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The Basics
Id: 62618
Status: new
Priority: 0/
Queue: Bio-Graphics

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Owner: Nobody in particular
Requestors: weeks [...] iastate.edu
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Bug Information
Severity: (no value)
Broken in: 2.11
Fixed in: (no value)



Subject: feature_draw.pl broken
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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
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# 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:


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