Extract sequences from a CDS FASTA file and translate them

extract-seqs-from-cds-and-translate.sh

# Required files:
#   - from https://github.com/mfcovington/extract_genotype_specific_seq (commit 0867551092)
#       - parse_fasta-lite.pl 
#   - from https://github.com/mfcovington/fasta-manipulation (v0.1.4)
#       - amino_acid_translation.pm
#       - translate_cds_fasta.pl

FASTA_DIR=         # Directory w/ FASTA files
SPECIES_LIST=      # A file w/ species IDs to extract one ID per line
OUT_DIR=           # Output directory
TRANSLATE_PATH=    # Path to translate_cds_fasta.pl (amino_acid_translation.pm should be in same directory)
PARSE_PATH=        # Path to parse_fasta-lite.pl

mkdir -p $OUT_DIR
cd $FASTA_DIR

for FASTA in *.fa; do
    $PARSE_PATH $SPECIES_LIST $FASTA    # Extract the sequences you want
    $TRANSLATE_PATH $SPECIES_LIST.$FASTA $OUT_DIR/aa.$FASTA    # Translate the sequences
    rm $SPECIES_LIST.$FASTA    # Remove the CDS version of the extracted sequences
done