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Full Discussion: trimming sequences
Top Forums Shell Programming and Scripting trimming sequences Post 302431727 by Xterra on Tuesday 22nd of June 2010 06:48:45 PM
Old 06-22-2010
trimming sequences

My file looks like this:
Quote:
>GHXCZCC01AJ8CJ
TTGATGTGCCAGCTGCCGTTGGTGTGTATCAGCTGGATTTTCTGGGACGC
CCCGGGGC
>GHXCZCC01APUO5
TGATGTGCCAGCTGCCGTTGGTGTGTATCAGCTGGATTTCTGGGACGCCC
CGGGGCGA
>GHXCZCC01AQSRP
TTGATGTTGCCAGCTGCCGTTGGTGTGTATCAGCTGGATTTTCTGGGACG
CCCCGGGG
But I would like to 'trim' all sequences to the same lenght 32 characters, keeping intact all the identifier (>GHXCZCC01AJ8CJ)
Quote:
>GHXCZCC01AJ8CJ
TTGATGTGCCAGCTGCCGTTGGTGTGTATCAG
CCCGGGGC
>GHXCZCC01APUO5
TGATGTGCCAGCTGCCGTTGGTGTGTATCAGC
CGGGGCGA
>GHXCZCC01AQSRP
TTGATGTTGCCAGCTGCCGTTGGTGTGTATCA
CCCCGGGG
Would it be possible to use awk to perform this task?
 

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GLUBEGINTRIM(3G)														  GLUBEGINTRIM(3G)

NAME
gluBeginTrim, gluEndTrim - delimit a NURBS trimming loop definition C SPECIFICATION
void gluBeginTrim( GLUnurbs* nurb ) void gluEndTrim( GLUnurbs* nurb ) PARAMETERS
nurb Specifies the NURBS object (created with gluNewNurbsRenderer). DESCRIPTION
Use gluBeginTrim to mark the beginning of a trimming loop, and gluEndTrim to mark the end of a trimming loop. A trimming loop is a set of oriented curve segments (forming a closed curve) that define boundaries of a NURBS surface. You include these trimming loops in the defini- tion of a NURBS surface, between calls to gluBeginSurface and gluEndSurface. The definition for a NURBS surface can contain many trimming loops. For example, if you wrote a definition for a NURBS surface that resem- bled a rectangle with a hole punched out, the definition would contain two trimming loops. One loop would define the outer edge of the rec- tangle; the other would define the hole punched out of the rectangle. The definitions of each of these trimming loops would be bracketed by a gluBeginTrim/gluEndTrim pair. The definition of a single closed trimming loop can consist of multiple curve segments, each described as a piecewise linear curve (see gluPwlCurve) or as a single NURBS curve (see gluNurbsCurve), or as a combination of both in any order. The only library calls that can appear in a trimming loop definition (between the calls to gluBeginTrim and gluEndTrim) are gluPwlCurve and gluNurbsCurve. The area of the NURBS surface that is displayed is the region in the domain to the left of the trimming curve as the curve parameter increases. Thus, the retained region of the NURBS surface is inside a counterclockwise trimming loop and outside a clockwise trimming loop. For the rectangle mentioned earlier, the trimming loop for the outer edge of the rectangle runs counterclockwise, while the trimming loop for the punched-out hole runs clockwise. If you use more than one curve to define a single trimming loop, the curve segments must form a closed loop (that is, the endpoint of each curve must be the starting point of the next curve, and the endpoint of the final curve must be the starting point of the first curve). If the endpoints of the curve are sufficiently close together but not exactly coincident, they will be coerced to match. If the endpoints are not sufficiently close, an error results (see gluNurbsCallback). If a trimming loop definition contains multiple curves, the direction of the curves must be consistent (that is, the inside must be to the left of all of the curves). Nested trimming loops are legal as long as the curve orientations alternate correctly. If trimming curves are self-intersecting, or intersect one another, an error results. If no trimming information is given for a NURBS surface, the entire surface is drawn. EXAMPLE
This code fragment defines a trimming loop that consists of one piecewise linear curve, and two NURBS curves: gluBeginTrim(nobj); gluPwlCurve(..., GLU_MAP1_TRIM_2); gluNurbsCurve(..., GLU_MAP1_TRIM_2); gluNurbsCurve(..., GLU_MAP1_TRIM_3); gluEndTrim(nobj); SEE ALSO
gluBeginSurface(3G), gluNewNurbsRenderer(3G), gluNurbsCallback(3G), gluNurbsCurve(3G), gluPwlCurve(3G) GLUBEGINTRIM(3G)
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