[maker-devel] <MAKER Trac Server> #7: add_utr_gff.pl and maker2zff.pl issues when trying to convert to GBrowse friendly format
MAKER
maker-devel at yandell-lab.org
Fri Nov 7 06:28:05 MST 2008
#7: add_utr_gff.pl and maker2zff.pl issues when trying to convert to GBrowse
friendly format
-----------------------------------------------+----------------------------
Reporter: projectcortana at gmail.com | Owner:
Type: defect | Status: new
Priority: major | Milestone:
Component: Code | Version: 0.001
Keywords: add_utr_gff.pl, maker2zff.pl, gff |
-----------------------------------------------+----------------------------
Allo,
I am experiencing problems using the two external scripts provided on
my GFF output file built from the default fastas in the data dir of
MAKER.
In order to add UTRs for GBrowse, the README states that users must
run both add_utr_gff and maker2zff scripts on the GFF, yet no changes
are made between my original GFF and the wutr.gff file. After checking
the source, it seems that the reason for this is because my
source_tags in the GFF provided don't pass the first, or other,
conditionals required in the script. For instance, the first if
statement in add_utr_gff.pl is checking for where the source_tag
equals "maker" - yet the code to place the word 'maker' has been
commented out in the gene_data subroutine, located in ../maker/lib/
Dumper/GFF/GFFV3.pm. After taking a quick look at the remaining
conditionals in either script file, it becomes obvious that the GFF
file fails the rest of them.
Do these scripts need updating or is it my GFF file to blame? If it is
my GFF, what's wrong with it compared to what MAKER should normally be
outputting?
Thank you,
Sam
##gff-version 3
##sequence-region contig-dpp-500-500 1 32156
contig-dpp-500-500 . contig 1 32156 . . .
ID=contig-
dpp-500-500;Name=contig-dpp-500-500
contig-dpp-500-500 repeatmasker match 903 928 . +
. ID=contig-
dpp-500-500:hit:0;Name=species:(CGAAT)n-
genus:Simple_repeat;Target=species:(CGAAT)n-genus:Simple_repeat 5 29 +
contig-dpp-500-500 repeatmasker match_part 903 928
185 + . ID=contig-
dpp-500-500:hsp:0;Parent=contig-dpp-500-500:hit:0;Name=species:
(CGAAT)n-genus:Simple_repeat;Target=species:(CGAAT)n-
genus:Simple_repeat 5 29 +
contig-dpp-500-500 repeatmasker match 5809 5897 . +
. ID=contig-
dpp-500-500:hit:1;Name=species:(CAA)n-
genus:Simple_repeat;Target=species:(CAA)n-genus:Simple_repeat 2 88 +
contig-dpp-500-500 repeatmasker match_part 5809 5897
244 + . ID=contig-
dpp-500-500:hsp:1;Parent=contig-dpp-500-500:hit:1;Name=species:(CAA)n-
genus:Simple_repeat;Target=species:(CAA)n-genus:Simple_repeat 2 88 +
contig-dpp-500-500 repeatmasker match 5170 5198 . +
. ID=contig-
dpp-500-500:hit:2;Name=species:AT_rich-
genus:Low_complexity;Target=species:AT_rich-genus:Low_complexity 1 29
+
contig-dpp-500-500 repeatmasker match_part 5170 5198 29
+ . ID=contig-
dpp-500-500:hsp:2;Parent=contig-dpp-500-500:hit:2;Name=species:AT_rich-
genus:Low_complexity;Target=species:AT_rich-genus:Low_complexity 1 29
+
contig-dpp-500-500 repeatmasker match 12416 12440 . +
. ID=contig-
dpp-500-500:hit:3;Name=species:AT_rich-
genus:Low_complexity;Target=species:AT_rich-genus:Low_complexity 1 25
+
contig-dpp-500-500 repeatmasker match_part 12416 12440 25
+ .
ID=contig-dpp-500-500:hsp:3;Parent=contig-dpp-500-500:hit:
3;Name=species:AT_rich-genus:Low_complexity;Target=species:AT_rich-
genus:Low_complexity 1 25 +
contig-dpp-500-500 repeatmasker match 15478 15502 . +
. ID=contig-
dpp-500-500:hit:4;Name=species:AT_rich-
genus:Low_complexity;Target=species:AT_rich-genus:Low_complexity 1 25
+
contig-dpp-500-500 repeatmasker match_part 15478 15502 25
+ .
