Bareword "_THICKNESS1_" not allowed while "strict subs" in use at...

[IH Lin]

Using circos-0.63-3

I though I would post this as it hasn't been mentioned before.
I am using homer the NGS analysis suit. The conf file automatically generated is using the old parameters syntax which is now deprecated in circos.

  *** CIRCOS ERROR ***

  There was a problem evaluating the string [_THICKNESS1_ > 20] as code (error:
  Bareword "_THICKNESS1_" not allowed while "strict subs" in use at (eval 1848)
  line 1, <F> line 24.

  )

  Stack trace:
 at circos-0.63-3/bin/../lib/Circos/Error.pm line 338
        Circos::Error::fatal_error('rules', 'parse_error', '_THICKNESS1_ > 20', 'Bareword "_THICKNESS1_" not allowed while "strict subs" in us...') called at circos-0.63-3/bin/../lib/Circos/Expression.pm line 83
        Circos::Expression::eval_expression('HASH(0x1ce71720)', '_THICKNESS1_ > 20', 'ARRAY(0x1ce67940)') called at circos-0.63-3/bin/../lib/Circos/Rule.pm line 282
        Circos::Rule::test_rule('HASH(0x1ce71720)', '_THICKNESS1_ > 20', 'ARRAY(0x1ce67940)') called at circos-0.63-3/bin/../lib/Circos/Rule.pm line 125
        Circos::Rule::apply_rules_to_track('HASH(0x1ce66ca0)', 'ARRAY(0x19836f80)', 'ARRAY(0x19836d00)') called at circos-0.63-3/bin/../lib/Circos.pm line 1140
        Circos::run('Circos', 'configfile', 'GA181-1_HindIII_interChrom.circos.conf') called at circos-0.63-3/bin/circos line 300

I found this can be fixed by changing the legacy_underline_expression_syntax in etc/housekeeping.conf from no to yes.

# In old versions, data point parameters were referenced using _NAME_
# syntax. This has been replaced with var(NAME). The _NAME_ syntax is
# deprecated (for example, it will break when dealing with fields like
# gene_a_1). If you must use it, set the parameter below.

legacy_underline_expression_syntax = yes

[Martin Krzywinski]

I suggest that you don't use _THICKNESS_ syntax anymore. Instead, use the var() notation, e.g. var(thickness). 

For example,

<rule>

condition = var(thickness) > 20

color = red

</rule>

Martin Krzywinski

science + art

http://mkweb.bcgsc.ca

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