From e4402603f14b5e10c54cd1ec38d6dce0710487c0 Mon Sep 17 00:00:00 2001
From: Frederic Lemoine <fredericlemoine@users.noreply.github.com>
Date: Sat, 14 Oct 2023 11:56:53 +0200
Subject: [PATCH] Updated docs for replace

---
 docs/api/replace.md      | 45 ++++++++++++++++++++++++++++++++++++++++
 docs/commands/replace.md |  8 +++++++
 2 files changed, 53 insertions(+)

diff --git a/docs/api/replace.md b/docs/api/replace.md
index 253f898..ac960cb 100644
--- a/docs/api/replace.md
+++ b/docs/api/replace.md
@@ -47,3 +47,48 @@ func main() {
 	fmt.Println(fasta.WriteAlignment(al))
 }
 ```
+
+Replace characters in sequences of input alignment using its position+sequence name.
+
+```go
+package main
+
+import (
+	"bufio"
+	"fmt"
+	"io"
+
+	"github.com/evolbioinfo/goalign/align"
+	"github.com/evolbioinfo/goalign/io/fasta"
+	"github.com/evolbioinfo/goalign/io/utils"
+)
+
+func main() {
+	var fi io.Closer
+	var r *bufio.Reader
+	var err error
+	var al align.SeqBag
+	// or var al align.Alignment if aligned sequences
+
+	/* First Alignment*/
+
+	/* Get reader (plain text or gzip) */
+	if fi, r, err = utils.GetReader("align.fa"); err != nil {
+		panic(err)
+	}
+	defer fi.Close()
+
+	/* Parse Fasta */
+	if al, err = fasta.NewParser(r).Parse(); err != nil {
+	/* for aligned seqs: if al, err = fasta.NewParser(r).Parse(); err != nil {*/
+		panic(err)
+	}
+
+	// Will write a G at position 9 (0 based) of sequence "Seq001"
+	if err = al.ReplaceChar("Seq001", 9, "G"); err != nil {
+		panic(err)
+	}
+
+	fmt.Println(fasta.WriteAlignment(al))
+}
+```
diff --git a/docs/commands/replace.md b/docs/commands/replace.md
index b722d6e..230c191 100644
--- a/docs/commands/replace.md
+++ b/docs/commands/replace.md
@@ -6,6 +6,13 @@
 This command replaces characters in sequences of an input alignment. The `--regexp (-e)` option considers the string to be replaced as a regular expression.
 Unless `--unaligned`is specified, the replacement should not change sequence lengths, otherwise it returns an error.
 
+If `--posfile` is given, then `--old` and `--new` are not considered. Instead, characters at sites+sequences specified in the input file
+are replaced in the alignement. The format of the input posfile is tabulated with columns:
+
+- 0: sequence name
+- 1: site index
+- 2: new character
+
 #### Usage
 ```
 Usage:
@@ -17,6 +24,7 @@ Flags:
   -s, --old string      String to replace in the sequences (default "none")
   -o, --output string   Output alignment file (default "stdout")
   -e, --regexp          Considers Replace alignment using regexp
+  -f, --posfile string  File containing sites to replace by give characters in given sequences (deactivates --old & --new) (default "none")
       --unaligned       Considers input sequences as unaligned and fasta format (phylip, nexus,... options are ignored)
 
 Global Flags: