User Commands MAP2PS(1) NAME mapit, map2ps - level 2 postscript converter for Genetic Map Description Language (GMDL) SYNOPSIS map2ps [-h] [-eps] [-std] [-f stylefile] [mapfile] [psfile] DESCRIPTION Mapit is a suite of utility programs designed to produce high quality genetic maps in Postscript format intended for publication purposes. The mf2map utility program is first used to convert a masterfile to a file format called GMDL (see below) designed specifically for describing the visual properties of various map elements. Map2ps is a postscript converter designed to translate a genetic map file written specifically in the Genetic Map Description Language (GMDL) also developed at OGMP. Once translated, the postscript file can be imported into an interactive graphical editor such as the popular CorelDraw and Adobe Illustrator for futher editing and enhancements, or printed directly through a Postscript enabled printer. Normally, map2ps is not to be invoked directly from command-line. Instead, a separate utility program mf2map has been designed to generate, from an OGMP's masterfile, an executable GMDL file which calls map2ps implicitly with appropriate optional switches for translation. The user will only be required to take care of output redirection. For example, to generate a postcript file from a GMDL file called mygenome.map created by mf2map, one only needs to enter: mygenome.map > mygenome.ps on command-line. OPTIONS -h Map2ps will print the banner and usage information and then exit. -ePS Instructs map2ps to generate Encapsulated Postscript (EPS) file instead of the default level-2 Postscript. EPS files are useful to desktop publishing programs that support high quality embedded graphics and images. -std By default, map2ps generates CorelDraw compatible Postscript code. This includes a Postscript header con- taining a proprietary font encoding scheme which may not be supported by a number of Postscript printers. This optional switch forces map2ps to remove this header and instead use fonts that are widely supported by printer manufacturers. -f stylefile Map2ps uses a set of style rules to highlight various elements of the genetic map. The default set of rules was defined by OGMP and is hard-coded into map2ps. This optional switch provides a systematic way to override this default behavior. Once specified, map2ps applies the style rules found in stylefile to construct the Postscript genetic map. See STYLE RULE section below for syntax. ARGUMENTS Map2ps can be invoked without any input and output file arguments. In this case, it functions as a UNIX filter, reading from its standard input and writing to its standard output. This can be very useful for automating processes using UNIX pipes. If file arguments are provided, the first argument will be taken as the GMDL file name and the second as the output Postscript file name. Subsequent arguments will be ignored. If the output file name is not given, map2ps writes to its standard output. EXAMPLES As described above, map2ps is normally invoked implicitly by an executable GMDL file created by the mf2map utility pro- gram. In that case, generating a Postscript genetic map is as simply as entering mygenome.map > mygenome.ps For overriding defaults or finer control over map2ps, map2ps can be invoked from command-line with optional switches and arguments. Here is how one can take advantage of UNIX pipes: mf2map -c -m my.mf | map2ps -std -f chlorplast.sty | lpr It calls mf2map to generate a GMDL file from a masterfile (my.mf). Mf2map's output is then directly processed by map2ps, producing a Postscript version of the genetic map using standard fonts and style rules found in chlorplast.sty. The output of map2ps is sent directly to the printer for printing. Here is another example to demonstrate creating a Postscript genetic map from a GMDL file without using any UNIX pipe or doing output redirection: map2ps -eps -std mygenome.map mygenome.eps This creates an EPS genetic map, mygenome.eps, using stan- dard fonts from the GMDL file mygenome.map. STYLE RULES The optional style file provides a way to override default style rules. This can be useful to research groups wanting to establish and implement their own set of rules on a system-wide basis. The style file consists of three separate sections, each preceded by its own identification tag [id] similar to Windows' _ini files. Each section contains assign- ment statements in the form key = value to specific the new default value to use for the attribute or map element key. Preceded by the [global] identification tag, the Global sec- tion defines the rule set applied to the basic visual map elements such as the circular axis and the circle represent- ing the genome. The following attributes are available: LineColor Unless overriden elsewhere, this specifies the default color to use for drawing straight lines, circles and arcs. Available colors include black, red, green, blue, yellow, cyan, gray20 and gray40. LineWidth Specifies the default linewidth to use for drawing