ID=contig-dpp-500-500:hsp:4;Parent=contig-dpp-500-500:hit:
4;Name=species:AT_rich-genus:Low_complexity;Target=species:AT_rich-
genus:Low_complexity 1 25 +
contig-dpp-500-500 repeatmasker match 17472 17494 . +
. ID=contig-
dpp-500-500:hit:5;Name=species:AT_rich-
genus:Low_complexity;Target=species:AT_rich-genus:Low_complexity 1 23
+
contig-dpp-500-500 repeatmasker match_part 17472 17494 23
+ .
ID=contig-dpp-500-500:hsp:5;Parent=contig-dpp-500-500:hit:
5;Name=species:AT_rich-genus:Low_complexity;Target=species:AT_rich-
genus:Low_complexity 1 23 +
contig-dpp-500-500 repeatmasker match 31755 31785 . +
. ID=contig-
dpp-500-500:hit:6;Name=species:AT_rich-
genus:Low_complexity;Target=species:AT_rich-genus:Low_complexity 1 31
+
contig-dpp-500-500 repeatmasker match_part 31755 31785 24
+ .
ID=contig-dpp-500-500:hsp:6;Parent=contig-dpp-500-500:hit:
6;Name=species:AT_rich-genus:Low_complexity;Target=species:AT_rich-
genus:Low_complexity 1 31 +
contig-dpp-500-500 repeatmasker match 31845 31888 . +
. ID=contig-
dpp-500-500:hit:7;Name=species:AT_rich-
genus:Low_complexity;Target=species:AT_rich-genus:Low_complexity 1 44
+
contig-dpp-500-500 repeatmasker match_part 31845 31888 30
+ .
ID=contig-dpp-500-500:hsp:7;Parent=contig-dpp-500-500:hit:
7;Name=species:AT_rich-genus:Low_complexity;Target=species:AT_rich-
genus:Low_complexity 1 44 +
contig-dpp-500-500 repeatmasker match 26624 26647 . +
. ID=contig-
dpp-500-500:hit:8;Name=species:(GTCTG)n-
genus:Simple_repeat;Target=species:(GTCTG)n-genus:Simple_repeat 1 24 +
contig-dpp-500-500 repeatmasker match_part 26624 26647
195 + .
ID=contig-dpp-500-500:hsp:8;Parent=contig-dpp-500-500:hit:
8;Name=species:(GTCTG)n-genus:Simple_repeat;Target=species:(GTCTG)n-
genus:Simple_repeat 1 24 +
contig-dpp-500-500 repeatmasker match 105 129 . +
. ID=contig-
dpp-500-500:hit:9;Name=species:(CA)n-
genus:Simple_repeat;Target=species:(CA)n-genus:Simple_repeat 1 25 +
contig-dpp-500-500 repeatmasker match_part 105 129
204 + . ID=contig-
dpp-500-500:hsp:9;Parent=contig-dpp-500-500:hit:9;Name=species:(CA)n-
genus:Simple_repeat;Target=species:(CA)n-genus:Simple_repeat 1 25 +
contig-dpp-500-500 repeatmasker match 26695 26756 . +
. ID=contig-
dpp-500-500:hit:10;Name=species:(CCG)n-
genus:Simple_repeat;Target=species:(CCG)n-genus:Simple_repeat 3 65 +
contig-dpp-500-500 repeatmasker match_part 26695 26756
247 + .
ID=contig-dpp-500-500:hsp:10;Parent=contig-dpp-500-500:hit:
10;Name=species:(CCG)n-genus:Simple_repeat;Target=species:(CCG)n-
genus:Simple_repeat 3 65 +
contig-dpp-500-500 repeatmasker match 2163 2192 . +
. ID=contig-
dpp-500-500:hit:11;Name=species:(CAG)n-
genus:Simple_repeat;Target=species:(CAG)n-genus:Simple_repeat 2 31 +
contig-dpp-500-500 repeatmasker match_part 2163 2192
183 + . ID=contig-
dpp-500-500:hsp:11;Parent=contig-dpp-500-500:hit:11;Name=species:
(CAG)n-genus:Simple_repeat;Target=species:(CAG)n-genus:Simple_repeat 2
31 +
contig-dpp-500-500 repeatmasker match 1849 1881 . +
. ID=contig-
dpp-500-500:hit:12;Name=species:(CTTTG)n-
genus:Simple_repeat;Target=species:(CTTTG)n-genus:Simple_repeat 1 33 +
contig-dpp-500-500 repeatmasker match_part 1849 1881
206 + . ID=contig-
dpp-500-500:hsp:12;Parent=contig-dpp-500-500:hit:12;Name=species:
