Hi Ge,
On 06/28/2013 04:45 AM, Ge Tan wrote:
Hi Hervé,
Thank you so much!!! I tweaked it a little and it works exactly in the
Biostrings way which I want to learn!
You are my idol!!
One minor question I want to ask is when I change the
alloc_XRawList("BStringSet", "BString", ans_width));
to DNAStringSet.
So you have a text file with one DNA sequence per line. I wonder what
kind of file is that. Wouldn't it be easier if you managed to store
your DNA sequences in FASTA format so you could just reuse
readDNAStringSet() to load it? If you leave the record headers
empty, the FASTA file won't be significantly bigger than the text file
with one DNA sequence per line.
It reprots an error,
myAxt
A DNAStringSet instance of length 315050
width seq
Error in .Call2("new_CHARACTER_from_XString", x, xs_dec_lkup(x), PACKAGE =
"Biostrings") :
key 65 (char 'A') not in lookup table
Chars stored in a DNAStringSet need to be encoded.
The encoding scheme is:
- DNA base letters A, C, G, and T are associated to bits 0, 1, 2,
and 3, respectively. So A -> 0x1, C -> 0x2, G -> 0x4, T -> 0x8.
- IUPAC ambiguity codes are represented by a bit pattern that
combines the bits of the base letters that they are associated
with. For example, R is associated with A and G so is represented
by bits 0 and 2 set to 1 and all other bits set to 0. So R -> 0x5.
- Special letters - and + are represented by 0x10 and 0x20,
respectively.
This encoding scheme is summarized by the following lookup table:
> lkup <- get_seqtype_conversion_lookup("B", "DNA")
> lkup
[1] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
NA NA NA NA
[26] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 32 NA 16
NA NA NA NA
[51] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA 1 14 2 13 NA NA
4 11 NA NA
[76] 12 NA 3 15 NA NA NA 5 6 8 NA 7 9 NA 10 NA NA NA NA NA NA
NA 1 14 2
[101] 13 NA NA 4 11 NA NA 12 NA 3 15 NA NA NA 5 6 8 NA 7 9 NA 10
'lkup' is an integer vector that allows fast encoding from ASCII to
DNA (accepts lower-case DNA letters):
> lkup[as.integer(charToRaw("ACGTRa-+Xz")) + 1L]
[1] 1 2 4 8 5 1 16 32 NA NA
To use this lookup table at the C level, just pass it as an extra arg
to your .Call entry point. Then, at the C level, encode the incoming
bytes with something like:
int lkup_len, key, val;
char encoded_byte;
...
lkup_len = LENGTH(lkup);
key = (unsigned char) incoming_byte;
if (key >= lkup_len || (val = INTEGER(lkup)[key]) == NA_INTEGER) {
/* Make sure to UNPROTECT() whetever is currently PROTECTed,
and to free() whatever user-controlled memory is currently
allocated before you call error(). */
error("invalid char: '%c'", incoming_byte);
}
encoded_byte = (char) val;
...
HTH,
H.
Do you have any idea?
Thanks again!
Ge
------------------ Original ------------------
From: "Herv Pag s"<hpa...@fhcrc.org>;
Date: Fri, Jun 28, 2013 05:44 AM
To: "Ge Tan"<184523...@qq.com>;
Cc: "r-devel"<r-de...@r-project.org>;
Subject: Re: [Rd] Read a text file into R with .Call()
Hi Ge,
Here is one way to do this with the Biostrings C API. It does
2 passes on the file. There is also a 1-pass way but not necessarily
worth it because not as memory efficient.
The code below is untested (not even guaranteed to compile)!
