| Subject: | feature_draw.pl broken |
Distribution version: Bio::Graphics 2.11
Perl version: 5.10.1
OS version: FreeBSD 8.1
When running feature_draw.pl on the example input (from the feature_draw.pl perldoc --
attached as "example.txt"), the following error occurs:
#######################################
$ feature_draw.pl example.txt > example.png
Not a HASH reference at /usr/local/bin/feature_draw.pl line 61, <> line 32.
#######################################
A one line change fixed this (attached as feature_draw.pl.patch -- also, this fixes the formatting
of the example so it displays correctly with "perldoc feature_draw.pl").
| Subject: | example.txt |
# example file
[general]
bases = -1000..21000
height = 12
[EST]
glyph = segments
bgcolor= yellow
connector = dashed
height = 5
[FGENES]
glyph = transcript2
bgcolor = green
description = 1
Cosmid B0511 . 516-619
Cosmid B0511 . 3185-3294
Cosmid B0511 . 10946-11208
Cosmid B0511 . 13126-13511
Cosmid B0511 . 66-208
Cosmid B0511 . 6354-6499
Cosmid B0511 . 13955-14115
EST yk595e6.5 + 3187-3294
EST yk846e07.3 - 11015-11208
EST yk53c10
yk53c10.5 + 18892-19154
yk53c10.3 - 15000-15500,15700-15800
EST yk53c10.5 + 16032-16105
SwissProt PECANEX + 13153-13656 Swedish fish
FGENESH "Gene 1" - 1-205,518-616,661-735,3187-3365,3436-3846 Transmembrane domain
FGENESH "Gene 2" - 16626-17396,17451-17597 Kinase and sushi domains
| Subject: | feature_draw.pl.patch |
--- feature_draw.pl.orig 2010-11-01 14:18:11.697637429 +0000
+++ feature_draw.pl 2010-11-01 14:04:43.340151771 +0000
@@ -58,7 +58,7 @@
# over is presented in alphabetic order
my %types = map {$_=>1} $data->configured_types;
-my @configured_types = grep {exists $data->features->{$_}} $data->configured_types;
+my @configured_types = grep {defined $data->features($_)} $data->configured_types;
my @unconfigured_types = sort grep {!exists $types{$_}} $data->types;
# create the segment,the panel and the arrow with tickmarks
@@ -264,22 +264,22 @@
Here is an example data section:
-Cosmid B0511 . 516-619
-Cosmid B0511 . 3185-3294
-Cosmid B0511 . 10946-11208
-Cosmid B0511 . 13126-13511
-Cosmid B0511 . 66-208
-Cosmid B0511 . 6354-6499
-Cosmid B0511 . 13955-14115
-EST yk595e6.5 + 3187-3294
-EST yk846e07.3 - 11015-11208
-EST yk53c10
- yk53c10.5 + 18892-19154
- yk53c10.3 - 15000-15500,15700-15800
-EST yk53c10.5 + 16032-16105
-SwissProt PECANEX + 13153-13656 Swedish fish
-FGENESH "Gene 1" - 1-205,518-616,661-735,3187-3365,3436-3846 Transmembrane domain
-FGENESH "Gene 2" - 16626-17396,17451-17597 Kinase and sushi domains
+ Cosmid B0511 . 516-619
+ Cosmid B0511 . 3185-3294
+ Cosmid B0511 . 10946-11208
+ Cosmid B0511 . 13126-13511
+ Cosmid B0511 . 66-208
+ Cosmid B0511 . 6354-6499
+ Cosmid B0511 . 13955-14115
+ EST yk595e6.5 + 3187-3294
+ EST yk846e07.3 - 11015-11208
+ EST yk53c10
+ yk53c10.5 + 18892-19154
+ yk53c10.3 - 15000-15500,15700-15800
+ EST yk53c10.5 + 16032-16105
+ SwissProt PECANEX + 13153-13656 Swedish fish
+ FGENESH "Gene 1" - 1-205,518-616,661-735,3187-3365,3436-3846 Transmembrane domain
+ FGENESH "Gene 2" - 16626-17396,17451-17597 Kinase and sushi domains
Each line of the file contains five columns. The columns are: