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Full Discussion: Modifying a sequence using positions!
Top Forums Shell Programming and Scripting Modifying a sequence using positions! Post 302723585 by Don Cragun on Tuesday 30th of October 2012 11:42:13 AM
Old 10-30-2012
Quote:
Originally Posted by empyrean
Hi..
...
Quote:
Example files are

Snp file

SNPRefAlt
10AC
19GC
30CT
42AG

Sequence :

>sequence1
CTAGAATCAAAGCAAGAATACACTCTTTTTTTTGGAAAAGAATATCTCATGTTTGCTCTT
...
Quote:
Another thing is if we take the snp position, and if there are any snps in 10 bases difference, we need to replace that snp position with "N". In the above example in first two positions as the difference is 9 we are replacing the other element with 'N'.

---------- Post updated at 04:01 PM ---------- Previous update was at 11:20 AM ----------

Took my code off as it might be confusing for everyone..
I'm working on a response but it may not be done much before midnight tonight.

Does the text above in red mean that the table entry:
19GC
should cause bases being changed by other table entries for bases 9 through 18 and 20 through 29 should be changed to "N" or should it only cause bases 10 through 18 and 20 through 28 to be changed to "N"? (In other words, is "in 10 bases difference" inclusive or exclusive?)

In response to the text above in blue, I wish you had left the first part of your code that gave the name of the script that you want to use and the arguments you want to pass to that script.

Also, do your sequence input files contain only one sequence, or would you like it to be able to contain multiple sequences and have the script produce an output table for each sequence found in the input sequence file(s)?
 

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