DRAWMAP

To run DrawMap, we use the following parameters:
-beg     (0) 
-end     (end of gene)
-scale   (bp per cm)
-list    (a file that tells DrawMap what to graph)
-outfile (name of the postscript output file)

For example, on the command line, you could have to type:

DrawMap -beg 0 -end 5375 -scale 250 -list c1.list -outfile c1.ps

This tells DrawMap where to begin and end the gene, the scale, which file to
 read (c1.list) and where to put the output (into a file called c1.ps).

However, typing this, or even remembering it, is hard.  So, we typically 
have a command line stored in a file called <genename>.com.  Then you can
type "more <genename>.com at the prompt and use your mouse to swipe the 
command to the next line.

The -list file contains a list of the items DrawMap is to put on the graph. 
Here is what a typical one looks like.

primers.xm                   cross_match     feature_map     1
M20902.REF.fasta.out.xm      cross_match     feature_map     color
exons.xm                     cross_match     feature_map     color
variations.tbl	             table           feature_map    1

Primers.xm will show where, on the gene, the primers are located.  
The M20902.REF.fasta.out.xm is the xm output from RepeatMasker and contains
a list of the repeat regions.  The exons.xm file is a xm of the mRNA with 
the gene and shows where the exons are.


In general, any <genename>.list file consists of four columns: filename, 
type of file, what kind of map, color or black and white.



A table file is also a 4 column file.  Here is an example:
00071   00071   00071   nd
00284   00284   00284   nd
00290   00290   00290   nd
00353   00353   00353   nd
00578   00578   00578   nd
00609   00609   00609   nd
00851   00851   00851   nd
00898   00898   00898   nd
00899   00899   00899   nd
01103   01103   01103   nd
01269   01269   01269   nd
01302   01302   01302   nd
01471   01471   01471   nd

The first three columsn represent begin, end, and name of item.  I don't know 
what the nd stands for, but it is necessary.

usage:
DrawMap <-beg start_of_graph(bp)>
<-end end_of_graph(bp)>
<-scale bp_per_cm>

required parameters unless -list option is used
<-ft >
<-gt >
<-fill >


[-list list_name, where the list is: file ft gt fill]
[-outfile output_file]
[-more]
[-help]

list - the list file contains a table with each line containing
file (path), filetype, graphtype (as above), and
file object fill (color, 1, or 0).
The elements must be separated by spaces.
(e.g. myfile cross_match detail autocolor)


-more many option -- puts DrawMap in a semi-interactive mode, and more
than one map can be printed.

ex:
DrawMap -beg 0 -end 100000 -scale 5000 -ft cross_match -gt 3d_histogram
-fill autocolor -outfile map.ps mydata.xmatch

The program currently uses an 8 x 11.5 inch paper as a default unit size
if the map is larger than a piece of paper, multiple sheets will be
printed (except remaps). The color option works but requires expert user
mode. (i.e. it's pretty crude)

supported file and graph types

file type: blast
graph types: feature_map, detail, genes, line_arrow, histogram, 3d_histogram

file type: cross_match
graph types: feature_map, detail, genes, line_arrow, histogram, 3d_histogram, dotplot

file type: fieldtable
graph types: feature_map, genes, line_arrow, histogram, 3d_histogram, linkage

file type: mapsites
graph types: remap

file type: sputnik
graph types: feature_map

file type: table
graph types: feature_map, genes, line_arrow

file type: xytable
graph types: xyplot