fort Hays State University
- Website: https://gruenstaeudl-lab.com/
- Repositories: 27
- Profile: https://github.com/michaelgruenstaeudl
Assistant Professor, Fort Hays State University
GitHub Events
Total
Last Year
Committers
Last synced: over 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| Michael Gruenstaeudl | m****l@g****m | 67 |
| TilMeh | g****b@t****e | 16 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 11 months ago
All Time
- Total issues: 2
- Total pull requests: 0
- Average time to close issues: about 2 months
- Average time to close pull requests: N/A
- Total issue authors: 2
- Total pull request authors: 0
- Average comments per issue: 1.5
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 0
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 0
- Pull request authors: 0
- Average comments per issue: 0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- michaelgruenstaeudl (1)
- kazumaxneo (1)
Pull Request Authors
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
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Total downloads:
- pypi 81 last-month
- Total dependent packages: 0
- Total dependent repositories: 1
- Total versions: 21
- Total maintainers: 2
pypi.org: airpg
A package to automatically access the inverted repeats of archived plastid genomes
- Homepage: https://github.com/michaelgruenstaeudl/airpg
- Documentation: https://airpg.readthedocs.io/
- License: GPLv3
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Latest release: 1.1.4
published about 5 years ago
Rankings
Maintainers (2)
Dependencies
- argparse >=1.4.0
- biopython >=1.72
- entrezpy *
- ete3 *
- pandas *
- biopython *
- coloredlogs *
- entrezpy *
- ete3 *
- fuzzywuzzy *
- pandas *
- python-Levenshtein *