Skip to content

Update fuzznuc.sh #2

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
Nespeca2020707 wants to merge 1 commit into
base: main
Choose a base branch
from
Open

Update fuzznuc.sh #2

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
5 changes: 4 additions & 1 deletion R/fuzznuc.sh
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -39,7 +39,10 @@ echo "BED file created: ${output_base}.bed"

# Generate sequence name and length table
echo "Generating sequence name and length table..."
awk 'BEGIN {OFS="\t"} /^>/ {if (seq) print id, length(seq); id=substr($1, 2); seq=""} !/^>/ {seq = seq $0} END {if (seq) print id, length(seq)}' "$genome" > "${output_base}_length.tsv"
awk 'BEGIN {OFS="\t"}
/^>/ { if (len) print id, len; id=substr($1, 2); len=0 }
!/^>/ { len += length($0) }
END { if (len) print id, len }' "$genome" > "${output_base}_length.tsv"
echo "Sequence name and length table created: ${output_base}_length.tsv"

# Clean up intermediate files
Expand Down