Metadata-Version: 2.1
Name: airpg
Version: 1.0.3
Summary: A package to automatically access the inverted repeats of archived plastid genomes
Home-page: https://github.com/michaelgruenstaeudl/airpg
Author: Tilman Mehl, Michael Gruenstaeudl
Author-email: tilmanmehl@zedat.fu-berlin.de, m.gruenstaeudl@fu-berlin.de
License: GPLv3
Download-URL: https://github.com/michaelgruenstaeudl/airpg/archive/v1.0.3.tar.gz
Description: *airpg*: Accessing the inverted repeats of archived plastid genomes
        ===================================================================
        
        [![Build Status](https://travis-ci.com/michaelgruenstaeudl/airpg.svg?branch=master)](https://travis-ci.com/michaelgruenstaeudl/airpg)
        [![PyPI status](https://img.shields.io/pypi/status/airpg.svg)](https://pypi.python.org/pypi/airpg/)
        [![PyPI pyversions](https://img.shields.io/pypi/pyversions/airpg.svg)](https://pypi.python.org/pypi/airpg/)
        [![PyPI version shields.io](https://img.shields.io/pypi/v/airpg.svg)](https://pypi.python.org/pypi/airpg/)
        [![PyPI license](https://img.shields.io/pypi/l/airpg.svg)](https://pypi.python.org/pypi/airpg/)
        
        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
        
        
        ## EXAMPLE USAGE
        
        ### Short survey for the impatient / for testing (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](https://zenodo.org/record/4335906)
        ```
        airpg_update_blocklist.py -f airpg_blocklist.txt \
        -m john.smith@example.com -q "inverted[TITLE] AND \
        repeat[TITLE] AND loss[TITLE]"
        
        airpg_identify.py -q "complete genome[TITLE] AND \
        (chloroplast[TITLE] OR plastid[TITLE]) AND \
        2019/01/01:2019/12/31[PDAT] AND 50000:250000[SLEN] \
        NOT unverified[TITLE] NOT partial[TITLE] AND \
        Magnoliophyta[ORGN]" \
        -b airpg_blocklist.txt -o output_script1.tsv
        
        airpg_analyze.py -i output_script1.tsv \
        -m john.smith@example.com -o output_script2.tsv
        ```
        
        
        ### Full survey with explanations (runtime ca. 19 hours)
        Survey of all plastid genomes of flowering plants submitted to NCBI Nucleotide from start of 2000 until end of October 2020. Note: The results of this survey are available on Zenodo via DOI [10.5281/zenodo.4335906](https://zenodo.org/record/4335906)
        
        #### STEP 1: Querying NCBI Nucleotide for complete plastid genomes given an Entrez search string
        ```
        TESTFOLDER=./angiosperms_Start2000toEndOct2020
        DATE=$(date '+%Y_%m_%d')
        ENTREZSTRING='complete genome[TITLE] AND (chloroplast[TITLE] OR plastid[TITLE]) AND 2000/01/01:2020/10/31[PDAT] AND 50000:250000[SLEN] NOT unverified[TITLE] NOT partial[TITLE] AND Magnoliophyta[ORGN]' # complete plastid genomes of all flowering plants between start of 2000 and end of October 2020
        RECORDSTABLE=plastome_availability_table_${DATE}.tsv
        mkdir -p $TESTFOLDER
        ```
        ```
        # Updating blocklist
        if [ ! -f ./airpg_blocklist.txt ]; then
            touch ./airpg_blocklist.txt
            airpg_update_blocklist.py -f ./airpg_blocklist.txt
        fi
        airpg_update_blocklist.py -f ./airpg_blocklist.txt -m john.smith@example.com -q "inverted[TITLE] AND repeat[TITLE] AND loss[TITLE]"
        ```
        ```
        airpg_identify.py -q "$ENTREZSTRING" -o $TESTFOLDER/$RECORDSTABLE \
            --blocklist ./airpg_blocklist.txt 1>>$TESTFOLDER/airpg_identify_${DATE}.runlog 2>&1
        ```
        
        #### STEP 2: Retrieving and parsing the genome records identified in step 1, analyzing the position and length of their IR annotations
        ```
        IRSTATSTABLE=reported_IR_stats_table_${DATE}.tsv
        mkdir -p $TESTFOLDER/records_${DATE}
        mkdir -p $TESTFOLDER/data_${DATE}
        ```
        ```
        airpg_analyze.py -i $TESTFOLDER/$RECORDSTABLE \
            -r $TESTFOLDER/records_${DATE}/ -d $TESTFOLDER/data_${DATE}/ \
            -m john.smith@example.com -o $TESTFOLDER/$IRSTATSTABLE 1>>$TESTFOLDER/airpg_analyze_${DATE}.runlog 2>&1
        ```
        
        <!--
        ## FOO BAR BAZ
        ```
        Foo bar baz
        ```
        -->
        
        ## CHANGELOG
        See [`CHANGELOG.md`](CHANGELOG.md) for a list of recent changes to the software.
        
Keywords: plastid genomes,inverted repeats,NCBI Nucleotide
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
Classifier: Programming Language :: Python :: 3
Classifier: Operating System :: POSIX
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Python: >=3.6
Description-Content-Type: text/markdown
