################################################################################ ### ### ### RUNNING gff2aplot ### ### ### ### User: lopep ### ### Date: Tue Jun 3 16:42:37 2003 ### ### Perl: v5.8.0 ### ################################################################################ ################################################################################ ### SETTING DEFAULTS ### ################################################################################ ################################################################################ ### CHECKING COMMAND-LINE OPTIONS ### ################################################################################ ### ### Validating INPUT FILENAMES ### ###---> "taf6.mmhs.genomic.tblastx.aplot.gff" exists, including as Input File. ###---> "taf6.mm.gene.gff" exists, including as Input File. ###---> "taf6.hs.gene.gff" exists, including as Input File. ### ### Validating CUSTOM FILENAMES ### ###---> ".gff2aplotrc" NOT FOUND, skipping!!! ###---> "taf6.tblastx.rc" exists, including as Custom File. ### ### Checking COMMAND-LINE Options ### ... [000003] ### ### Checking Custom Variables SET by COMMAND-LINE ### ################################################################################ ### COMMAND-LINE OPTIONS CHECKED ### ### 1 wallclock secs ( 0.03 usr + 0.00 sys = 0.03 CPU) ### ################################################################################ ### ################################################################################ ### COMMAND-LINE CHECKED ### ### 0 wallclock secs ( 0.00 usr + 0.00 sys = 0.00 CPU) ### ################################################################################ ### ################################################################################ ### READING CUSTOM FILES ### ################################################################################ ### ### Reading Customization Parameters from "taf6.tblastx.rc" ### .*LLLLLL..*GG.*FFFFFFFF [000023] ################################################################################ ### CUSTOM FILES LOADED ### ### 0 wallclock secs ( 0.00 usr + 0.01 sys = 0.01 CPU) ### ################################################################################ ### ################################################################################ ### MAPPING CUSTOMIZATION INPUTS TO MAIN VARS ### ################################################################################ ################################################################################ ### VALUES SET for MAIN VARS ### ### 0 wallclock secs ( 0.01 usr + 0.00 sys = 0.01 CPU) ### ################################################################################ ### ################################################################################ ### PARSING INPUT GFF RECORDS ### ################################################################################ ### ### Reading GFF records from "taf6.mmhs.genomic.tblastx.aplot.gff" ### OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO [000050] OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO [000100] OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO [000150] OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO [000191] ### ### Reading GFF records from "taf6.mm.gene.gff" ### XXXXXXXXXXXXXXXX [000016] ### ### Reading GFF records from "taf6.hs.gene.gff" ### XXXXXXXXXXXXXXXXX [000017] ################################################################################ ### DATA LOADED ### ### 0 wallclock secs ( 0.09 usr + 0.21 sys = 0.30 CPU) ### ################################################################################ ### ################################################################################ ### SETTING CUSTOM VALUES TO GFF ELEMENTS ### ################################################################################ ################################################################################ ### VALUES SET for GFF ELEMENTS ### ### 1 wallclock secs ( 0.03 usr + 0.13 sys = 