SEXP read_text_file_in_BStringSet(FILE *FN)
{
SEXP ans, width;
IntAE width_buf;
char *foo;
cachedXVectorList cached_ans;
cachedCharSeq cached_ans_elt;
int i;
/* 1st pass: compute the 'width' vector. */
width_buf = new_IntAE(0, 0, 0);
while (foo = readLine(FN)) {
IntAE_insert_at(&width_buf, IntAE_get_nelt(width_buf),
strlen(foo));
}
PROTECT(width = new_INTEGER_from_IntAE(&width_buf));
/* Allocate 'ans'. */
PROTECT(ans = alloc_XRawList("BStringSet", "BString", ans_width));
/* 2nd pass: Fill 'ans' with data. */
cached_ans = cache_XVectorList(ans);
rewind(FN);
i = 0;
while (foo = readLine(FN)) {
cached_ans_elt = get_cachedXRawList_elt(&cached_ans, i);
memcpy((char *) cached_ans_elt->seq, foo, INTEGER(width)[i] *
sizeof(char));
i++;
}
UNPROTECT(2);
return ans;
}
The returned object is a BStringSet object.
Note that I kept your
foo = readLine(FN)
approach for reading the file line by line. A more efficient way would
be to use something like
n = getLineLength(FN)
for the 1st pass (no need to load the line of text into the foo
buffer), and something like
readLine(FN, (char *) cached_ans_elt->seq)
for the 2nd pass so the data is loaded directly to where it needs to
go (i.e. without going first thru the foo buffer, hence avoiding the
memcpy()).
Cheers,
H.
On 06/27/2013 12:37 PM, Ge Tan wrote:
Hi Simons,
Thanks for your reply.
10000 is just an example I wrote. In fact, there can be millions of strings
(all of them are different and each has thousands of characters) I want to read
from the file. So if I use mkChar it will store the same amount of the copies
in the global cache.
The problem is when I get the returned qNames in R, and then rm(qNames) and do
the gc().
gc() shows a normal amout of memory it uses. But from the top command, this R
session can still use several GB. The rm() and gc() does not take effect on the
memory release. (I suspect the release of the global cache is not done, even
now there is not objects pointing to them.)
I am sure there is no other memory leak problem. Once I run the mkChar, the
memory issue emerges.
So I am comfused how to read lines from text files and make it into R character
vectors to pass back to R. We cannot store each of them into the global cache
nor is not necessary as they are not duplicated.
Regarding the raw vector method, I am not quite clear how to manipulate it.
Could you give some more detailed examples?
I attached more complete code I wrote. BTW, I am using R version 2.15.2.
Thanks!
Ge
PROTECT(qNames = NEW_CHARACTER(nrAxts));
PROTECT(qStart = NEW_INTEGER(nrAxts));
PROTECT(qEnd = NEW_INTEGER(nrAxts));
PROTECT(qStrand = NEW_CHARACTER(nrAxts));
PROTECT(qSym = NEW_CHARACTER(nrAxts));
PROTECT(tNames = NEW_CHARACTER(nrAxts));
PROTECT(tStart = NEW_INTEGER(nrAxts));
PROTECT(tEnd = NEW_INTEGER(nrAxts));
PROTECT(tStrand = NEW_CHARACTER(nrAxts));
PROTECT(tSym = NEW_CHARACTER(nrAxts));
PROTECT(score = NEW_INTEGER(nrAxts));
PROTECT(symCount = NEW_INTEGER(nrAxts));
PROTECT(returnList = NEW_LIST(12));
int *p_qStart, *p_qEnd, *p_tStart, *p_tEnd, *p_score, *p_symCount;
p_qStart = INTEGER_POINTER(qStart);
p_qEnd = INTEGER_POINTER(qEnd);
p_tStart = INTEGER_POINTER(tStart);
p_tEnd = INTEGER_POINTER(tEnd);
p_score = INTEGER_POINTER(score);
p_symCount = INTEGER_POINTER(symCount);
int j = 0;
i = 0;
