# gnomaptest-X.tsv
# Features for worm from WormBase GFF data [csome_X.gff, 28-May-2000]
## ^^ this comment line is parsed for species, data source, date for display

## ------ summary of gnomap, genome map drawer usage -------
## example java calling command lines (e.g. for Unix system, like will work on MacOS and MSWin)
##  jre -Dawt.toolkit=flybase.graf.NullToolkit -cp .:gnomap.jar:readseq.jar flybase.GnoMap httpcall style=pdf spp=worm chr=X bp=1..36900 dataname=gnomaptest env=MAP_DATA=testd/ 
##  jre -Dawt.toolkit=flybase.graf.NullToolkit -cp .:gnomap.jar:readseq.jar flybase.GnoMap httpcall debug=1 style=pdf spp=worm chr=X bp=1..36900

## jre parameter -Dawt.toolkit=flybase.graf.NullToolkit 
##   is required to run without an OS graphics environment (e.g. Unix commandline w/o XWindows)

## example command set for MacOS MRJ's commandline equivalent
# com.apple.mrj.application.main = flybase.GnoMap
# com.apple.mrj.application.classpath = $APPLICATION/gnomap.jar:$APPLICATION/readseq.jar:$BOOTCLASSPATH 
# com.apple.mrj.application.parameters = style=pdf spp=worm chr=X bp=1..36900 env=MAP_DATA=testd/ dataname=gnomaptest 

## program parameters:
## dataname=xxx and env=MAP_DATA=testd/  - locate input data of this format (tab-separated-values, fields as below)
## data file must now be named 'gnomaptest-X.tsv' in folder testd/worm/ 
##   to match spp=worm chr=X and dataname=gnomaptest
## Note that program chooses file name based on chr,spp,bp options and will not make new output if one of same name exists
##
## httpcall -- caller is http server, need now for unix call (small bug)
## chr=X -- chromosome name
## spp=worm -- species name
## bp=1..36900 -- base range to display (otherwise it draws overview map)
## style=pdf or style=html -- for output formats 
## add debug=1 option to get debug output
##
## See also gnomap.properties to set defaults of some of above (MAP_DATA, MAP_PIX, dataname, ...)

## ---- start of data ----
## Feature and range are required fields
## gene, map, ID, db_xref and notes are not required (notes not now used, id, dbxref for hyperlinks)

#gnomap-version 1
#Feature	gene	map	range	id	db_xref	notes

source	worm	Chr X	1..36900	-
## ^^ required line to specify total map range (in bases)

gene	CTEL7X	-	1..2649	-	-	-
tandem_repeat	-	-	129..203	-	-	Note  "4 copies of 15mer"
inverted_repeat	-	-	392..434	-	-	Note  "loop 1779, 1 gap"
gene	cTel7X.1	-	complement(709..1328)	MEOW:CEgn0007267	-	-
CDS	cTel7X.1	-	complement(join(709..822,1182..1328))	MEOW:CEgn0007267		
mRNA	cTel7X.1	-	complement(join(709..822,1182..1328))	MEOW:CEgn0007267		
tandem_repeat	-	-	2382..2645	-	-	Note  "43 copies of 6mer"
inverted_repeat	-	-	2131..2643	-	-	Note  "loop 1779, 1 gap"
repeat_family	-	-	2382..2643	-	scan_similarity	-
gene	Y47C4A	-	2750..17489	-	-	-
inverted_repeat	-	-	3294..3606	-	-	Note  "loop 311"
inverted_repeat	-	-	4270..4455	-	-	Note  "loop 184"
gene	Y47C4A.b	-	4503..4673	MEOW:CEgn0018832	-	-
CDS	Y47C4A.b	-	4503..4673	MEOW:CEgn0018832		
mRNA	Y47C4A.b	-	4503..4673	MEOW:CEgn0018832		
inverted_repeat	-	-	4887..5654	-	-	Note  "loop 251"
gene	Y47C4A.a	-	complement(5870..7861)	MEOW:CEgn0018831	-	-
inverted_repeat	-	-	6384..7134	-	-	Note  "loop 997, 2 gaps"
CDS	Y47C4A.a	-	complement(join(5870..6177,7595..7638,7758..7861))	MEOW:CEgn0018831		
mRNA	Y47C4A.a	-	complement(join(5870..6177,7595..7638,7758..7861))	MEOW:CEgn0018831		
inverted_repeat	-	-	8007..8145	-	-	Note  "loop 955"
inverted_repeat	-	-	8825..8963	-	-	Note  "loop 955"
inverted_repeat	-	-	9855..10853	-	-	Note  "loop 997, 5 gaps"
gene	R57	-	17290..29611	-	-	-
inverted_repeat	-	-	17714..18436	-	-	Note  "loop 721, 15 gaps"
gene	R57.2	-	18585..20514	MEOW:CEgn0014980	-	-
tandem_repeat	-	-	19053..19129	-	-	Note  "38 copies of 2mer"
inverted_repeat	-	-	19061..19130	-	-	Note  "loop 68"
CDS	R57.2	-	join(18585..18683,19134..19230,19276..19328,19513..19692,19778..19906,20380..20514)	MEOW:CEgn0014980		
mRNA	R57.2	-	join(18585..18683,19134..19230,19276..19328,19513..19692,19778..19906,20380..20514)	MEOW:CEgn0014980		
inverted_repeat	-	-	21312..21655	-	-	Note  "loop 342"
repeat_family	-	-	21624..21649	-	hmmfs.3_similarity	-
inverted_repeat	-	-	22160..22598	-	-	Note  "loop 437"
repeat_family	-	-	22260..22744	-	hmmfs.3_similarity	-
gene	R57.1	-	24104..29568	MEOW:CEgn0014979	-	-
inverted_repeat	-	-	24667..24888	-	-	Note  "loop 220"
repeat_family	-	-	24310..24359	-	hmmfs.3_similarity	-
inverted_repeat	-	-	26743..26931	-	-	Note  "loop 187"
repeat_family	-	-	26761..26825	-	hmmfs.3_similarity	-
gene	M02E1	-	28212..59047	-	-	-
CDS	R57.1	-	join(24104..24221,24993..25307,25523..25777,25859..25995,26313..26424,26471..26564,27006..27187,27514..27658,27996..28364,28952..29236,29281..29407,29452..29568)	MEOW:CEgn0014979		
mRNA	R57.1	-	join(24104..24221,24993..25307,25523..25777,25859..25995,26313..26424,26471..26564,27006..27187,27514..27658,27996..28364,28952..29236,29281..29407,29452..29568)	MEOW:CEgn0014979		
inverted_repeat	-	-	31093..31364	-	-	Note  "loop 270, 1 gap"
inverted_repeat	-	-	34970..35106	-	-	Note  "loop 135"
inverted_repeat	-	-	36616..36812	-	-	Note  "loop 195, 2 gaps"