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Top Forums Shell Programming and Scripting Modifying a sequence using positions! Post 302723085 by empyrean on Monday 29th of October 2012 04:01:46 PM
Old 10-29-2012
Modifying a sequence using positions!

Hi.. i have two files one with positions information and another is sequence information. Now i need to read the positions and take the snps at the positions and replace that position base with the snp information in the sequence and write it in the snp information file.. for example

Snp file contains

10 A C A/C
Sequence file contains

ATCGAACTCTACATTAC
Here 10th element is T so i will replace T with [A/C] so the final output should be

10 A C A/C ATCGAACTC[A/C]ACATTAC
Example files are

Snp file

SNPRefAlt
10AC
19GC
30CT
42AG

Sequence :

>sequence1
CTAGAATCAAAGCAAGAATACACTCTTTTTTTTGGAAAAGAATATCTCATGTTTGCTCTT

Final output :

SNPRefAltOutput
10ACCTAGAATCA[A/C]AGCAAGAANACACTCTTTTTTTTGGAAAAGAATATCTCATGTTTGCTCTT
19GCCTAGAATCANAGCAAGAA[C/G]ACACTCTTTTTTTTGGAAAAGAATATCTCATGTTTGCTCTT
30CTCTAGAATCAAAGCAAGAATACACTCTTTT[T/C]TTTGGAAAAGAATATCTCATGTTTGCTCTT
42AGCTAGAATCAAAGCAAGAATACACTCTTTTTTTTGGAAAAGA[A/G]TATCTCATGTTTGCTCTT

While replacing the snps here from Ref and Alt column, we need to consider the order of {A,T,C,G} like the [Ref/Alt] always the first base should be either A or T or C and followed by that order.

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..

Last edited by empyrean; 10-29-2012 at 05:01 PM..
 

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CREATE TABLE 
AS(7) SQL Commands CREATE TABLE AS(7) NAME
CREATE TABLE AS - create a new table from the results of a query SYNOPSIS
CREATE [ [ LOCAL ] { TEMPORARY | TEMP } ] TABLE table_name [ (column_name [, ...] ) ] AS query DESCRIPTION
CREATE TABLE AS creates a table and fills it with data computed by a SELECT command. The table columns have the names and data types asso- ciated with the output columns of the SELECT (except that you can override the column names by giving an explicit list of new column names). CREATE TABLE AS bears some resemblance to creating a view, but it is really quite different: it creates a new table and evaluates the query just once to fill the new table initially. The new table will not track subsequent changes to the source tables of the query. In contrast, a view re-evaluates its defining SELECT statement whenever it is queried. PARAMETERS
[LOCAL] TEMPORARY or [LOCAL] TEMP If specified, the table is created as a temporary table. Refer to CREATE TABLE [create_table(7)] for details. table_name The name (optionally schema-qualified) of the table to be created. column_name The name of a column in the new table. Multiple column names can be specified using a comma-delimited list of column names. If col- umn names are not provided, they are taken from the output column names of the query. query A query statement (that is, a SELECT command). Refer to SELECT [select(7)] for a description of the allowed syntax. DIAGNOSTICS
Refer to CREATE TABLE [create_table(7)] and SELECT [select(7)] for a summary of possible output messages. NOTES
This command is functionally equivalent to SELECT INTO [select_into(7)], but it is preferred since it is less likely to be confused with other uses of the SELECT ... INTO syntax. COMPATIBILITY
This command is modeled after an Oracle feature. There is no command with equivalent functionality in SQL92 or SQL99. However, a combina- tion of CREATE TABLE and INSERT ... SELECT can accomplish the same thing with little more effort. HISTORY
The CREATE TABLE AS command has been available since PostgreSQL 6.3. SEE ALSO
CREATE TABLE [create_table(7)], CREATE VIEW [create_view(l)], SELECT [select(l)], SELECT INTO [select_into(l)] SQL - Language Statements 2002-11-22 CREATE TABLE AS(7)
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