Re: [R-sig-phylo] read.FASTA accept connection

[Emmanuel Paradis]

This is great! This can also read other types of connection. I made a 
few modifications so that the function can read remote files through 
HTTPS or FTPS and this fixes the crash when reading empty files (or 
compressed files without specifying a connection). For this fix, it is 
needed to recompile ape, but the modified read.FASTA (pasted below) can 
be used without recompilation.


Cheers,

Emmanuel


read.FASTA <- function(file)
{
if (length(grep("^(ht|f)tp(s|):", file))) {
url <- file
file <- tempfile()
download.file(url, file)
}
if (is(file, "connection")) {
if (!isOpen(file, "rt")) {
open(file, "rt")
on.exit(close(file))
}
x <- scan(file, what = character(), sep = "\n", quiet = TRUE)
x <- charToRaw(paste(x, collapse = "\n"))
sz <- length(x)
} else {
sz <- file.size(file)
x <- readBin(file, "raw", sz)
}
## if the file is larger than 1 Gb we assume that it is
## UNIX-encoded and skip the search-replace of carriage returns
if (sz < 1e9) {
icr <- which(x == as.raw(0x0d)) # CR
if (length(icr)) x <- x[-icr]
}
res <- .Call("rawStreamToDNAbin", x)
if (identical(res, 0L)) {
warning("failed to read sequences, returns NULL")
return(NULL)
}
names(res) <- sub("^ +", "", names(res)) # to permit phylosim
class(res) <- "DNAbin"
res
}

Le 04/01/2017 à 00:37, Rj Ewing a écrit :

Emmanuel,

Thanks, I've attached a patch containing the changes.

I'm not very familiar with R, so maybe there is a better way to do it.
Let me know if you want me to make any changes.

Thanks,
RJ

On Tue, Jan 3, 2017 at 12:53 AM, Emmanuel Paradis
> wrote:

Hi,

You can send your contribution directly to me. See this post for a
recent discussion on how to contribute to ape:

http://www.mail-archive.com/r-sig-phylo@r-project.org/msg04580.htmlra 


Sure your contribution will be useful. I've just found out that
read.FASTA crashes R if the FASTA file is gz'ed. It will be the
opportunity to fix this too.

Best,

Emmanuel


Le 02/01/2017 à 19:26, Rj Ewing a écrit :

Is there a way to contribute to the project? I would like to add the
ability for read.FASTA to accept a connection or a file.

I have a zip file that I would rather not unzip before passing into
read.FASTA. I can obtain a connection using unz("file.zip",
"myFasta.fasta"), however read.FASTA does not support this.

Thanks,
RJ

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Re: [R-sig-phylo] read.FASTA accept connection

[Rj Ewing]

Emmanuel,

Thanks, I've attached a patch containing the changes.

I'm not very familiar with R, so maybe there is a better way to do it. Let
me know if you want me to make any changes.

Thanks,
RJ

On Tue, Jan 3, 2017 at 12:53 AM, Emmanuel Paradis 
wrote:

> Hi,
>
> You can send your contribution directly to me. See this post for a recent
> discussion on how to contribute to ape:
>
> http://www.mail-archive.com/r-sig-phylo@r-project.org/msg04580.htmlra
>
> Sure your contribution will be useful. I've just found out that read.FASTA
> crashes R if the FASTA file is gz'ed. It will be the opportunity to fix
> this too.
>
> Best,
>
> Emmanuel
>
>
> Le 02/01/2017 à 19:26, Rj Ewing a écrit :
>
>> Is there a way to contribute to the project? I would like to add the
>> ability for read.FASTA to accept a connection or a file.
>>
>> I have a zip file that I would rather not unzip before passing into
>> read.FASTA. I can obtain a connection using unz("file.zip",
>> "myFasta.fasta"), however read.FASTA does not support this.
>>
>> Thanks,
>> RJ
>>
>> [[alternative HTML version deleted]]
>>
>> ___
>> R-sig-phylo mailing list - R-sig-phylo@r-project.org
>> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
>> Searchable archive at http://www.mail-archive.com/r-
>> sig-ph...@r-project.org/
>>
>>
>> Pour nous remonter une erreur de filtrage, veuillez vous rendre ici :
>> http://f.security-mail.net/302UOvTyxTd
>>
>>
>>


connections.patch
Description: Binary data
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Re: [R-sig-phylo] read.FASTA accept connection

[Emmanuel Paradis]

Hi,

You can send your contribution directly to me. See this post for a 
recent discussion on how to contribute to ape:


http://www.mail-archive.com/r-sig-phylo@r-project.org/msg04580.htmlra

Sure your contribution will be useful. I've just found out that 
read.FASTA crashes R if the FASTA file is gz'ed. It will be the 
opportunity to fix this too.


Best,

Emmanuel

Le 02/01/2017 à 19:26, Rj Ewing a écrit :

Is there a way to contribute to the project? I would like to add the
ability for read.FASTA to accept a connection or a file.

I have a zip file that I would rather not unzip before passing into
read.FASTA. I can obtain a connection using unz("file.zip",
"myFasta.fasta"), however read.FASTA does not support this.

Thanks,
RJ

[[alternative HTML version deleted]]

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http://f.security-mail.net/302UOvTyxTd




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[R-sig-phylo] read.FASTA accept connection

[Rj Ewing]

Is there a way to contribute to the project? I would like to add the
ability for read.FASTA to accept a connection or a file.

I have a zip file that I would rather not unzip before passing into
read.FASTA. I can obtain a connection using unz("file.zip",
"myFasta.fasta"), however read.FASTA does not support this.

Thanks,
RJ

[[alternative HTML version deleted]]

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