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FastaIndex的Python项目详细描述
fasta索引（.fai）处理程序与samtools faidx兼容。 .fai扩展为4列，存储每个序列的a、c、g&t计数。
用法
依赖性
- python 2.7版
参数
-h, --help show this help message and exit --version show program’s version number and exit -v, --verbose verbose -i FASTA, --fasta FASTA FASTA file(s) -o OUT, --out OUT output stream [stdout] -r REGIONS, --regions REGIONS contig(s) or contig region(s) to output (returns reverse complement if end larger than start) -N N calculate NXX and exit ie N50 -L L calculate LXX and exit ie L50 -S, --stats return FastA stats aka fasta_stats
示例
# retrieve sequence of scaffold00001 starting at 100 and ending at 200 base (0-based) FastaIndex -i contigs.fa -r 'scaffold00001:100-200'# retrieve reverse complement of the same region FastaIndex -i contigs.fa -r 'scaffold00001:200-100'# calculate N50 of FastA file FastaIndex -i contigs.fa -N50 # more statistics of FastA file FastaIndex -i contigs.fa -S # or fasta_stats -i contigs.fa
安装
sudo pip install -U FastaIndex
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