PostScript as a Programming Language for Bioinformatics: mynotebook
"PostScript (PS) is an interpreted, stack-based programming language. It is best known for its use as a page description language in the electronic and desktop publishing areas."[wikipedia]. In this post, I'll show how I've used to create a simple and lightweight view
of the genome.
Introduction: just a simple postscript program
The following PS program fills a rectangular gray shape; You can display the result using ghostview, a2ps, etc...%!PS newpath 50 50 moveto 0 100 rlineto 100 0 rlineto 0 -100 rlineto closepath 0.5 setgray fill showpage
Some global variables
The page width
/screenWidth 1000 def
The page width
/screenHeight 1000 def
The minimum 5' position
/minChromStart 1E9 def
The maximum 3' position
/maxChromEnd -1 def
The size of a genomic feature
/featureHeight 20 def
The distance between two 'ticks' for drawing the orientation
/ticksx 20 def
The font size
/theFontSize 9 defThe variable knownGene is a PS array of genes.
/knownGene [ [(uc002zkr.3) (chr22) (-) 161242... ...] ] def
Each Gene is a PS array holding the structure of the UCSC knownGene table, that is to say: name , chromosome, txStart, txEnd, cdsStart, cdsEnd, exonStarts, exonEnds:
[(uc002zmh.2) (chr22) (-) 17618410 17646177 17618910 17646134 [17618410 17619439 17621948 17623987 17625913 17629337 17630431 17646098 ] [17619247 17619628 17622123 17624021 17626007 17629450 17630635 17646177 ] ]. a simple command line can be used to fetch those data:
% curl -s "http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/knownGene.txt.gz" |\
gunzip -c | grep chr22 | head -n 20 |\
awk '{printf("[(%s) (%s) (%s) %s %s %s %s [%s] [%s] ]\n",$1,$2,$3,$4,$5,$6,$7,$9,$10);}' |\
tr "," " " > result.txt
Some utilities
converting a PS object to string
/toString
{
20 string cvs
} bind def
Converting a string to interger (loop over each character an increase the current value)
/toInteger
{
3 dict begin
/s exch def
/i 0 def
/n 0 def
s {
n 10 mul /n exch def
s i get 48 sub n add /n exch def %48=ascii('0')
i 1 add /i exch def
} forall
n % leave n on the stack
end
} bind def
Convert a genomic position to a index on the page 'x' axis
/convertPos2pixel
{
minChromStart sub maxChromEnd minChromStart sub div screenWidth mul
} bind def
Extract the chromosome (that is to say, extract the 1st element of the current array on the stack)
/getChrom
{
1 get
} bind def
Create a hyperlink to the UCSC genome browser
/getHyperLink
{
3 dict begin
/E exch def %% END
/S exch def %% START
/C exch def %% CHROMOSOME
[ (http://genome.ucsc.edu/cgi-bin/hgTracks?position=) C (:) S toString (-) E toString (&) (&db=hg19) ] concatstringarray
end
} bind def
Paint a rectangle
/box
{
4 dict begin
/height exch def
/width exch def
/y exch def
/x exch def
x y moveto
width 0 rlineto
0 height rlineto
width -1 mul 0 rlineto
0 height -1 mul rlineto
end
} bind def
Paint a gray gradient
/gradient
{
4 dict begin
/height exch def
/width exch def
/y exch def
/x exch def
/i 0 def
height 2 div /i exch def
0 1 height 2 div {
1 i height 2.0 div div sub setgray
newpath
x
y height 2 div i sub add
width
i 2 mul
box
closepath
fill
i 1 sub /i exch def
}for
newpath
0 setgray
0.4 setlinewidth
x y width height box
closepath
stroke
end
} bind def
Methods extracting a data about the current gene on the PS stack.
Extract the transcription start:/getTxStart
{
3 get
} bind def
Extract the transcription end:
/getTxEnd
{
4 get
} bind def
Extract the CDS start:
/getCdsStart
{
5 get
} bind def
Extract the transcription end:
/getCdsEnd
{
6 get
} bind def
Extract the strand:
/getStrand
{
2 get (+) eq {1} {-1} ifelse
} bind def
Get the gene name/getKgName
{
0 get
} bind def
Get the number of exons:
/getExonCount
{
7 get length
} bind def
Get the start position of the i-th exon:
/getExonStart
{
2 dict begin
/i exch def
/gene exch def
gene 7 get i get
end
} bind def
Get the end position of the i-th exon:
/getExonEnd
{
2 dict begin
/i exch def
/gene exch def
gene 8 get i get
end
} bind def
Should we draw this gene on the page ?
