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去除细胞器序列

作用:将 contig 比对 NCBI nt,经 GI → taxid → 学名汇总每个物种的命中数,据此识别并去除质体/线粒体来源的 contig。 入口:03.1.blast.sh(内部调用 03.2.get_gi.py、03.3.get_name.py),随后运行 03.4.get_ratio.py 输入:contigs.fa;nt 库 ``{SOFTWARE_ZC}/nt_lib/nt;cutted_nucl_gb.accession2taxid 与 names.dmp(须放在工作目录)。 输出:nt.blast.xml、tiqu_gi.txt、scientific_name.txt、final_result.txt(Name/Hit_reads/percentage1/percentage2,按命中数排序)。 运行:bash 03.1.blast.sh,然后 python 03.4.get_ratio.py 工具:blastn -outfmt 5 -evalue 1e-5 -num_threads 88;Python 仅用标准库(re、collections),以 python 调用。

English **Purpose**: BLAST the contigs against NCBI `nt`, resolve GI → taxid → scientific name and count hits per species to identify and remove plastid/mitochondrial (organelle) contigs. **Entry point**: `03.1.blast.sh` (calls `03.2.get_gi.py` and `03.3.get_name.py`), after which `03.4.get_ratio.py` runs separately **Inputs**: `contigs.fa`; `nt` database ``{SOFTWARE_ZC}`/nt_lib/nt`; `cutted_nucl_gb.accession2taxid` and `names.dmp` (must be in the working directory). **Outputs**: `nt.blast.xml`, `tiqu_gi.txt`, `scientific_name.txt`, `final_result.txt` (`Name/Hit_reads/percentage1/percentage2`, sorted by hit count). **Run**: `bash 03.1.blast.sh`, then `python 03.4.get_ratio.py` **Tools**: `blastn -outfmt 5 -evalue 1e-5 -num_threads 88`; Python with the standard library only (`re`, `collections`), invoked as `python`.