Section: User Commands (1)
Updated: September 2000
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col2psalign - Make postscript alignment from col file



[-ple] [-rrange | -range=range] [-ffontsize | --fit] [--space] [--width=width] [--height=height] [--margin=margin] [--topmargin=topmargin] [--sidemargin=sidemargin] [--namewidth=namewidth] [--textwidth=textwidth] [--lineheight=lineheight] [--figure] [file]



col2psalign creates a postscript file that shows the sequences in the input file. It is assumed that the input file contains aligned sequences, such that they are equal in length (including gaps).

Input is either from file or stdin. The output is sent to stdout.



col2psalign accepts the following options.

Makes portrait output instead of landscape.

Uses letter paper format instead of the default A4.

Prints colors as empty boxes instead of filled boxes behind letters.

Only prints the positions defined by range. The range is specified as position intervals seperated by commas, like `-r1-20,50-100,139' which makes col2psalign output positions 1-20, 50-100, and 139.

Sets the font size to fontsize. The default is 8.

Inserts spaces for every ten positions.

Fits the entire alignment to the page width, unless the --textwidth option is used, in which case it fits textwidth characters of the alignment to the page width.

Sets the page width to width, which by default is points, but if followed by cm, it is centimeters. If followed by in or inch, it is in inches. for example, if range is 720, the page width is 720 points, if range is 10in or 10inch, the page width is 10 inches, if range is 25.4cm, the page width is 25.4 centimeters. These values are by the way identical.

Sets the page height to height, the format of which is described under --width.

Sets all margins, the top/bottom margins, and the sidemargins respectively. The format of the values are as described under --width. The default is 20 points.

Sets the width of the sequnece names to namewidth. The units of namewidth is the fontsize. The default value is 8. This means that the sequence name width is 64 points (since the default font size is 8).

Sets the width of the sequence field to textwidth. The units of textwidth is characters. Notice that a space is inserted for each 10 positions. These spaces are also counted. This means that textwidth should be 54 if 50 positions should be displayed in every line (since 4 spaces are inserted).

Sets the height of the lines to lineheight times the default.

Makes the outputs useful as a figure.



Make a figure of width 12 cm that has no margins and each sequence is in one line:

col2psalign --figure --margin=0 --width=12cm --fit foo.col

Make a postscript file with fontsize 36. On portrait pages. The name space is smaller than default:

col2psalign -p -f36 --namewidth=5 foo.col

Make a portrait postscript file with 20 sequence position on each line (notice the 21 because of the space character between blocks of 10 positions):

col2psalign --space -p --textwidth=21 --fit foo.col



Report bugs to col-bugs@bioinf.au.dk.



Bjarne Knudsen (bk@daimi.au.dk)






Comments, questions, etc., email gorodkin@rth.dk.

Last updated March 26th, 2007 by Jan Gorodkin