/isVisible
{
1 dict begin
/gene exch def
minChromStart gene getTxEnd gt
{
false
}
{
gene getTxStart maxChromEnd gt
{
false
}
{
true
}ifelse
}ifelse
end
}bind def
Methods for an array of genes
Loop over the genes and extract the lowest 5' index:/getMinChromStart
{
3 dict begin
/genes exch def
/pos 10E9 def
/i 0 def
genes length {
genes i get getTxStart pos min /pos exch def
i 1 add /i exch def
}repeat
pos
end
} bind def
Loop over the genes and extract the highest 3' index:
/getMaxChromEnd
{
3 dict begin
/genes exch def
/pos -1E9 def
/i 0 def
genes length {
genes i get getTxEnd pos max /pos exch def
i 1 add /i exch def
}repeat
pos
end
} bind def
Painting ONE Gene
/paintGene
{
5 dict begin
/gene exch def %% the GENE argument
/midy featureHeight 2.0 div def %the middle of the row
/x0 gene getTxStart convertPos2pixel def % 5' side of the gene in pixel
/x1 gene getTxEnd convertPos2pixel def % 3' side of the gene in pixel
/i 0 def
0.1 setlinewidth
1 0 0 setrgbcolor
newpath
x0 midy moveto
x1 midy lineto
closepath
stroke
% paint ticks
0 1 x1 x0 sub ticksx div{
newpath
gene getStrand 1 eq
{
x0 ticksHeight sub i add midy ticksHeight add moveto
x0 i add midy lineto
x0 ticksHeight sub i add midy ticksHeight sub lineto
}
%else
{
x0 ticksHeight add i add midy ticksHeight add moveto
x0 i add midy lineto
x0 ticksHeight add i add midy ticksHeight sub lineto
} ifelse
stroke
i ticksx add /i exch def
} for
%paint Transcript start-end
0 0 1 setrgbcolor
newpath
gene getCdsStart convertPos2pixel
midy cdsHeight 2 div sub
gene getCdsEnd convertPos2pixel gene getCdsStart convertPos2pixel sub
cdsHeight box
closepath
fill
% loop over exons
0 /i exch def
gene getExonCount
{
gene i getExonStart convertPos2pixel
midy exonHeight 2 div sub
gene i getExonEnd convertPos2pixel gene i getExonStart convertPos2pixel sub
exonHeight gradient
i 1 add /i exch def
} repeat
0 setgray
gene getTxEnd convertPos2pixel 10 add midy moveto
gene getKgName show
%URL
[ /Rect [x0 0 x1 1 add featureHeight]
/Border [1 0 0]
/Color [1 0 0]
/Action << /Subtype /URI /URI gene getChrom gene getTxStart gene getTxEnd getHyperLink >>
/Subtype /Link
/ANN pdfmark
end
} bind def
Paint all Genes
/paintGenes
{
3 dict begin
/genes exch def %the GENE argument (an array)
/i 0 def % loop iterator
/j 0 def % row iterator
% draw 10 vertical lines
i 0 /i exch def
0 setgray
0 1 10 {
%draw a vertical line
screenWidth 10 div i mul 0 moveto
screenWidth 10 div i mul screenHeight lineto
stroke
% print the position at the top rotate by 90°
screenWidth 10 div i mul 10 add screenHeight 5 sub moveto
-90 rotate
maxChromEnd minChromStart sub i 10 div mul minChromStart add toString show
90 rotate
i 1 add /i exch def
} for
0 /i exch def
genes length {
genes i get isVisible
{
gsave
0 j featureHeight 2 add mul translate
genes i get paintGene
j 1 add /j exch def
grestore
} if
i 1 add /i exch def
}repeat
end
} bind def
All in one: the postscript code
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| %!PS | |
| %%Creator: Pierre Lindenbaum PhD plindenbaum@yahoo.fr http://plindenbaum.blogspot.com | |
| %%Title: Genome Browser | |
| %%CreationDate: 2011-09-25 | |
| %%BoundingBox: 0 0 1000 1000 | |
| %%Pages! 1 | |
| % | |
