The genome assembly process often generates FASTA-formatted contig files, in which the contigs have cryptic sequence names. By using specific Bash commands, one can automatically rename these contigs based on the name of the file they are contained in.
If your contig file contains only a single contig:
for i in *__contig.fasta; do
VAR=${i%__contig.fasta*};
sed -i "1s/.*/>$VAR/" $i;
done
If your contig file contains multiple contigs:
for i in *__contigs.fasta; do
VAR=${i%__contigs.fasta*};
sed -i "s/>.*/>$VAR/" $i;
awk '$0=$0' $i | awk '!(NR%2){print prev "__Length" length($0) ORS $0} {prev=$0}' > ${i}.new
done
Die