(CTTTG)n-genus:Simple_repeat;Target=species:(CTTTG)n-
genus:Simple_repeat 1 33 +
contig-dpp-500-500 blastx:repeatmask protein_match 28310
28507
0.00421711 - . ID=contig-
dpp-500-500:hit:13;Name=gi|18254413|gb|
AAL66754.1|AF464738_5;Target=gi|18254413|gb|AAL66754.1|AF464738_5 784
855 +
contig-dpp-500-500 blastx:repeatmask match_part 28310
28507
0.00421711 - . ID=contig-
dpp-500-500:hsp:13;Parent=contig-
dpp-500-500:hit:13;Name=gnl|BL_ORD_ID|15987;Target=gnl|BL_ORD_ID|15987
784 855 +
contig-dpp-500-500 blastx:repeatmask protein_match 30776
30931
0.016025 - . ID=contig-
dpp-500-500:hit:14;Name=gi|7670973|gb|
AAF66306.1|;Target=gi|7670973|gb|AAF66306.1| 135 185 +
contig-dpp-500-500 blastx:repeatmask match_part 30776
30931
0.016025 - . ID=contig-
dpp-500-500:hsp:14;Parent=contig-
dpp-500-500:hit:14;Name=gnl|BL_ORD_ID|4439;Target=gnl|BL_ORD_ID|4439
135 185 +
contig-dpp-500-500 blastx:repeatmask protein_match 31190
31270 9.72204
+ . ID=contig-dpp-500-500:hit:15;Name=gi|4521269|dbj|
BAA76304.1|;Target=gi|4521269|dbj|BAA76304.1| 661 687 +
contig-dpp-500-500 blastx:repeatmask match_part 31190
31270 9.72204
+ . ID=contig-dpp-500-500:hsp:15;Parent=contig-
dpp-500-500:hit:
15;Name=gnl|BL_ORD_ID|22384;Target=gnl|BL_ORD_ID|22384 661 687 +
contig-dpp-500-500 blastx:repeatmask protein_match 31558
31587
4.36403 - . ID=contig-dpp-500-500:hit:16;Name=gi|27670321|ref|
XP_229474.1|;Target=gi|27670321|ref|XP_229474.1| 451 460 +
contig-dpp-500-500 blastx:repeatmask match_part 31558
31587
4.36403 - . ID=contig-dpp-500-500:hsp:16;Parent=contig-
dpp-500-500:hit:
16;Name=gnl|BL_ORD_ID|20333;Target=gnl|BL_ORD_ID|20333 451 460 +
contig-dpp-500-500 blastx:repeatmask protein_match 31717
31818
0.231401 + . ID=contig-
dpp-500-500:hit:17;Name=gi|327819|gb|
AAB03749.1|;Target=gi|327819|gb|AAB03749.1| 18 51 +
contig-dpp-500-500 blastx:repeatmask match_part 31717
31818 0.231401
+ . ID=contig-dpp-500-500:hsp:17;Parent=contig-
dpp-500-500:hit:
17;Name=gnl|BL_ORD_ID|29022;Target=gnl|BL_ORD_ID|29022 18 51 +
contig-dpp-500-500 blastx:repeatmask protein_match 32026
32109
2.55843 - . ID=contig-dpp-500-500:hit:18;Name=gi|6015506|emb|
CAB57796.1|;Target=gi|6015506|emb|CAB57796.1| 138 165 +
contig-dpp-500-500 blastx:repeatmask match_part 32026
32109
2.55843 - . ID=contig-dpp-500-500:hsp:18;Parent=contig-
dpp-500-500:hit:
18;Name=gnl|BL_ORD_ID|30389;Target=gnl|BL_ORD_ID|30389 138 165 +
contig-dpp-500-500 blastn expressed_sequence_match 31379
31507
1.07552e-18 + . ID=contig-dpp-500-500:hit:19;Name=dpp-
mRNA-3;Target=dpp-mRNA-3 3961 4089 +
contig-dpp-500-500 blastn match_part 31379 31429
1.07552e-18 + .
ID=contig-dpp-500-500:hsp:19;Parent=contig-dpp-500-500:hit:19;Name=gnl|
BL_ORD_ID|2;Target=gnl|BL_ORD_ID|2 3961 4011 +
contig-dpp-500-500 blastn match_part 31449 31507
1.80977e-23 + .
ID=contig-dpp-500-500:hsp:20;Parent=contig-dpp-500-500:hit:19;Name=gnl|
BL_ORD_ID|2;Target=gnl|BL_ORD_ID|2 4031 4089 +
##FASTA
>contig-dpp-500-500
TGAGAGAGCTGAAATATTGTAATTGTGAGTCTGGCTTGTTTGTTATTGTTGCCTTAGCGG
TTGCTTGTTGTTTTTTTGGCTTGATTAATAATTAATCGCACTCGCACACACACACACACA
...cut for brevity.
--
Ticket URL: <http://malachite.genetics.utah.edu/projects/maker/ticket/7>
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