To run DrawMap, we use the following parameters:
-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.
DrawMap <-beg start_of_graph(bp)>
required parameters unless -list option is used
[-list list_name, where the list is: file ft gt fill]
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.
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