| % curl -s "http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/knownGene.txt.gz" | gunzip -c | head -n 20 | awk '{printf("[(%s) (%s) (%s) %s %s %s %s [%s] [%s] ]\n",$1,$2,$3,$4,$5,$6,$7,$9,$10);}' | tr "," " " | |
| % | |
| /pdfmark where {pop} {userdict /pdfmark /cleartomark load put} ifelse | |
| /screenWidth 1000 def | |
| /screenHeight 1000 def | |
| /minChromStart 1E9 def | |
| /maxChromEnd -1 def | |
| /featureHeight 20 def | |
| /ticksx 20 def | |
| /theFontSize 9 def | |
| /Courier findfont theFontSize scalefont setfont | |
| %% http://en.wikibooks.org/wiki/PostScript_FAQ#How_to_concatenate_strings.3F | |
| /concatstringarray % [(a) (b) ... (z)] --> (ab...z) | |
| { 0 1 index { length add } forall string | |
| 0 3 2 roll | |
| { 3 copy putinterval | |
| length add | |
| } | |
| forall pop | |
| } bind def | |
| /toString | |
| { | |
| 20 string cvs | |
| } bind def | |
| /toInteger | |
| { | |
| 3 dict begin | |
| /s exch def | |
| /i 0 def | |
| /n 0 def | |
| s { | |
| n 10 mul /n exch def | |
| s i get 48 sub n add /n exch def %48=ascii('0') | |
| i 1 add /i exch def | |
| } forall | |
| n | |
| end | |
| } bind def | |
| /convertPos2pixel | |
| { | |
| minChromStart sub maxChromEnd minChromStart sub div screenWidth mul | |
| } bind def | |
| /getChrom | |
| { | |
| 1 get | |
| } bind def | |
| /getTxStart | |
| { | |
| 3 get | |
| } bind def | |
| /getTxEnd | |
| { | |
| 4 get | |
| } bind def | |
| /getCdsStart | |
| { | |
| 5 get | |
| } bind def | |
| /getCdsEnd | |
| { | |
| 6 get | |
| } bind def | |
| /getStrand | |
| { | |
| 2 get (+) eq {1} {-1} ifelse | |
| } bind def | |
| /getKgName | |
| { | |
| 0 get | |
| } bind def | |
| /getExonCount | |
| { | |
| 7 get length | |
| } bind def | |
| /getExonStart | |
| { | |
| 2 dict begin | |
| /i exch def | |
| /gene exch def | |
| gene 7 get i get | |
| end | |
| } bind def | |
| /getExonEnd | |
| { | |
| 2 dict begin | |
| /i exch def | |
| /gene exch def | |
| gene 8 get i get | |
| end | |
| } bind def | |
| /isVisible | |
| { | |
| 1 dict begin | |
| /gene exch def | |
| minChromStart gene getTxEnd gt | |
| { | |
| false | |
| } | |
| { | |
| gene getTxStart maxChromEnd gt | |
| { | |
| false | |
| } | |
| { | |
| true | |
| }ifelse | |
| }ifelse | |
| end | |
| }bind def | |
| /getHyperLink | |
| { | |
| 3 dict begin | |
| /E exch def | |
| /S exch def | |
| /C exch def | |
| [ (http://genome.ucsc.edu/cgi-bin/hgTracks?position=) C (:) S toString (-) E toString (&) (&db=hg19) ] concatstringarray | |
| end | |
| } bind def | |
| /getMinChromStart | |
| { | |
| 3 dict begin | |
| /genes exch def | |
| /pos 10E9 def | |
| /i 0 def | |
| genes length { | |
| genes i get getTxStart pos min /pos exch def | |
| i 1 add /i exch def | |
| }repeat | |
| pos | |
| end | |
| } bind def | |
| /getMaxChromEnd | |
| { | |
| 3 dict begin | |
| /genes exch def | |
| /pos -1E9 def | |
| /i 0 def | |
| genes length { | |
| genes i get getTxEnd pos max /pos exch def | |
| i 1 add /i exch def | |
| }repeat | |
| pos | |
| end | |
| } bind def | |
| /box | |
| { | |
| 4 dict begin | |
| /height exch def | |
| /width exch def | |
| /y exch def | |
| /x exch def | |
| x y moveto | |
| width 0 rlineto | |
| 0 height rlineto | |
| width -1 mul 0 rlineto | |
| 0 height -1 mul rlineto | |
