[BioPython] From alignment column pos to seq nucleotide pos
Iddo Friedberg
idoerg@cc.huji.ac.il
Thu, 4 Oct 2001 17:48:40 +0200 (GMT+0200)
Hi Anders,
Quick & dirty:
--acat---acca-aaatgcgt # record 0
a-ccattag-ccataa--gcgt # record 1
agc--ttag-ccataa--gcgt # record 2
^
column 7
Now, you want to find the sequence number if the "a" in record 1, on column 7.
s = 0
for i in c_align._records[1].seq[:7]:
if i <> "-": # is this is a bad way for gapchecking??
s += 1
"s" is your sequence position. There is probably a more elegant way of checking for
a gap within Biopython. See the Alphabet modules.
Hope this helped,
Iddo
On Thu, 4 Oct 2001, Anders Lundmark wrote:
: Hi,
:
: Given the column position in an alignment object,
: how do I easiest get the corresponding nucleotide
: position in one of the sequence members?
:
: Regards,
:
: Anders Lundmark
:
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--
Iddo Friedberg | Tel: +972-2-6757374
Dept. of Molecular Genetics and Biotechnology | Fax: +972-2-6757308
The Hebrew University - Hadassah Medical School | email: idoerg@cc.huji.ac.il
POB 12272, Jerusalem 91120 |
Israel |
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