help with orderchr...

[Etienne Mahe]

Greetings All,

I am trying to re-order the my data by linkage (see attached configuration files); the error message I receive follows (in cygwin emulator):

$ perl orderchr -conf orderchr.conf

Can't use an undefined value as an ARRAY reference at orderchr line 588.

Any help would be appreciated

Cheers,

Etienne

PS. Does circos have any functionality to combine a linkage plot with a histogram?

[Martin Krzywinski]

You didn't include an attachment.

I'll also need the link file as well as the karyotype you're using to reproduce the error.

Martin Krzywinski

science + art

http://mkweb.bcgsc.ca

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[Etienne Mahe]

Apologies, please find attached

On Sunday, September 14, 2014 6:46:58 PM UTC-4, Martin wrote:

You didn't include an attachment.

I'll also need the link file as well as the karyotype you're using to reproduce the error.

Martin Krzywinski

science + art

http://mkweb.bcgsc.ca

On Sat, Sep 13, 2014 at 7:07 AM, Etienne Mahe <etienn...@medportal.ca> wrote:

Greetings All,

I am trying to re-order the my data by linkage (see attached configuration files); the error message I receive follows (in cygwin emulator):

$ perl orderchr -conf orderchr.conf

Can't use an undefined value as an ARRAY reference at orderchr line 588.

Any help would be appreciated

Cheers,

Etienne

PS. Does circos have any functionality to combine a linkage plot with a histogram?

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[Martin Krzywinski]

Hi Etienne,

The orderchr script was using an old format of links files. I've updated the script and attached it, together with all the circos configuration files to generate the attached images.

The image on left is the native karyotype order and the image on the right is the reordered version.

I've reversed the order of sexm (this is something that the orderchr script doesn't check for), since it seemed to help a lot with untangling the links.

To order the links, just run

./orderchr

and to generate the image, just run

> circos

M

Martin Krzywinski

science + art

http://mkweb.bcgsc.ca

To unsubscribe from this group and stop receiving emails from it, send an email to circos-data-visual...@googlegroups.com.

[Kathryn Uckele]

This post is over 8 years old but I am getting a similar error when running orderchr (circos tools version 0.23) on my files. 

I apologize in advance that I could not figure out how to attach files to this message. Many thanks in advance.

The error message is: "Can't use an undefined value as an ARRAY reference at /usr/local/bin/orderchr line 584, <F> line 59."

Here is what I ran: 

orderchr -links links/Bomo.Slit.links.circos.txt -karyotype data/karyotype/karyotype.joint.txt -static_rx Bomo_Chr

Here is my "joint" karyotype file (karyotype.joint.txt):

chr - Bomo_Chr1 b1 0 2066628 chr0
chr - Bomo_Chr2 b2 0 839644 chr11
chr - Bomo_Chr3 b3 0 1521295 chr21
chr - Bomo_Chr4 b4 0 1873723 chr22
chr - Bomo_Chr5 b5 0 1906197 chr23
chr - Bomo_Chr6 b6 0 1665060 chr24
chr - Bomo_Chr7 b7 0 1394489 lgreen
chr - Bomo_Chr8 b8 0 1626222 vlgreen
chr - Bomo_Chr9 b9 0 1679606 vlorange
chr - Bomo_Chr10 b10 0 1761477 chr1
chr - Bomo_Chr11 b11 0 2044000 chr2
chr - Bomo_Chr12 b12 0 1758060 chr3
chr - Bomo_Chr13 b13 0 1773508 chr4
chr - Bomo_Chr14 b14 0 1334551 chr5
chr - Bomo_Chr15 b15 0 1844029 chr6
chr - Bomo_Chr16 b16 0 1433729 chr7
chr - Bomo_Chr17 b17 0 1684067 chr8
chr - Bomo_Chr18 b18 0 1569905 chr9
chr - Bomo_Chr19 b19 0 1480148 chr10
chr - Bomo_Chr20 b20 0 1237053 chr12
chr - Bomo_Chr21 b21 0 1531039 chr13
chr - Bomo_Chr22 b22 0 1848252 chr14
chr - Bomo_Chr23 b23 0 2146569 chr15
chr - Bomo_Chr24 b24 0 1735917 chr16
chr - Bomo_Chr25 b25 0 1454889 chr17
chr - Bomo_Chr26 b26 0 1147347 chr18
chr - Bomo_Chr27 b27 0 1093012 chr19
chr - Bomo_Chr28 b28 0 1060973 chr20
chr - Slit_Chr1Q s1 0 1354933 black
chr - Slit_Chr2Q s2 0 1543153 black
chr - Slit_Chr3Q s3 0 646456 black
chr - Slit_Chr4Q s4 0 1032218 black
chr - Slit_Chr5Q s5 0 1189835 black
chr - Slit_Chr6Q s6 0 1346277 black
chr - Slit_Chr7Q s7 0 1548569 black
chr - Slit_Chr8Q s8 0 1242197 black
chr - Slit_Chr9Q s9 0 1493693 black
chr - Slit_Chr10Q s10 0 856305 black
chr - Slit_Chr11Q s11 0 1330094 black
chr - Slit_Chr12Q s12 0 1047668 black
chr - Slit_Chr13Q s13 0 735280 black
chr - Slit_Chr14Q s14 0 1564086 black
chr - Slit_Chr15Q s15 0 1392607 black
chr - Slit_Chr16Q s16 0 1627152 black
chr - Slit_Chr17Q s17 0 1359203 black
chr - Slit_Chr18Q s18 0 1219171 black
chr - Slit_Chr19Q s19 0 819389 black
chr - Slit_Chr20Q s20 0 1362892 black
chr - Slit_Chr21Q s21 0 1420889 black
chr - Slit_Chr22Q s22 0 1427141 black
chr - Slit_Chr23Q s23 0 1388014 black
chr - Slit_Chr24Q s24 0 1220212 black
chr - Slit_Chr25Q s25 0 1368314 black
chr - Slit_Chr26Q s26 0 1022944 black
chr - Slit_Chr27Q s27 0 1461909 black
chr - Slit_Chr28Q s28 0 1345760 black
chr - Slit_Chr29Q s29 0 1421318 black
chr - Slit_Chr30Q s30 0 1301315 black
chr - Slit_ChrZQ s31 0 1893476 black

And here is a few lines of my links file (Bomo.Slit.links.circos.txt):

Bomo_Chr1 1298211 1334985 Slit_Chr4Q 7654 30939 color=chr0
Bomo_Chr1 2056418 2062127 Slit_Chr10Q 32058 43360 color=chr0
Bomo_Chr1 3771 203620 Slit_ChrZQ 543 139264 color=chr0
Bomo_Chr1 246101 318691 Slit_ChrZQ 79086 131217 color=chr0
Bomo_Chr1 320455 346975 Slit_ChrZQ 317693 339297 color=chr0
Bomo_Chr1 349182 440247 Slit_ChrZQ 316666 435966 color=chr0
Bomo_Chr1 467063 973535 Slit_ChrZQ 488554 1095023 color=chr0
Bomo_Chr1 973749 1059613 Slit_ChrZQ 1095583 1169530 color=chr0
Bomo_Chr1 1062655 1087513 Slit_ChrZQ 964846 986942 color=chr0

............