idoneal - main.go

     1  // This package contains a CLI program to extract basic metadata from FASTQ formatted files.
     2  package main // import "vimagination.zapto.org/idoneal"
     3  
     4  import (
     5  	"compress/gzip"
     6  	"flag"
     7  	"fmt"
     8  	"io"
     9  	"io/fs"
    10  	"os"
    11  	"strings"
    12  
    13  	"vimagination.zapto.org/idoneal/pkg/meta"
    14  )
    15  
    16  type OS struct{}
    17  
    18  func (OS) Open(name string) (fs.File, error) {
    19  	return os.Open(name)
    20  }
    21  
    22  // Vars to be mocked for testing
    23  var (
    24  	Stdout           io.Writer = os.Stdout
    25  	Stderr           io.Writer = os.Stderr
    26  	FS               fs.FS     = OS{}
    27  	Exit                       = os.Exit
    28  	flagErrorHandler           = flag.ExitOnError
    29  )
    30  
    31  func openFile(file string) (io.ReadCloser, error) {
    32  	var (
    33  		f   io.ReadCloser
    34  		err error
    35  	)
    36  	f, err = FS.Open(file)
    37  	if err != nil {
    38  		return nil, fmt.Errorf("error opening file: %w\n", err)
    39  	}
    40  	if strings.HasSuffix(file, ".gz") {
    41  		f, err = gzip.NewReader(f)
    42  		if err != nil {
    43  			return nil, fmt.Errorf("error starting decompression: %w", err)
    44  		}
    45  	}
    46  	return f, nil
    47  }
    48  
    49  func main() {
    50  	var countSequences, countNucleotides bool
    51  
    52  	flags := flag.NewFlagSet(os.Args[0], flagErrorHandler)
    53  	flags.SetOutput(Stderr)
    54  	flags.Usage = func() {
    55  		fmt.Fprintf(Stderr, `Usage: %s [OPTIONS] FILE
    56  
    57  OPTIONS:
    58    -h, --help          Print this help.
    59    -n, --nucleotides   Print the number of nucleotides in the FILE.
    60    -s, --sequences     Print the number of sequences in the FILE.
    61  `, os.Args[0])
    62  	}
    63  	flags.BoolVar(&countSequences, "s", false, "")
    64  	flags.BoolVar(&countSequences, "sequences", false, "")
    65  	flags.BoolVar(&countNucleotides, "n", false, "")
    66  	flags.BoolVar(&countNucleotides, "nucleotides", false, "")
    67  	flags.Parse(os.Args[1:])
    68  
    69  	file := flags.Arg(0)
    70  
    71  	if file == "" {
    72  		flags.Usage()
    73  		return
    74  	}
    75  
    76  	if countSequences {
    77  		f, err := openFile(file)
    78  		if err != nil {
    79  			fmt.Fprintln(Stderr, err)
    80  		}
    81  		defer f.Close()
    82  		count, err := meta.CountSequences(f)
    83  		if err != nil {
    84  			fmt.Fprintf(Stderr, "error while counting sequences: %s\n", err)
    85  			Exit(2)
    86  			return
    87  		}
    88  		fmt.Fprintln(Stdout, count)
    89  	}
    90  	if countNucleotides {
    91  		f, err := openFile(file)
    92  		if err != nil {
    93  			fmt.Fprintln(Stderr, err)
    94  		}
    95  		defer f.Close()
    96  		count, err := meta.CountNucleotides(f)
    97  		if err != nil {
    98  			fmt.Fprintf(Stderr, "error while counting nucleotides: %s\n", err)
    99  			Exit(2)
   100  			return
   101  		}
   102  		fmt.Fprintln(Stdout, count)
   103  	}
   104  }
   105