The number [21.4] with a number regular expression of type [int] but this type is not defined, How to solve this problem

[Jim]

Circos work ver well in my computer.However, when my data was created and used in "data/karyotype/karyotype.test.txt", it doesn't run. The errors was list as following:
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
 *** CIRCOS ERROR ***

 You tried to test the number [21.4] with a number regular expression of type
 [int] but this type is not defined. Regexp::Common module returned error [ at
 D:/Strawberry/circos 0.67/bin/../lib/Circos/Error.pm line 418, <F> line 28.

     Circos::Error::fatal_error("parsedata", "bad_number", 21.4, "int") called
     at D:/Strawberry/circos 0.67/bin/../lib/Circos/Utils.pm line 403

     eval {...} called at D:/Strawberry/circos 0.67/bin/../lib/Circos/Utils.pm
     line 400

     Circos::Utils::is_number(21.4, "int") called at D:/Strawberry/circos
     0.67/bin/../lib/Circos/Karyotype.pm line 131

     Circos::Karyotype::read_karyotype_file("data/karyotype/karyotype.data.txt"

     HASH(0x36aa71c)) called at D:/Strawberry/circos
     0.67/bin/../lib/Circos/Karyotype.pm line 92

     Circos::Karyotype::read_karyotype("file",
     "data/karyotype/karyotype.data.txt") called at D:/Strawberry/circos
     0.67/bin/../lib/Circos.pm line 211
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
My data :
band hs1 p36.33 p36.33 0 21.4 gvar
band hs1 p36.33 p36.33 21.4 50.2 gpos75
band hs1 p36.33 p36.33 50.2 100 stalk
band hs2 p36.31 p36.31 0 11.8 stalk
band hs2 p36.33 p36.33 11.8 27.4 gpos75
band hs2 p36.33 p36.33 27.4 46 stalk
band hs2 p36.23 p36.23 46 72.2 gpos25
band hs2 p36.23 p36.23 72.2 100 gpos25
band hs3 p36.22 p36.22 0 9.1 gpos75
band hs3 p36.33 p36.33 9.1 20.1 gpos75
band hs3 p36.33 p36.33 20.1 32.7 stalk
band hs3 p36.21 p36.21 32.7 50.9 gpos50
band hs3 p36.13 p36.13 50.9 74.9 gpos75
band hs3 p36.13 p36.13 74.9 100 gpos75
band hs4 p36.33 p36.33 0 15.1 gpos75
band hs4 p36.33 p36.33 15.1 56.7 stalk
band hs4 p36.12 p36.12 56.7 100 gpos25
band hs5 p36.11 p36.11 0 6.8 gpos66
band hs5 p36.33 p36.33 6.8 18 gpos75
band hs5 p36.33 p36.33 18 31.2 stalk
band hs5 p35.3 p35.3 31.2 46.6 gpos25
band hs5 p36.33 p36.33 46.6 70.7 stalk
band hs5 p35.3 p35.3 70.7 100 gpos25
band hs6 p35.2 p35.2 0 100 acen
.......
-----------------------------------------------------------------------------------------------------------------------------
so ,how to define such number [21.4] in the circos.conf? Thanks for your attention!

[Martin Krzywinski]

Since Circos is designed for data on sequences, positions must be integers.

So bands must start and end at integer positions, e.g. 21 or 22 and not 21.4

Also, it looks like you're defining band positions in %. Positions need to be absolute in bases, not relative.

I realize this is a shortcoming for cases where floating point values are needed.

Martin Krzywinski

science + art

http://mkweb.bcgsc.ca

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