[BioPython] From alignment column pos to seq nucleotide pos (fwd)

[Iddo Friedberg]

Sorry,

Bad code, off-by-one.

Here's the (hopefully) good one:

s = -1
for i in c_align._records[1].seq[:8]:
    if i <> "-":   # is this is a bad way for gapchecking??
        s += 1


"s" will now have a value of -1 if the column is located before the start
of the actual sequence.


Iddo

:: 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
:
: _______________________________________________
: BioPython mailing list-  BioPython@biopython.org
: http://biopython.org/mailman/listinfo/biopython
:

--

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                                          |
http://bioinfo.md.huji.ac.il/marg/people-home/iddo/

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