Metadata-Version: 1.1
Name: bioinfo-tools
Version: 0.2.6.1
Summary: Python library that parses GFF, Fasta files into python classes
Home-page: https://github.com/sebriois/bioinfo_tools
Author: Sebastien Briois, Guillaume Tiberi
Author-email: sebriois@gmail.com
License: BSD
Description: # bioinfo_tools 0.2.6.1
        
        ## Installation
        
        ```bash
        pip install bioinfo_tools
        ```
        
        ## Parsers
        
        *HEADS UP!* These parsers are still under development and usage is not consistent from one parser to another.
        
        ### Fasta parser
        
        ```python
        from bioinfo_tools.parsers.fasta import FastaParser
        
        fasta_parser = FastaParser()
        
        # by default, sequence IDs are separated by the firstly found '|' or ':'
        for seqid, sequence in fasta_parser.read("/path/to/file.fasta"):
            print(seqid, sequence)
        
        # you may specify a specific separator for your sequence ID (e.g white space):
        for seqid, sequence in fasta_parser.read("/path/to/file.fasta", id_separator=" "):
            print(seqid, sequence)
        ```
        
        ### GFF parser
        
        ```python
        from bioinfo_tools.parsers.gff import Gff3
        
        gff_parser = Gff3()
        with open("/path/to/file.gff") as fh:
            for gene in gff_parser.read(fh):
                print(gene)
        
        import gzip
        with gzip.open("/path/to/file.gz", "rb") as fh:
            for gene in gff_parser.read(fh):
                print(gene)
        ```
        
        ### OBO parser
        
        
        ```python
        from bioinfo_tools.parsers.obo import OboParser
        
        obo_parser = OboParser()
        with open("/path/to/file.obo") as fh:
            go_terms = obo_parser.read(fh)
        
        for go_term in go_terms.values():
            print(go_term)
        
            # you may also get the GO term parents via the parser
            parents = obo_parser.get_parents(go_term)
        ```
Keywords: bioinformatics
Platform: UNKNOWN
Classifier: Environment :: Web Environment
Classifier: Intended Audience :: Developers
Classifier: License :: OSI Approved :: BSD License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
