error Creating RINs file

[Rimsk]

Hi,
I am trying to create my own RegINs file using regin-creator, but I get an error. Can you please help me out.
I downloaded regin-creator, unziped the dependencies in same folder where converter.jar is present.
In same folder I kept the miRbase-v19.bridge and Mm_Derby_10130701.bridge

Mar 19, 2014 10:57:45 AM org.regin.creator.GenericCreator convert
SEVERE: Could not convert file to RegIN: 1
java.lang.ArrayIndexOutOfBoundsException: 1
at org.regin.creator.GenericCreator.createSourceNode(GenericCreator.java:265)
at org.regin.creator.GenericCreator.convert(GenericCreator.java:113)
at org.regin.creator.GenericCreator$1.buildGraph(GenericCreator.java:76)
at org.regin.creator.utils.ArgsParser.convertAndWrite(ArgsParser.java:70)
at org.regin.creator.GenericCreator.startConversion(GenericCreator.java:74)
at org.regin.creator.GenericCreator.main(GenericCreator.java:50)

[mkutmon]

There seems to be a problem in the config file. You need to start numbering the columns with 0. Can you try this and tell me if it works?

[Rimsk]

here is my config file:

name=miRTarBase
organism=Mus musculus
version=4.5
source_columns=1,2
target_columns=3,4,5
edge_columns=0,6,7,8
interaction_type=MTI
source_id_column=1
source_type=miRNA
source_bridgedb=mirbase-v19.bridge
source_syscode_in=Mb
source_syscodes_out=Mbm,Mb
source_label_column=1
target_id_column=4
target_type=gene
target_bridgedb=Mm_Derby_20130701.bridge
target_syscode_in=L
target_syscodes_out=L,En,S
target_label_column=3

[Rimsk]

here is my config file name=miRTarBase
organism=Mus musculus
version=4.5
source_columns=1,2
target_columns=3,4,5
edge_columns=0,6,7,8
interaction_type=MTI
source_id_column=1
source_type=miRNA
source_bridgedb=mirbase-v19.bridge
source_syscode_in=Mb
source_syscodes_out=Mbm,Mb
source_label_column=1
target_id_column=4
target_type=gene
target_bridgedb=Mm_Derby_20130701.bridge
target_syscode_in=L
target_syscodes_out=L,En,S
target_label_column=3

On Wed, Mar 19, 2014 at 11:55 AM, Martina Summer-Kutmon <
[email protected]> wrote:

There seems to be a problem in the config file. You need to start
numbering the columns with 0. Can you try this and tell me if it works?

Reply to this email directly or view it on GitHubhttps://github.com//issues/1#issuecomment-38038039
.

[mkutmon]

Okay could you give me the headers of your data file from miRWalk?

[Rimsk]

ensembl miRNA Species (miRNA) Target Gene Target Gene (Entrez ID) Species (Target Gene) Experiments Support Type References (PMID)
ENSMUSG00000001729 mmu-miR-200c-3p Mus musculus Akt1 11651 Mus musculus n_a n_a 21248297
ENSMUSG00000001729 mmu-miR-141-3p Mus musculus Akt1 11651 Mus musculus n_a n_a 20053927
ENSMUSG00000001729 mmu-miR-200a-3p Mus musculus Akt1 11651 Mus musculus n_a n_a 19074548
ENSMUSG00000001729 mmu-miR-200b-3p Mus musculus Akt1 11651 Mus musculus n_a n_a 19074548
ENSMUSG00000026628 mmu-miR-200b-3p Mus musculus Atf3 11910 Mus musculus n_a n_a 20498046
ENSMUSG00000057329 mmu-miR-200c-3p Mus musculus Bcl2 12043 Mus musculus n_a n_a 21114921

[Rimsk]

ensembl miRNA Species (miRNA) Target Gene Target Gene (Entrez ID) Species
(Target Gene) Experiments Support Type References (PMID)
ENSMUSG00000001729 mmu-miR-200c-3p Mus musculus Akt1 11651 Mus musculus n_a
n_a 21248297
ENSMUSG00000001729 mmu-miR-141-3p Mus musculus Akt1 11651 Mus musculus n_a
n_a 20053927
ENSMUSG00000001729 mmu-miR-200a-3p Mus musculus Akt1 11651 Mus musculus n_a
n_a 19074548
ENSMUSG00000001729 mmu-miR-200b-3p Mus musculus Akt1 11651 Mus musculus n_a
n_a 19074548
ENSMUSG00000026628 mmu-miR-200b-3p Mus musculus Atf3 11910 Mus musculus n_a
n_a 20498046
ENSMUSG00000057329 mmu-miR-200c-3p Mus musculus Bcl2 12043 Mus musculus n_a
n_a 21114921

On Wed, Mar 19, 2014 at 12:22 PM, Martina Summer-Kutmon <
[email protected]> wrote:

Okay could you give me the headers of your data file from miRWalk?

Reply to this email directly or view it on GitHubhttps://github.com//issues/1#issuecomment-38040127
.

[mkutmon]

Okay, I know what the problem is. Your data file is not a TAB-delimited file. The columns are separated by spaces which is not recognized by the program. If you could make sure it is tab-delimited without a text-delimiter and try again, it should work.

[Rimsk]

It is a tab-delimited file. I have attached it just check it...

On Wed, Mar 19, 2014 at 1:50 PM, Martina Summer-Kutmon <
[email protected]> wrote:

Reopened #1 #1.

