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#### File I/O -- Input and output sequence data.
---
##### Input <code>Phyclust</code> accepts three types of input:
- Data read from a text file in PHYLIP format.
- Data read from a text file in FASTA format.
- Data simulated by the
<a href="./ex_msseqgen.html"><code>ms+seqgen</code></a>
approach.
The data reading functions <code>read.*()</code> will return a list object of
class <code>seq.data</code>.
Suppose we call the returned list object <code>ret</code>.
Then, <code>ret$org.code</code> and <code>ret$org</code> are two matrices that
store the data.
Matrix <code>ret$org.code</code> contains the original data, e.g. A,G,C,T for
nucleotide, and
<code>ret$org</code> contains the data formatted for
the computer, e.g. 0,1,2,3 for nucleotide.
Matrix <code>ret$org</code> is translated from <code>ret$org.code</code>
according to the standard encoding of the chosen data type, and most
calculations are done with <code>ret$org</code>.
---
##### Output <code>Phyclust</code> outputs sequence data in two formats: PHYLIP or FASTA.
We use "<code>Great pony EIAV rev datasets</code>" as examples,
<a href="./pony524.txt" target="_blank">pony524.phy</a>
in <code>PHYLIP</code> format and
<a href="./pony625.txt" target="_blank">pony625.fas</a>
in <code>FASTA</code> format.
The other example for the data sets can be found at
<a href="./ex_eiav.html">here</a>.
The following code will read in two file, create objects with class
<code>seq.data</code>, and save the data matrix in two new files in
the working directory.
---
##### Read a PHYLIP file
```
> data.path <- paste(.libPaths()[1], "/phyclust/data/pony524.phy", sep = "")
> (my.pony.524 <- read.phylip(data.path))
code.type: NUCLEOTIDE, n.seq: 146, seq.len: 405.
> str(my.pony.524)
List of 7
$ code.type: chr "NUCLEOTIDE"
$ info : chr " 146 405"
$ nseq : num 146
$ seqlen : num 405
$ seqname : Named chr [1:146] "AF314258" "AF314259" "AF314260" "AF314261" ...
..- attr(*, "names")= chr [1:146] "1" "2" "3" "4" ...
$ org.code : chr [1:146, 1:405] "g" "g" "g" "g" ...
$ org : num [1:146, 1:405] 1 1 1 1 1 1 1 1 1 1 ...
- attr(*, "class")= chr "seq.data"
```
---
##### Read a FASTA file
```
> data.path <- paste(.libPaths()[1], "/phyclust/data/pony625.fas", sep = "")
> (my.pony.625 <- read.fasta.nucleotide(data.path))
code.type: NUCLEOTIDE, n.seq: 62, seq.len: 406.
> str(my.pony.625)
List of 6
$ code.type: chr "NUCLEOTIDE"
$ nseq : num 62
$ seqlen : int 406
$ seqname : chr [1:62] "AF512608" "AF512609" "AF512610" "AF512611" ...
$ org.code : chr [1:62, 1:406] "G" "G" "G" "G" ...
$ org : num [1:62, 1:406] 1 1 1 1 1 1 1 1 1 1 ...
- attr(*, "class")= chr "seq.data"
```
---
##### Save files
```
> # PHYLIp
> write.phylip(my.pony.625$org, "new.625.txt")
> edit(file = "new.625.txt")
> # FASTA
> write.fasta(my.pony.524$org, "new.524.txt")
> edit(file = "new.524.txt")
```
---
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