for(j = 0; j < nrAxtFiles; j++){
char *filepath_elt = (char *) R_alloc(strlen(CHAR(STRING_ELT(filepath,
j))), sizeof(char));
strcpy(filepath_elt, CHAR(STRING_ELT(filepath, j)));
lf = lineFileOpen(filepath_elt, TRUE);
while((axt = axtRead(lf)) != NULL){
SET_STRING_ELT(qNames, i, mkChar(axt->qName));
p_qStart[i] = axt->qStart + 1;
p_qEnd[i] = axt->qEnd;
if(axt->qStrand == '+')
SET_STRING_ELT(qStrand, i, mkChar("+"));
else
SET_STRING_ELT(qStrand, i, mkChar("-"));
SET_STRING_ELT(qSym, i, mkChar(axt->qSym));
SET_STRING_ELT(tNames, i, mkChar(axt->tName));
p_tStart[i] = axt->tStart + 1;
p_tEnd[i] = axt->tEnd;
if(axt->tStrand == '+')
SET_STRING_ELT(tStrand, i, mkChar("+"));
else
SET_STRING_ELT(tStrand, i, mkChar("-"));
SET_STRING_ELT(tSym, i, mkChar(axt->tSym));
p_score[i] = axt->score;
p_symCount[i] = axt->symCount;
i++;
axtFree(&axt);
}
lineFileClose(&lf);
}
SET_VECTOR_ELT(returnList, 0, tNames);
SET_VECTOR_ELT(returnList, 1, tStart);
SET_VECTOR_ELT(returnList, 2, tEnd);
SET_VECTOR_ELT(returnList, 3, tStrand);
SET_VECTOR_ELT(returnList, 4, tSym);
SET_VECTOR_ELT(returnList, 5, qNames);
SET_VECTOR_ELT(returnList, 6, qStart);
SET_VECTOR_ELT(returnList, 7, qEnd);
SET_VECTOR_ELT(returnList, 8, qStrand);
SET_VECTOR_ELT(returnList, 9, qSym);
SET_VECTOR_ELT(returnList, 10, score);
SET_VECTOR_ELT(returnList, 11, symCount);
UNPROTECT(13);
//axtFree(&curAxt);
//return R_NilValue;
return returnList;
------------------ Original ------------------
From: "r-devel"<r-de...@r-project.org>;
Date: Fri, Jun 28, 2013 03:08 AM
To: "Ge Tan"<184523...@qq.com>;
Cc: "r-devel"<r-de...@r-project.org>;
Subject: Re: [Rd] Read a text file into R with .Call()
On Jun 27, 2013, at 9:18 AM, Ge Tan wrote:
Hi,
I want to read a text file into R with .Call().
So I define some NEW_CHARACTER() to store the chracters read and use
SET_STRING_ELT to fill the elements.
e.g.
PROTECT(qNames = NEW_CHARACTER(10000));
char *foo; // This foo holds the string I want.
while(foo = readLine(FN)){
SET_STRING_ELT(qNames, i, mkChar(foo)));
}
In this way, I can get the desired character from qNames. The only problem is that
"mkChar" will make every foo string into a global CHARSXP cache. When I have a
huge amount of file to read, the CHARSXP cache use too much memory. I do not know whether
there is any other way to SET_STRING_ELT without the mkChar operation.
No. *all* strings in R are in the cache. The whole point of it is that is uses
less memory by not duplicating strings - and the overhead for as little as
10000 strings is minuscule. So I suspect that is not your problem since if that
was the case, you would not have enough memory to just load the file. Check you
code, chances are the issue is elsewhere.
That said, you can always load the file into a raw vector and use accessor
function to create strings on demand - but this is only meaningful when you
plan to use a very small subset.
Cheers,
Simon
I know I cam refer to the Biostrings pakcage's way of readDNAStringSet, but
that is a bit complicated I have not full understood it.
Any help will be appreciated!!
Ge
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--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024
E-mail: hpa...@fhcrc.org
Phone: (206) 667-5791
Fax: (206) 667-1319
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