fix_capitalisation.bash

#!/bin/bash

# simple files
for f in *.bed *.contamination *recommendation *report.txt *taxonomy.rpt */*/*combined_summary.csv *.fa *.gb
do
    perl -i_original -pne 's/scaffold_/SCAFFOLD_/' $f
done

# compressed fastas
for f in *.gz
do      
	zcat $f | perl -pne 's/scaffold_/SCAFFOLD_/' | gzip -9 -c > "${f%.gz}_new"
	mv $f "${f%.gz}_original.gz"
	mv "${f%.gz}_new" $f
done

species_to_rename.txt

cbNecPumi1 - done
xcThyRhom1 - done
glLicPygm2 - done (need to tell Yumi)
ilLysCori56 - done