airpg: 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

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

CHANGELOG

See CHANGELOG.md for a list of recent changes to the software.