| end | |
| } bind def | |
| /gradient | |
| { | |
| 4 dict begin | |
| /height exch def | |
| /width exch def | |
| /y exch def | |
| /x exch def | |
| /i 0 def | |
| height 2 div /i exch def | |
| 0 1 height 2 div { | |
| 1 i height 2.0 div div sub setgray | |
| newpath | |
| x | |
| y height 2 div i sub add | |
| width | |
| i 2 mul | |
| box | |
| closepath | |
| fill | |
| i 1 sub /i exch def | |
| }for | |
| newpath | |
| 0 setgray | |
| 0.4 setlinewidth | |
| x y width height box | |
| closepath | |
| stroke | |
| end | |
| } bind def | |
| /ticksHeight | |
| { | |
| featureHeight 0.2 mul | |
| } bind def | |
| /cdsHeight | |
| { | |
| featureHeight 0.5 mul | |
| } bind def | |
| /exonHeight | |
| { | |
| featureHeight 0.8 mul | |
| } bind def | |
| %********************************* | |
| % | |
| % paint one gene | |
| % @arg one knownGene array | |
| % @return void | |
| % | |
| /paintGene | |
| { | |
| 5 dict begin | |
| /gene exch def %% the GENE argument | |
| /midy featureHeight 2.0 div def %the middle of the row | |
| /x0 gene getTxStart convertPos2pixel def % 5' side of the gene in pixel | |
| /x1 gene getTxEnd convertPos2pixel def % 3' side of the gene in pixel | |
| /i 0 def | |
| 0.1 setlinewidth | |
| 1 0 0 setrgbcolor | |
| newpath | |
| x0 midy moveto | |
| x1 midy lineto | |
| closepath | |
| stroke | |
| % paint ticks | |
| 0 1 x1 x0 sub ticksx div{ | |
| newpath | |
| gene getStrand 1 eq | |
| { | |
| x0 ticksHeight sub i add midy ticksHeight add moveto | |
| x0 i add midy lineto | |
| x0 ticksHeight sub i add midy ticksHeight sub lineto | |
| } | |
| %else | |
| { | |
| x0 ticksHeight add i add midy ticksHeight add moveto | |
| x0 i add midy lineto | |
| x0 ticksHeight add i add midy ticksHeight sub lineto | |
| } ifelse | |
| stroke | |
| i ticksx add /i exch def | |
| } for | |
| %paint Transcript start-end | |
| 0 0 1 setrgbcolor | |
| newpath | |
| gene getCdsStart convertPos2pixel | |
| midy cdsHeight 2 div sub | |
| gene getCdsEnd convertPos2pixel gene getCdsStart convertPos2pixel sub | |
| cdsHeight box | |
| closepath | |
| fill | |
| % loop over exons | |
| 0 /i exch def | |
| gene getExonCount | |
| { | |
| gene i getExonStart convertPos2pixel | |
| midy exonHeight 2 div sub | |
| gene i getExonEnd convertPos2pixel gene i getExonStart convertPos2pixel sub | |
| exonHeight gradient | |
| i 1 add /i exch def | |
| } repeat | |
| 0 setgray | |
| gene getTxEnd convertPos2pixel 10 add midy moveto | |
| gene getKgName show | |
| %URL | |
| [ /Rect [x0 0 x1 1 add featureHeight] | |
| /Border [1 0 0] | |
| /Color [1 0 0] | |
| /Action << /Subtype /URI /URI gene getChrom gene getTxStart gene getTxEnd getHyperLink >> | |
| /Subtype /Link | |
| /ANN pdfmark | |
| end | |
| } bind def | |
| %******************************************** | |
| % | |
| % count the number of visible genes | |
| % | |
| % | |
| /countVisibleGenes | |
| { | |
| 3 dict begin | |
| /genes exch def %the GENE argument (an array) | |
| /i 0 def % loop iterator | |
| /n 0 def % the count | |
| genes length { | |
| genes i get isVisible | |
| { | |
| n 1 add /n exch def | |
| } if | |
| i 1 add /i exch def | |
| }repeat | |
| n | |
| end | |
| } bind def | |
| %******************************************** | |
