Metadata-Version: 2.1
Name: extract-fasta-seq
Version: 0.0.1
Summary: To extract specific fasta sequences from a fasta file. By Guanliang MENG, see https://github.com/linzhi2013
Home-page: https://github.com/linzhi2013
Author: Guanliang Meng
Author-email: mengguanliang@foxmail.com
License: UNKNOWN
Description: # extract_fasta_seq
        
        ## 1 Introduction
        
        `extract_fasta_seq` is a tool to extract specific fasta sequences from a fasta file. By Guanliang MENG, see https://github.com/linzhi2013/extract_fasta_seq
        
        ## 2 Installation
        
            pip install extract_fasta_seq
        
        There will be a command `extract_fasta_seq` created under the same directory as your `pip` command.
        
        ## 3 Usage
            
            $ 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 Author
        Guanliang MENG
        
        ## 5 Citation
        Currently I have no plan to publish `extract_fasta_seq`.
        
        
        
        
        
        
        
        
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)
Classifier: Programming Language :: Python :: 3
Classifier: Operating System :: MacOS :: MacOS X
Classifier: Operating System :: Microsoft :: Windows
Classifier: Operating System :: POSIX :: Linux
Requires-Python: >=3
Description-Content-Type: text/markdown
