23 lines
681 B
Bash
23 lines
681 B
Bash
#!/usr/bin/env bash
|
||
# 轻量组装 QC：contig 数 / 总长度 / N50 / N 占比 / GC%
|
||
# 用法: bash asm_qc.sh <fasta文件或目录...> > qc.tsv
|
||
set -euo pipefail
|
||
|
||
files=()
|
||
for p in "$@"; do
|
||
if [ -d "$p" ]; then
|
||
while IFS= read -r f; do files+=("$f"); done \
|
||
< <(find "$p" -type f \( -name '*.fa' -o -name '*.fasta' -o -name '*.fna' -o -name '*.fa.gz' -o -name '*.fasta.gz' -o -name '*.fna.gz' \))
|
||
else
|
||
files+=("$p")
|
||
fi
|
||
done
|
||
|
||
seqkit stats -a -T -j 8 "${files[@]}" | awk 'BEGIN{OFS="\t"}
|
||
NR==1 {print $0, "N%"; next}
|
||
{
|
||
# $5=sum_len, $19=sum_n（N 碱基数）
|
||
n = ($5 > 0) ? sprintf("%.4f", $19 / $5 * 100) : "NA"
|
||
print $0, n
|
||
}'
|