straight lines, circles and arcs. The value is to be given in postscript point size (1in = 72pts). FontColor Specifies the default color to use for all fonts (title, tick labels, gene labels etc). The available color values are exactly the same as those for LineColor above and can be overridden on a per gene family or on a per gene basis (see genes and exception below). FontType The default type of font to use for all fonts. As with FontColor The value given here can be overriden by rules given in the later two sections. The currently supported font types are: TimesRoman, TimesBold, TimesItalic, TimesBoldItalic, Arial, Arialitalic, Courier and Helvetica. FontSize Unless specified elsewhere, this is the default font size to use for all fonts. As with LineWidth , font size is measured in postscript points. GenomeRadius This is the radius of the circle that represents the "backbone" of the genome. It is to be given in postscript points also. GenomeWidth The linewidth used to draw arcs (or bands) representing the actually placements of genetic elements (genes, orf's and tRNA's) within the genome. It is to be given in postscript points. ScaleRadius Given in postscript points, this specifies the radius of the circle serving as the axis (bp) for the genome. ScaleWidth Specifies the linewidth to use for the circular axis above. It is to be given in postscript points. Circle1LineWidth Two smaller additional concentric circles are superim- posed on the genetic map, in preparation to support displaying restriction sites. This key specifies the linewidth in postscript points to use for the smaller of the two circles. Circle2LineWidth The linewidth in postscript points to use for the bigger of the two additional circles described above. The two circles are allowed to have different linewidths to enhance visual impact. OuterRingLineWidth The linewidth to use in drawing the outer circle that represents the "backbone" of the genome. Also given in postscript points. ScaleFontType The font type to use for labelling tick marks appearing on the inner circular axis. The supported font types are exactly the same as those available to FontType described above. TitleFontSize The font size to use to generate the map's title which is to appear at the center of the map. tRNAFontSize tRNA genes are treated differently from all the other genes. Their gene names are abbreviated using the corresponding 1-letter IUPAC amino acid code. tRNAFontSize allows the font size used for tRNA gene labels to be changed. tRNASubFontSize Labels for tRNA genes may contain subscripts. tRNASub- FontSize allows the font size for subscripts to be specified. LinkLineWidth Here, "link" refers to the pointer connecting a gene label to its associated arc segment in the genome. LinkLineWidth specifies the linewidth to use for draw- ing these pointers. ArcSkip When a gene is segregated over an extended intronic region, a circular bracket is used instead to connect the gene label to the range of arc segments. ArcSkip refers to the radial gap (measured in postscript points) inserted between the arc segments and the cir- cular bracket. ArcLabelSkip This refers to the radial gap inserted between the aforementioned circular bracket and the associated gene label. The "genes" section in the style file begins with the iden- tification tag [genes]. It is then followed by a number of assignment statements similar to the ones found in the glo- bal section. The keys on the left-hand-side of the equations however are gene family names such as atp, nad and cox; the values on the right-hand-side are lists of comma separated attributes used to provide general defaults for the corresponding gene families. For example: the assignment statement cox = red, 15pt, TimesItalic makes 15pt-red-times-italic the default font style to use for the cox family of genes. The final section of the style file begins with the identif- ication tag [exceptions]. This is where variations in font style within a family of genes are made possible. The assignment statements found in this section are essentially the same as those in the "genes" section described above except here that specific (enumerated) gene names rather than family names are used. For example, the statement atp17 = green, bold, Arial instructs map2ps to generate a label in green bold Arial font for the atp17 gene. SAMPLE STYLE FILE A short example style file is as follows: [global] LineColor = red LineWidth = 20 FontColor = green FontType = COURIER FontSize = 20 GenomeRadius = 172 GenomeWidth = 20 ScaleRadius = 125 ScaleWidth = 3 Circle1lineWidth = 5 Circle2LineWidth = 2 OuterRingLineWidth = 6 ScaleFontType = 2 TitleFontSize = 5 tRNAfontSize = 18 tRNAsubFontSize = 14 LinkLineWidth = 2 ArcSkip = 15 ArcLabelSkip = 30 [genes] atp = blue, courier, 22, bold cox = red, helvetica, 18, italic [exceptions] cox2 = blue,arial,30,normal atp8 = green FILE None SEE ALSO mf2map(1), ogmp(1), gobase2mf(1) AUTHORS Gertraud Burger Franz Lang Alexander Nip Lin Liu Daniel Leonard OGMP Last change: 2000/8/30