0.16 CPU) ### ################################################################################ ### ################################################################################ ### SORTING ELEMENTS BY ACCEPTOR (START) ### ################################################################################ *- Sorting ANNOTATION DATA | *- Sequence: NM_009315 | | *- Source: chr5 | | | *- Strand: + | | | | *- Group: M.musculus | | | | | Sorted 16 elements. | | | | `Sorted 1 groups. | *- Sequence: NM_005641 | | *- Source: chr7 | | | *- Strand: + | | | | *- Group: H.sapiens | | | | | Sorted 17 elements. | | | | `Sorted 1 groups. *- Sorting ALIGNMENT DATA | *- Sequence: NM_009315:NM_005641 | | *- Source: TBLASTX | | | *- Strand: -- | | | | *- Group: 22.3 | | | | | Sorted 3 elements. | | | | *- Group: 23.7 | | | | | Sorted 4 elements. | | | | *- Group: 96.9 | | | | | Sorted 1 elements. | | | | *- Group: 30.8 | | | | | Sorted 1 elements. | | | | *- Group: 107.1 | | | | | Sorted 1 elements. | | | | *- Group: 20.2 | | | | | Sorted 9 elements. | | | | *- Group: 276.8 | | | | | Sorted 1 elements. | | | | *- Group: 108.2 | | | | | Sorted 1 elements. | | | | *- Group: 88.1 | | | | | Sorted 1 elements. | | | | *- Group: 24.4 | | | | | Sorted 2 elements. | | | | *- Group: 113.8 | | | | | Sorted 1 elements. | | | | *- Group: 72.6 | | | | | Sorted 1 elements. | | | | *- Group: 78.6 | | | | | Sorted 1 elements. | | | | *- Group: 22.0 | | | | | Sorted 4 elements. | | | | *- Group: 20.9 | | | | | Sorted 6 elements. | | | | *- Group: 25.8 | | | | | Sorted 1 elements. | | | | *- Group: 27.9 | | | | | Sorted 2 elements. | | | | *- Group: 87.8 | | | | | Sorted 1 elements. | | | | *- Group: 34.3 | | | | | Sorted 1 elements. | | | | *- Group: 28.6 | | | | | Sorted 1 elements. | | | | *- Group: 21.3 | | | | | Sorted 8 elements. | | | | *- Group: 20.5 | | | | | Sorted 4 elements. | | | | *- Group: 49.1 | | | | | Sorted 1 elements. | | | | *- Group: 27.6 | | | | | Sorted 1 elements. | | | | *- Group: 24.8 | | | | | Sorted 2 elements. | | | | *- Group: 28.3 | | | | | Sorted 1 elements. | | | | *- Group: 93.1 | | | | | Sorted 1 elements. | | | | *- Group: 31.8 | | | | | Sorted 1 elements. | | | | *- Group: 63.5 | | | | | Sorted 1 elements. | | | | *- Group: 71.9 | | | | | Sorted 1 elements. | | | | *- Group: 52.6 | | | | | Sorted 1 elements. | | | | *- Group: 53.3 | | | | | Sorted 1 elements. | | | | *- Group: 26.5 | | | | | Sorted 1 elements. | | | | *- Group: 22.7 | | | | | Sorted 4 elements. | | | | *- Group: 57.2 | | | | | Sorted 1 elements. | | | | *- Group: 23.4 | | | | | Sorted 4 elements. | | | | *- Group: 25.5 | | | | | Sorted 1 elements. | | | | *- Group: 23.0 | | | | | Sorted 4 elements. | | | | *- Group: 21.6 | | | | | Sorted 3 elements. | | | | *- Group: 24.1 | | | | | Sorted 3 elements. | | | | *- Group: 26.2 | | | | | Sorted 2 elements. | | | | *- Group: 25.1 | | | | | Sorted 3 elements. | | | | `Sorted 42 groups. | | | *- Strand: ++ | | | | *- Group: 22.3 | | | | | Sorted 5 elements. | | | | *- Group: 70.9 | | | | | Sorted 1 elements. | | | | *- Group: 23.7 | | | | | Sorted 4 elements. | | | | *- Group: 105.4 | | | | | Sorted 1 elements. | | | | *- Group: 30.8 | | | | | Sorted 1 elements. | | | | *- Group: 115.9 | | | | | Sorted 1 elements. | | | | *- Group: 61.0 | | | | | Sorted 2 elements. | | | | *- Group: 20.2 | | | | | Sorted 9 elements. | | | | *- Group: 24.4 | | | | | Sorted 1 elements. | | | | *- Group: 85.0 | | | | | Sorted 1 elements. | | | | *- Group: 22.0 | | | | | Sorted 4 elements. | | | | *- Group: 20.9 | | | | | Sorted 5 elements. | | | | *- Group: 25.8 | | | | | Sorted 5 elements. | | | | *- Group: 300.4 | | | | | Sorted 1 elements. | | | | *- Group: 27.9 | | | | | Sorted 1 elements. | | | | *- Group: 27.2 | | | | | Sorted 1 elements. | | | | *- Group: 92.0 | | | | | Sorted 1 elements. | | | | *- Group: 21.3 | | | | | Sorted 8 elements. | | | | *- Group: 73.4 | | | | | Sorted 1 elements. | | | | *- Group: 38.1 | | | | | Sorted 1 