| % | |
| % draw an array of genes | |
| % | |
| % @arg an array of knownGene | |
| % @return void | |
| % | |
| /paintGenes | |
| { | |
| 3 dict begin | |
| /genes exch def %the GENE argument (an array) | |
| /i 0 def % loop iterator | |
| /j 0 def % row iterator | |
| % draw 10 vertical lines | |
| i 0 /i exch def | |
| 0 setgray | |
| 0 1 10 { | |
| %draw a vertical line | |
| screenWidth 10 div i mul 0 moveto | |
| screenWidth 10 div i mul screenHeight lineto | |
| stroke | |
| % print the position at the top rotate by 90° | |
| screenWidth 10 div i mul 10 add screenHeight 5 sub moveto | |
| -90 rotate | |
| maxChromEnd minChromStart sub i 10 div mul minChromStart add toString show | |
| 90 rotate | |
| i 1 add /i exch def | |
| } for | |
| 0 /i exch def | |
| genes length { | |
| genes i get isVisible | |
| { | |
| gsave | |
| 0 j featureHeight 2 add mul translate | |
| genes i get paintGene | |
| j 1 add /j exch def | |
| grestore | |
| } if | |
| i 1 add /i exch def | |
| }repeat | |
| end | |
| } bind def | |
| /knownGene [ | |
| [(uc002zkr.3) (chr22) (-) 16124263 16193004 16124263 16124263 [16124263 16162396 16186810 16187164 16192905 ] [16124973 16162487 16186946 16187302 16193004 ] ] | |
| [(uc002zks.3) (chr22) (-) 16150261 16193004 16150261 16150261 [16150261 16162396 16186810 16187164 16189031 16189263 16190680 16192905 ] [16151821 16162487 16186946 16187302 16189143 16189411 16190791 16193004 ] ] | |
| [(uc002zkt.2) (chr22) (+) 16162065 16172264 16162065 16162065 [16162065 16164481 16171951 ] [16162388 16164569 16172264 ] ] | |
| [(uc002zku.2) (chr22) (-) 16179619 16181004 16179619 16179619 [16179619 ] [16181004 ] ] | |
| [(uc002zkv.3) (chr22) (-) 16187164 16193004 16187164 16187164 [16187164 16189031 16189263 16190680 16192905 ] [16187302 16189143 16189378 16190791 16193004 ] ] | |
| [(uc002zkw.2) (chr22) (-) 16240244 16240281 16240244 16240244 [16240244 ] [16240281 ] ] | |
| [(uc002zkx.1) (chr22) (-) 16240300 16240339 16240300 16240300 [16240300 ] [16240339 ] ] | |
| [(uc002zky.1) (chr22) (+) 16241086 16241125 16241086 16241086 [16241086 ] [16241125 ] ] | |
| [(uc002zkz.1) (chr22) (-) 16242000 16242030 16242000 16242000 [16242000 ] [16242030 ] ] | |
| [(uc002zla.1) (chr22) (-) 16243380 16243414 16243380 16243380 [16243380 ] [16243414 ] ] | |
| [(uc002zlb.2) (chr22) (-) 16243908 16243948 16243908 16243908 [16243908 ] [16243948 ] ] | |
| [(uc002zlc.1) (chr22) (-) 16245151 16245185 16245151 16245151 [16245151 ] [16245185 ] ] | |
| [(uc002zld.2) (chr22) (-) 16245679 16245719 16245679 16245679 [16245679 ] [16245719 ] ] | |
| [(uc002zle.1) (chr22) (-) 16248998 16249023 16248998 16248998 [16248998 ] [16249023 ] ] | |
| [(uc002zlf.1) (chr22) (-) 16251234 16254941 16251234 16251234 [16251234 ] [16254941 ] ] | |
| [(uc002zlg.1) (chr22) (-) 16256331 16287425 16256331 16256331 [16256331 16258184 16262903 16266928 16268136 16269872 16275206 16277747 16279194 16282144 16282477 16287253 ] [16256677 16258303 16262952 16267095 16268181 16269943 16275277 16277885 16279301 16282318 16282592 16287425 ] ] | |
| [(uc002zlh.1) (chr22) (-) 16256331 16287425 16258185 16280411 [16256331 16258184 16266928 16268136 16269872 16275206 16277747 16279194 16280333 16282144 16282477 16287253 ] [16256677 16258303 16267095 16268181 16269943 16275277 16277885 16279301 16280589 16282318 16282592 16287425 ] ] | |
