I'm looking for an existing C program which can parse FASTA files for an academic project. The requirements are:
- It must be capable of parsing very large DNA sequences (entire genomes)
- It must be open source (i.e. I must have the author's permission to use it)
- It must be C only (not C++)
I've done some Googling but haven't yet found an ideal candidate. I would appreciate any advice.
Thank you
4 answers
Heng Li has a fasta/fastq parser in that fits in a single C-header file: http://lh3lh3.users.sourceforge.net/parsefastq.shtml
If you look the example, KSEQ_INIT request two variable, the first is a type variable, for your purpose use FILE* (it's defined in stdio.h), the second is a method, the text file are readed by "read" method:
KSEQ_INIT(FILE*, read); //STEP 1
I tried with fscanf and fgets, but they are wrong.
after that, you must use a connection to the file, a pointer file:
FILE* fp;
the file is open by fopen:
fp = fopen(argv[1], "r"); // STEP 2
at the end you need to close the connection.
fclose(fp); // STEP 6
that's all for the moment, I'm finding the function to read.
if I use int the prompt prints Program too big to fit in memory
Modifying your example:
#include <stdio.h>
#include "kseq.h"
KSEQ_INIT(int, read)
int main(int argc, char *argv[])
{
FILE* fp;
kseq_t *seq;
int l;
if (argc == 1) {
fprintf(stderr, "Usage: %s <in.seq>\n", argv[0]);
return 1;
}
fp = fopen(argv[1], "r");
seq = kseq_init(fp);
while ((l = kseq_read(seq)) >= 0) {
printf("name: %s\n", seq->name.s);
if (seq->comment.l) printf("comment: %s\n", seq->comment.s);
printf("seq: %s\n", seq->seq.s);
if (seq->qual.l) printf("qual: %s\n", seq->qual.s);
}
printf("return value: %d\n", l);
kseq_destroy(seq);
fclose(fp);
return 0;
}
I obtain when I compile
kseq_test_mod.c: In function 'main':
kseq_test_mod.c:16:2: warning: passing argument 1 of 'kseq_init' makes integer from pointer without a cast
kseq_test_mod.c:4:1: note: expected 'int' but argument is of type 'struct FILE *
If I run the executable:
C:\Documents and Settings\Proteomica\My Documents\Download\kseq>prova.exe sequence.fasta
return value: -1
The fasta is dowloaded from ncbi.
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Gunzapper •
The first thing I did, probably there are some thing that I don't understand
How about Bill Pearson's FASTA (written in C)? Given it is the origin of the format, I am inclined to believe it parses FASTA.
You can try Sean Eddy's squid library. It's a general purpose sequence analysis library, but deprecated by easel (the library now used by HMMER3). See sreformat_main.c for an example of how to read sequence files of (almost) any format.
Another (general purpose) library to consider might be seqan (C++ though and haven't used it myself).
I think there used to be a C version of readseq as well, but I can only find a newer Java version.
However, all of the above might be overkill if you just want to parse fasta format, which is pretty simple.
Andreas
The readseq C version is still available as version1: http://iubio.bio.indiana.edu/soft/molbio/readseq/. It is quite old, though.
The UCSC source tree has a large number of fasta utilities written in C that can parse and process large multi-fasta files in the src/utils directory.
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The top answer to the following question is in pure C and works for fasta. MIT license. Which C++ Libraries Are Best For Dealing With Fastq Files?
See also: Which C++ Libraries Are Best For Dealing With Fastq Files?
The library mentioned in top answer is efficient, MIT licensed, written in C and works for both fasta and fastq.