elements. | | | | *- Group: 20.5 | | | | | Sorted 9 elements. | | | | *- Group: 118.1 | | | | | Sorted 1 elements. | | | | *- Group: 71.9 | | | | | Sorted 1 elements. | | | | *- Group: 71.2 | | | | | Sorted 1 elements. | | | | *- Group: 52.6 | | | | | Sorted 1 elements. | | | | *- Group: 30.1 | | | | | Sorted 2 elements. | | | | *- Group: 52.9 | | | | | Sorted 1 elements. | | | | *- Group: 26.5 | | | | | Sorted 2 elements. | | | | *- Group: 22.7 | | | | | Sorted 4 elements. | | | | *- Group: 67.7 | | | | | Sorted 1 elements. | | | | *- Group: 97.3 | | | | | Sorted 1 elements. | | | | *- Group: 23.4 | | | | | Sorted 2 elements. | | | | *- Group: 23.0 | | | | | Sorted 3 elements. | | | | *- Group: 21.6 | | | | | Sorted 7 elements. | | | | *- Group: 93.8 | | | | | Sorted 2 elements. | | | | *- Group: 24.1 | | | | | Sorted 2 elements. | | | | *- Group: 126.2 | | | | | Sorted 1 elements. | | | | *- Group: 26.2 | | | | | Sorted 2 elements. | | | | *- Group: 232.1 | | | | | Sorted 1 elements. | | | | *- Group: 69.8 | | | | | Sorted 1 elements. | | | | `Sorted 40 groups. ################################################################################ ### ELEMENTS SORTED ### ### 0 wallclock secs ( 0.06 usr + 0.02 sys = 0.08 CPU) ### ################################################################################ ### ################################################################################ ### SETTING PAGE LAYOUT ### ################################################################################ ###---> Page size set to "a4" ( 595 x 842 )... ###---> Setting plot AXES: ### ALIGNMENT "NM_009315:NM_005641" was found. PLOTTING IT... ### X-SEQUENCE "NM_009315" was found. PLOTTING IT... ### Y-SEQUENCE "NM_005641" was found. PLOTTING IT... ###---> SEQUENCE BOUNDARIES selected for this plot: ### X : 1 to 5878 ### Y : 1 to 12278 ###---> SEQUENCE ZOOM is not enabled for this plot... ###---> NO ZOOM AREA was selected for this plot... ###---> SCORE BOUNDARIES selected for this plot: ### ALIGNMENT: 43 to 839 ### PERCENT box: 0 to 1000 ###---> TICKMARKS were set: ### Nucleotide-Scale: Major step 1000 - Minor step 200 ### Score-Scale: Major step 250 - Minor step 62.5 ###---> X/Y scale settings are: ### XY-RATIO is not taken into account for this plot ... ### Are X/Y axes going to have same length ? YES ################################################################################ ### PAGE LAYOUT SET for CURRENT PLOT ### ### 0 wallclock secs ( 0.00 usr + 0.00 sys = 0.00 CPU) ### ################################################################################ ### ################################################################################ ### WRITING POSTSCRIPT TO STDOUT ### ################################################################################ ###---> PostScript Header DONE... ###---> PostScript Colors Table SET... ###---> PostScript Page-formats Table SET... ###---> PostScript Variables SET... ###---> PostScript Functions SET... ###---> Writting PostScript Page: ### + APLOT-BOX section : ### + drawing X-sequence annotation (NM_009315)... ### + drawing X-sequence ribbons... ### + drawing Y-sequence annotation (NM_005641)... ### + drawing Y-sequence ribbons... ### + drawing alignment features (NM_009315:NM_005641)... ### + APLOT-BOX section DONE... ### + PERCENT-BOX section : ### + drawing X-sequence ribbons... ### + drawing alignment features (NM_009315:NM_005641)... ### + PERCENT-BOX section DONE... ###---> PostScript Page FINISHED... ################################################################################ ### WRITING POSTSCRIPT FINISHED ### ### 0 wallclock secs ( 0.08 usr + 0.10 sys = 0.18 CPU) ### ################################################################################ ### ################################################################################ ### gff2aplot HAS FINISHED ### ### [ 2 wallclock secs ( 0.30 usr + 0.47 sys = 0.77 CPU) ] ### ################################################################################