| [(uc010gqp.2) (chr22) (-) 16256331 16287937 16258185 16287885 [16256331 16258184 16266928 16268136 16269872 16275206 16277747 16279194 16282144 16282477 16287253 ] [16256677 16258303 16267095 16268181 16269943 16275277 16277885 16279301 16282318 16282592 16287937 ] ] | |
| [(uc002zlj.1) (chr22) (-) 16266928 16287937 16266930 16287390 [16266928 16268136 16269872 16275206 16277747 16279194 16282144 16282477 16287253 16287537 ] [16267095 16268181 16269943 16275277 16277885 16279301 16282318 16282592 16287425 16287937 ] ] | |
| [(uc002zlk.2) (chr22) (+) 16274557 16278598 16274557 16274557 [16274557 16276480 ] [16275003 16278598 ] ] | |
| [(uc002zll.1) (chr22) (+) 16373080 16377057 16373080 16373080 [16373080 16373829 16375448 ] [16373121 16373911 16377057 ] ] | |
| [(uc011agd.1) (chr22) (-) 16448825 16449804 16448826 16449804 [16448825 ] [16449804 ] ] | |
| [(uc002zln.1) (chr22) (+) 16492811 16492932 16492811 16492811 [16492811 ] [16492932 ] ] | |
| [(uc011age.1) (chr22) (+) 17029052 17029078 17029052 17029052 [17029052 ] [17029078 ] ] | |
| [(uc002zlo.1) (chr22) (+) 17029615 17029643 17029615 17029615 [17029615 ] [17029643 ] ] | |
| [(uc002zlp.1) (chr22) (-) 17071647 17073700 17071766 17073440 [17071647 ] [17073700 ] ] | |
| [(uc010gqq.2) (chr22) (+) 17082800 17095998 17082800 17082800 [17082800 17092547 17094966 17095588 ] [17083105 17092783 17095068 17095998 ] ] | |
| [(uc002zlq.3) (chr22) (+) 17082800 17095998 17082800 17082800 [17082800 17092547 17094966 ] [17083105 17092783 17095998 ] ] | |
| [(uc002zlr.2) (chr22) (+) 17082800 17129719 17082800 17082800 [17082800 17092547 17094966 17103730 17117929 17119468 17128057 17128552 17129416 ] [17083105 17092783 17095068 17103787 17117980 17119630 17128147 17128675 17129719 ] ] | |
| [(uc002zls.1) (chr22) (+) 17082800 17179521 17082800 17082800 [17082800 17119468 17178385 ] [17083105 17119630 17179521 ] ] | |
| [(uc002zlt.2) (chr22) (+) 17100506 17134580 17100506 17100506 [17100506 17100941 17103730 17117929 17119468 17128494 17129416 17134399 ] [17100610 17101050 17103787 17117980 17119630 17128675 17129538 17134580 ] ] | |
| [(uc002zlu.2) (chr22) (-) 17227759 17229328 17227759 17227759 [17227759 17229165 ] [17228629 17229328 ] ] | |
| [(uc002zlv.2) (chr22) (-) 17264312 17302584 17264508 17288963 [17264312 17280660 17288628 17302496 ] [17265299 17280914 17288973 17302584 ] ] | |
| [(uc011agf.1) (chr22) (-) 17264312 17302584 17264508 17288963 [17264312 17280660 17288628 17302496 ] [17265299 17280914 17288976 17302584 ] ] | |
| [(uc010gqr.1) (chr22) (+) 17308363 17310225 17308363 17308363 [17308363 17309431 ] [17308950 17310225 ] ] | |
| [(uc011agg.1) (chr22) (-) 17385314 17385395 17385314 17385314 [17385314 ] [17385395 ] ] | |
| [(uc002zlw.2) (chr22) (-) 17442828 17489112 17443622 17489004 [17442828 17444614 17445655 17446067 17446989 17449187 17450832 17468849 17472762 17488830 ] [17443766 17444719 17445752 17446158 17447254 17449273 17451083 17469057 17473066 17489112 ] ] | |
| [(uc010gqs.1) (chr22) (-) 17446991 17489112 17449218 17489004 [17446991 17449187 17468849 17472762 17488830 ] [17448371 17449273 17469006 17473066 17489112 ] ] | |
