cd /data/home/anne/PROJECTS/JanMaarten/Bimal/202008

/data/molgentools/genomics/g2d_conversions.pl -l D3.gbk -r Cvrt_gbk2fasta -o D3.fna
/data/molgentools/genomics/g2d_conversions.pl -l D17.gbk -r Cvrt_gbk2fasta -o D17.fna

/data/molgentools/genomics/g2d_conversions.pl -l D3.fna -r Cvrt_fasta2tab -o D3.tab
/data/molgentools/genomics/g2d_conversions.pl -l D17.fna -r Cvrt_fasta2tab -o D17.tab

split on _length_

awk '{print ">" $1 "\n" $3}' D3.tab >D3_clean.fna
awk '{print ">" $1 "\n" $3}' D17.tab >D17_clean.fna

# Blast proteins against new RAST annotation
/data/molgentools/blast/anne_blast.pl -p blastp -query D3_solomon.faa -db RAST_202009/Staphylococcus_aureus_D3.faa -out RAST_202009/Staphylococcus_aureus_D3.blast	
/data/molgentools/blast/anne_blast.pl -p blastp -query D17_solomon.faa -db RAST_202009/Staphylococcus_aureus_D17.faa -out RAST_202009/Staphylococcus_aureus_D17.blast