用于对照一组样品检查标记是否存在的包装
seqPresenceAbsence的Python项目详细描述
SeqPresence缺勤
要求
- python=3.6
- Perl 5（fasconcat-g所需）
- ncbi-blast+（makeblastdb和blastn必须在$path中）
- MUSCLE（肌肉必须在$path中）
安装
pip install seqPresenceAbsence
使用量
Usage: seqPresenceAbsence [OPTIONS]
seqPresenceAbsence is a simple script for querying an input nucleotide
FASTA file against a database of sequences. Will return an .xlsx and .csv
report of presence/absence of the sequences. Version: 0.2.0.
Options:
-i, --indir PATH Path to directory containing FASTA files you want
to query [required]
-t, --targets PATH Path to multi-FASTA containing targets of
interest [required]
-o, --outdir PATH Root directory to store all output files
[required]
-p, --perc_identity FLOAT Equivalent to the -perc_identity argument in
blastn. Defaults to 95.00.
-k, --keep_db_seqs Set this flag to keep the target sequence in
addition to the query sequence from BLAST.
-v, --verbose Set this flag to enable more verbose logging.
--version Specify this flag to print the version and exit.
--help Show this message and exit.
注释
该软件包包括由patrick kück开发的fasconcat-g v1.04发行版。
参考文献
- Kück P.，Meusemann K.（2010）：fasconcat：数据矩阵的方便处理。Phylogen分子。伊沃。56:1115-1118
- Edgar，R.C.（2004）肌肉：具有高精度和高吞吐量的多序列比对 核酸研究32（5）：1792-1797
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