/
fastaUnresolvedRegions.go
134 lines (110 loc) · 3.78 KB
/
fastaUnresolvedRegions.go
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/* Copyright (C) 2019 Philipp Benner
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
package main
/* -------------------------------------------------------------------------- */
import "fmt"
import "log"
import "os"
import "github.com/pborman/getopt"
import . "github.com/pbenner/gonetics"
/* -------------------------------------------------------------------------- */
type Config struct {
OutFormat string
Verbose int
}
/* -------------------------------------------------------------------------- */
func PrintStderr(config Config, level int, format string, args ...interface{}) {
if config.Verbose >= level {
fmt.Fprintf(os.Stderr, format, args...)
}
}
/* -------------------------------------------------------------------------- */
func importFasta(config Config, filename string) StringSet {
s := StringSet{}
PrintStderr(config, 1, "Reading fasta file `%s'... ", filename)
if err := s.ImportFasta(filename); err != nil {
PrintStderr(config, 1, "failed\n")
log.Fatal(err)
}
PrintStderr(config, 1, "done\n")
return s
}
/* -------------------------------------------------------------------------- */
func exportBed3(config Config, granges GRanges, filename string) {
if filename == "" {
if err := granges.WriteBed3(os.Stdout); err != nil {
log.Fatal(err)
}
} else {
PrintStderr(config, 1, "Writing table `%s'... ", filename)
if err := granges.ExportBed3(filename, false); err != nil {
PrintStderr(config, 1, "failed\n")
log.Fatal(err)
} else {
PrintStderr(config, 1, "done\n")
}
}
}
/* -------------------------------------------------------------------------- */
func fastaUnresolvedRegions(config Config, filenameFasta, filenameOutput string) {
genomicSequence := importFasta(config, filenameFasta)
seqnames := []string{}
from := []int{}
to := []int{}
for name, sequence := range genomicSequence {
for i := 0; i < len(sequence); i++ {
if sequence[i] == 'n' || sequence[i] == 'N' {
i_from := i
i_to := i+1
for i++; i < len(sequence); i++ {
if sequence[i] == 'n' || sequence[i] == 'N' {
i_to = i+1
} else {
break
}
}
seqnames = append(seqnames, name)
from = append(from, i_from)
to = append(to, i_to)
}
}
}
exportBed3(config, NewGRanges(seqnames, from, to, nil), filenameOutput)
}
/* -------------------------------------------------------------------------- */
func main() {
config := Config{}
options := getopt.New()
optHelp := options. BoolLong("help", 'h', "print help")
optVerbose := options.CounterLong("verbose", 'v', "be verbose")
options.SetParameters("<SEQUENCES.fa> [OUTPUT.bed]\n")
options.Parse(os.Args)
if *optHelp {
options.PrintUsage(os.Stdout)
os.Exit(0)
}
if len(options.Args()) != 1 && len(options.Args()) != 2 {
options.PrintUsage(os.Stderr)
os.Exit(1)
}
config.Verbose = *optVerbose
filenameFasta := options.Args()[0]
filenameOutput := ""
if len(options.Args()) == 2 {
filenameOutput = options.Args()[1]
}
fastaUnresolvedRegions(config, filenameFasta, filenameOutput)
}