Metadata-Version: 2.1
Name: airpg
Version: 0.1.4
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: BSD
Download-URL: https://github.com/michaelgruenstaeudl/airpg/archive/v0.1.4.tar.gz
Description: *airpg*: Accessing the inverted repeats of archived plastid genomes
        ===================================================================
        
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        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
        #### SCRIPT 01: Generating plastome availability table
        ```
        # Angiosperms
        TESTFOLDER=./03_testing/angiosperms_Start2000toEnd2019
        DATE=$(date '+%Y_%m_%d')
        MYQUERY='complete genome[TITLE] AND (chloroplast[TITLE] OR plastid[TITLE]) AND 2000/01/01:2019/12/31[PDAT] AND 0000050000:00000250000[SLEN] NOT unverified[TITLE] NOT partial[TITLE] AND (Embryophyta[ORGN] AND Magnoliophyta[ORGN])'
        AVAILTABLE=plastome_availability_table_${DATE}.tsv
        mkdir -p $TESTFOLDER
        ```
        ```
        # Non-angiosperm landplants
        TESTFOLDER=./03_testing/nonangiosperm_landplants_Start2000toEnd2019
        DATE=$(date '+%Y_%m_%d')
        MYQUERY='complete genome[TITLE] AND (chloroplast[TITLE] OR plastid[TITLE]) AND 2000/01/01:2019/12/31[PDAT] AND 0000050000:00000250000[SLEN] NOT unverified[TITLE] NOT partial[TITLE] AND (Embryophyta[ORGN] NOT Magnoliophyta[ORGN])'
        AVAILTABLE=plastome_availability_table_${DATE}.tsv
        mkdir -p $TESTFOLDER
        ```
        ```
        # Defining blacklist
        if [ ! -f ./02_blacklists/BLACKLIST__master_${DATE} ]; then
            cat $(ls ./02_blacklists/BLACKLIST__* | grep -v "master") > ./02_blacklists/BLACKLIST__master_${DATE}
        fi
        ```
        ```
        python ./01_package/01_generate_plastome_availability_table.py -q "$MYQUERY" -o $TESTFOLDER/$AVAILTABLE --blacklist ./02_blacklists/BLACKLIST__master_${DATE} 1>>$TESTFOLDER/Script01_${DATE}.runlog 2>&1
        ```
        
        #### SCRIPT 02: Downloading records and extracting IR information
        ```
        REPRTDSTAT=reported_IR_stats_table_${DATE}.tsv
        mkdir -p $TESTFOLDER/records_${DATE}
        mkdir -p $TESTFOLDER/data_${DATE}
        ```
        ```
        python ./01_package/02_download_records_and_extract_IRs.py -i $TESTFOLDER/$AVAILTABLE -r $TESTFOLDER/records_${DATE}/ -d $TESTFOLDER/data_${DATE}/ -o $TESTFOLDER/$REPRTDSTAT 1>>$TESTFOLDER/Script02_${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 :: BSD License
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