| [(uc002zlx.1) (chr22) (+) 17517459 17539682 17517459 17517459 [17517459 17525762 17528213 17537962 ] [17518234 17525890 17528316 17539682 ] ] | |
| [(uc002zly.2) (chr22) (+) 17565848 17591387 17565981 17590710 [17565848 17577951 17578686 17579664 17581244 17582885 17583028 17584383 17585615 17586480 17586742 17588616 17589196 ] [17566119 17577976 17578833 17579777 17581371 17582933 17583192 17584467 17585700 17586492 17586844 17588658 17591387 ] ] | |
| [(uc010gqt.2) (chr22) (+) 17565848 17591387 17565981 17590710 [17565848 17577951 17578686 17579664 17581244 17582885 17583028 17584383 17585615 17589196 ] [17566119 17577976 17578833 17579777 17581371 17582933 17583192 17584467 17585700 17591387 ] ] | |
| [(uc002zlz.1) (chr22) (+) 17593917 17596582 17593917 17593917 [17593917 ] [17596582 ] ] | |
| [(uc002zmb.2) (chr22) (-) 17597188 17602213 17600280 17602017 [17597188 ] [17602213 ] ] | |
| [(uc002zma.2) (chr22) (-) 17597188 17602257 17600280 17600952 [17597188 17602141 ] [17601033 17602257 ] ] | |
| [(uc002zmc.2) (chr22) (+) 17602484 17612993 17602484 17602484 [17602484 17605544 17611251 17612504 ] [17602929 17605661 17611374 17612993 ] ] | |
| [(uc002zmd.2) (chr22) (-) 17618410 17622467 17618910 17622286 [17618410 17619439 17621948 17622282 ] [17619247 17619628 17622123 17622467 ] ] | |
| [(uc002zme.2) (chr22) (-) 17618410 17629450 17618910 17622070 [17618410 17619439 17621948 17625913 17629337 ] [17619247 17619628 17622123 17626007 17629450 ] ] | |
| [(uc002zmf.2) (chr22) (-) 17618410 17640169 17618910 17640141 [17618410 17619439 17621948 17623987 17625913 17629337 17630431 17640015 ] [17619247 17619628 17622123 17624021 17626007 17629450 17630635 17640169 ] ] | |
| [(uc002zmg.2) (chr22) (-) 17618410 17640169 17618910 17640141 [17618410 17621948 17623987 17640015 ] [17619247 17622123 17624021 17640169 ] ] | |
| [(uc002zmh.2) (chr22) (-) 17618410 17646177 17618910 17646134 [17618410 17619439 17621948 17623987 17625913 17629337 17630431 17646098 ] [17619247 17619628 17622123 17624021 17626007 17629450 17630635 17646177 ] ] | |
| ] def | |
| knownGene getMinChromStart 10 sub /minChromStart exch def | |
| knownGene getMaxChromEnd 10 add /maxChromEnd exch def | |
| systemdict /userChromStart known { | |
| userChromStart toInteger /minChromStart exch def | |
| } if | |
| systemdict /userChromEnd known { | |
| userChromEnd toInteger /maxChromEnd exch def | |
| } if | |
| screenHeight knownGene countVisibleGenes 1 add div 20.0 min /featureHeight exch def | |
| 0 0 screenWidth 1 sub screenHeight 1 sub box | |
| 0.95 setgray | |
| fill | |
| knownGene paintGenes | |
| 0 0 screenWidth screenHeight box | |
| 0 setgray | |
| stroke | |
| showpage |
Open the PS file in ghostview, evince, ...
Zooming ? Yes we can.
Ghostview has an option -Sname=string -Sname=string
-sname=string
Define a name in "systemdict" with a given string as value.
This is different from -d.
In my postscript file, the default values for minChromStart and maxChromEnd are overridden by the user's parameters:
systemdict /userChromStart known {
userChromStart toInteger /minChromStart exch def
} if
systemdict /userChromEnd known {
userChromEnd toInteger /maxChromEnd exch def
} if
That's it,Pierre
