I tried to write this C code to find complementary of DNA sequence. Please verify and help to improve.
#include<stdio.h>
main()
{
int n;
printf("\n\nEnter length of sequence:");
scanf("%d",&n);
char seq[n], com[n];
int i;
printf("\nENTER THE SEQUENCE:");
scanf("%s",&seq);
for(i;i<n;i++)
{
if(seq[i]=='A')
com[i]='T';
else if(seq[i]=='T')
com[i]='A';
else if(seq[i]=='G')
com[i]='C';
else if(seq[i]=='C')
com[i]='G';
else if(seq[i]==' ')
com[i]='_';
else if(seq[i]!='T' && seq[i]!='A' && seq[i]!='G' && seq[i]!='C')
com[i]='*';
}
printf("\n\n%s\n\n",com);
printf("\n\n* is non-DNA bases\n\n");
}
•
written
by
Arindam Ghosh
declare 'main(int argc,char** argv)'
don't print messages like "ENTER SEQUENCE:"
read from stdin or from one or more file
read fasta
use switch/case instead of 'if/else' or even faster, a conversion array char compl[UCHAR_MAX];
a C program returns 0 on success
•
written
by
Pierre Lindenbaum
If you want really fast, avoid conditionals and instead declare a static array that uses a character's ASCII decimal value to map to its complementary base:
This takes the reverse complement of a string made up of bases {A, C, T, G, U, a, c, t, g, u, N} by reading the input string backwards and printing mapped bases to standard output.
To compile:
$ gcc -Wall rc.c -o rc
To run, as an example:
$ echo 'AGGTCCA' | ./rc TGGACCT
Thanks Alex, getline is new to me. Is it just a GNU extension or is it part of a recent standard ?
memory leak: line should be freed
Fixed, thanks. Valgrind suggests the heap is clean:
$ echo -e 'ATTCG\nTTCCA\nGGGAT\nNNaTT' | valgrind -v --track-origins=yes --leak-check=full ./rc ==26625== Memcheck, a memory error detector ==26625== Copyright (C) 2002-2012, and GNU GPL'd, by Julian Seward et al. ==26625== Using Valgrind-3.8.1 and LibVEX; rerun with -h for copyright info ==26625== Command: ./rc ==26625== ... CGAAT TGGAA ATCCC AAtNN ==26625== ==26625== HEAP SUMMARY: ==26625== in use at exit: 0 bytes in 0 blocks ==26625== total heap usage: 1 allocs, 1 frees, 120 bytes allocated ==26625== ==26625== All heap blocks were freed -- no leaks are possible ==26625== ==26625== For counts of detected and suppressed errors, rerun with: -v ==26625== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 6 from 6)
answering my question: http://stackoverflow.com/questions/13112784 "First, getline() is not in the C standard library, but is a POSIX 2008 extension. Normally, it will be available with a POSIX-compatible compiler, as the macros _POSIX_C_SOURCE will be defined with the appropriate values. You possibly have an older compiler from before getline() was standardized, in which case this is a GNU extension, and you must #define _GNU_SOURCE before #include <stdio.h> to enable it, and must be using a GNU-compatible compiler, such as gcc."
•
written
by
Pierre Lindenbaum
I didn't have to add an extension to compile under the version of clang that ships in OS X 10.11, so I guess OS X supports that POSIX standard, but on an older Linux box running gcc 4.8.2, I did have to add -std=gnu99 to the build statement. I did not have to add #define _GNU_SOURCE.
•
written
by
Alex Reynolds
Don't forget N and U! :)
•
written
by
Brian Bushnell
Done and done!
FYI: seqtk/bioawk has a more complete complement table. It includes R/Y/D/etc:
Unless it is an assignment, I do not see why you won't use existing tools. Here is faRc from Kent utils and much more:
http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/
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Inputting DNA sequence by hand.. very convenient.
we can copy paste it atleast................
Just for fun, I made a Python version of the script (outputs reverse complement):
A 1-liner might look like: