从fasta文件中提取特定的fasta序列。孟冠良，见https://github.com/linzhi2013
extract-fasta-seq的Python项目详细描述
提取快速顺序
1简介
extract_fasta_seq是一个从fasta文件中提取特定fasta序列的工具。孟冠良，见https://github.com/linzhi2013/extract_fasta_seq
2安装
pip install extract_fasta_seq
将在与您的pip命令相同的目录下创建命令extract_fasta_seq。
3用法
$ extract_fasta_seq
usage: extract_fasta_seq.py [-h] [-q <str> [<str> ...]] [-f <query file>]
[-s [<subject file>]] [-s1 <pattern>]
[-s2 <pattern>] [-d1 [<int>]] [-d2 [<int>]]
[-o [<outfile>]] [-v] [-V] [--lazy] [--version]
To extract specific fasta sequences from a fasta file. By Guanliang MENG, see
https://github.com/linzhi2013
optional arguments:
-h, --help show this help message and exit
-q <str> [<str> ...] query list. "-s1" and "-d1" have no effect on this
option.
-f <query file> query list file, one line should contain only one
queryid! (but can be mixed with others, and we can use
"-s1" and "-d1" option to extract the queryid)
-s [<subject file>] subject file [stdin]
-s1 <pattern> query file sep_pattern [\s+]
-s2 <pattern> subject file sep_pattern [\s+]
-d1 [<int>] which field in the query_file is to used? [0]
-d2 [<int>] which field in the subject_file is to used? useful for
finding out all sequences in the subject_file whose
seqids equal to the queryids [0]
-o [<outfile>] outfile [stdout]
-v invert the output [False]
-V verbose output
--lazy Stop searching once each required seqid has at least
one sequence found, which can be problems if some
required seqids have more than sequences! Works only
for non-invert mode. [False]
--version show program's version number and exit
4作者
孟冠良
5条引文
目前我没有计划发布extract_fasta_seq。
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