Metadata-Version: 1.0
Name: Fastaq
Version: 1.5.0
Summary: Scripts to manipulate FASTA and FASTQ files, plus API for developers
Home-page: https://github.com/sanger-pathogens/Fastaq
Author: Martin Hunt
Author-email: mh12@sanger.ac.uk
License: GPLv3
Description: Fastaq
        ======
        
        Python3 scripts to manipulate FASTA and FASTQ files, plus API for developers
        
        Installation
        ------------
        
        Run the tests:
        
            python3 setup.py test
        
        Install:
        
            python3 setup.py install
        
        Notes:
         * A few scripts assume that samtools is installed and in your path. This is NOT tested in the tests, because most scripts don't need it.
         * The installation will put all scripts in your path and are named fastaq_*.
        
        Scripts
        -------
        
        Key points:
         * Use -h or --help with a script to get its usage.
         * All scripts automatically detect whether the input is a FASTA or FASTQ file.
         * Input and output files can be gzipped. An input file is assumed to be gzipped if its name ends with .gz. To gzip an output file, just name it with .gz at the end.
         * You can use a minus sign for a filename to use stdin or stdout, so scripts can be piped together. See the following examples.
        
        Reverse complement all sequences in a file:
        
            fastaq_reverse_complement in.fastq out.fastq
        
        Reverse complement all sequences in a gzipped file, then translate each sequence
        
            fastaq_reverse_complement in.fastq.gz - | fastaq_translate - out.fasta
        
        For developers
        --------------
        
        Here is a template for counting the sequences in a FASTA or FASTQ file:
        
            from fastaq import sequences
            seq_reader = sequences.file_reader(infile)
            count = 0
            for seq in seq_reader:
                count += 1
            print(count)
        
        Hopefully you get the idea and there are plenty of examples in tasks.py. Detection of FASTA or FASTQ and gzipped or not input file 'infile' is automatic. See help(sequences) for the various methods already defined in the classes Fasta and Fastq.
        
Platform: UNKNOWN
