[emboss-dev] makenucseq, error with completely random sequence?
Henrikki Almusa
henrikki.almusa at helsinki.fi
Mon Jul 10 18:09:13 UTC 2006
Hello,
I went through the code that I submitted and wondered if there is in
fact an error in it :). When creating a completely random sequence we
use following string to make the random sequence
char seqCharNucPure[] = "ACGTUacgtu";
This is then converted into list and random element is taken to make the
sequence. However later this is done
ajStrExchangeSetCC(&seqstr,"u","t")
which replaces all the occurrances of 'u' with 't'. Doesn't this mean
that the 't' is now overrepresented?
I used the seqCharNucPure in there hoping that some point that stucture
might be available without copy and paste of the code. However should
the program be changed to use little different version of the string
(which could then in that later situation added to ajseqtype.c).
char seqCharNucDnaPure[] = "ACGTacgt";
So something like this (untested)?
--- makenucseq.c 2006-07-10 05:49:55.000000000 +0000
+++ makenucseq.c.fix 2006-07-10 11:24:53.000000000 +0000
@@ -125,7 +125,6 @@
ajStrFmtLower(&seqstr);
seq = ajSeqNew();
- ajStrExchangeSetCC(&seqstr,"u","t");
if (extra < 0)
ajStrCutStart(&seqstr,extra);
ajSeqAssignSeqS(seq, seqstr);
@@ -184,12 +183,12 @@
int i;
int max;
char *chars;
- char seqCharNucPure[] = "ACGTUacgtu";
- int seqCharNucPureLength = 10;
+ char seqCharNucDnaPure[] = "ACGTacgt";
+ int seqCharNucDnaPureLength = 8;
AjPStr tmp;
- chars = seqCharNucPure;
- max = seqCharNucPureLength;
+ chars = seqCharNucDnaPure;
+ max = seqCharNucDnaPureLength;
for (i = 0; i < max; i++)
{
Regards,
--
Henrikki Almusa
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