Reply to this email directly or view it on GitHubhttps://github.com//issues/1
.

ensembl miRNA Species (miRNA) Target Gene Target Gene (Entrez ID) Species (Target Gene) Experiments Support Type References (PMID)
ENSMUSG00000001729 mmu-miR-200c-3p Mus musculus Akt1 11651 Mus musculus n_a n_a 21248297
ENSMUSG00000001729 mmu-miR-141-3p Mus musculus Akt1 11651 Mus musculus n_a n_a 20053927
ENSMUSG00000001729 mmu-miR-200a-3p Mus musculus Akt1 11651 Mus musculus n_a n_a 19074548
ENSMUSG00000001729 mmu-miR-200b-3p Mus musculus Akt1 11651 Mus musculus n_a n_a 19074548
ENSMUSG00000026628 mmu-miR-200b-3p Mus musculus Atf3 11910 Mus musculus n_a n_a 20498046
ENSMUSG00000057329 mmu-miR-200c-3p Mus musculus Bcl2 12043 Mus musculus n_a n_a 21114921
ENSMUSG00000057329 mmu-miR-200b-3p Mus musculus Bcl2 12043 Mus musculus n_a n_a 18942116
ENSMUSG00000027358 mmu-miR-429-3p Mus musculus Bmp2 12156 Mus musculus n_a n_a 20016822
ENSMUSG00000021835 mmu-miR-200a-3p Mus musculus Bmp4 12159 Mus musculus n_a n_a 19559694
ENSMUSG00000021835 mmu-miR-141-3p Mus musculus Bmp4 12159 Mus musculus n_a n_a 19559694
ENSMUSG00000006932 mmu-miR-200a-3p Mus musculus Ctnnb1 12387 Mus musculus n_a n_a 22211245
ENSMUSG00000024304 mmu-miR-429-3p Mus musculus Cdh2 12558 Mus musculus n_a n_a 18698484
ENSMUSG00000024304 mmu-miR-200c-3p Mus musculus Cdh2 12558 Mus musculus n_a n_a 18698484
ENSMUSG00000024304 mmu-miR-429-3p Mus musculus Cdh2 12558 Mus musculus n_a n_a 18698484

[mkutmon]

Okay, with the example rows you gave me the script works fine for me. Can you email me the complete file then I can check if there is another problem.

[Rimsk]

On Wed, Mar 19, 2014 at 3:12 PM, Martina Summer-Kutmon <
[email protected]> wrote:

Okay, with the example rows you gave me the script works fine for me. Can
you email me the complete file then I can check if there is another
problem.

Reply to this email directly or view it on GitHubhttps://github.com//issues/1#issuecomment-38054558
.

miRTarBase ID miRNA Species (miRNA) Target Gene Target Gene (Entrez ID) Species (Target Gene) Experiments Support Type References (PMID)
MIRT001696 mmu-miR-141-3p Mus musculus Klf5 12224 Mus musculus Reporter assay Non-Functional MTI 15131085
MIRT001677 mmu-miR-200b-3p Mus musculus Zeb1 21417 Mus musculus qRT-PCR//Luciferase reporter assay Functional MTI 19787069
MIRT001680 mmu-miR-200a-3p Mus musculus Zeb1 21417 Mus musculus Reporter assay Functional MTI 21049046
MIRT002336 mmu-miR-200c-3p Mus musculus Zeb1 21417 Mus musculus qRT-PCR//Luciferase reporter assay Functional MTI 19787069
MIRT001664 mmu-miR-429-3p Mus musculus Zeb1 21417 Mus musculus Reporter assay Functional MTI 21049046
MIRT001694 mmu-miR-141-3p Mus musculus Zeb1 21417 Mus musculus Reporter assay Functional MTI 18411277
MIRT006425 mmu-miR-141-3p Mus musculus Mapk14 26416 Mus musculus Luciferase reporter assay//Microarray//qRT-PCR//Western blot Functional MTI 22101765
MIRT006426 mmu-miR-200c-3p Mus musculus Mapk14 26416 Mus musculus Microarray//qRT-PCR Non-Functional MTI (Weak) 22101765
MIRT006427 mmu-miR-200b-3p Mus musculus Mapk14 26416 Mus musculus Microarray//qRT-PCR Non-Functional MTI (Weak) 22101765
MIRT006425 mmu-miR-141-3p Mus musculus Mapk14 26416 Mus musculus Luciferase reporter assay//Microarray//qRT-PCR//Western blot Functional MTI 22101765
MIRT006426 mmu-miR-200c-3p Mus musculus Mapk14 26416 Mus musculus Microarray//qRT-PCR Non-Functional MTI (Weak) 22101765
MIRT006427 mmu-miR-200b-3p Mus musculus Mapk14 26416 Mus musculus Microarray//qRT-PCR Non-Functional MTI (Weak) 22101765
MIRT005945 mmu-miR-200b-3p Mus musculus Flt1 14254 Mus musculus Luciferase reporter assay Functional MTI 21115742
MIRT005946 mmu-miR-200c-3p Mus musculus Flt1 14254 Mus musculus Luciferase reporter assay Functional MTI 21115742
MIRT005948 mmu-miR-429-3p Mus musculus Flt1 14254 Mus musculus Luciferase reporter assay Non-Functional MTI 21115742
MIRT005947 mmu-miR-200a-3p Mus musculus Flt1 14254 Mus musculus Luciferase reporter assay Non-Functional MTI 21115742
MIRT005948 mmu-miR-429-3p Mus musculus Flt1 14254 Mus musculus Luciferase reporter assay Non-Functional MTI 21115742
MIRT005947 mmu-miR-200a-3p Mus musculus Flt1 14254 Mus musculus Luciferase reporter assay Non-Functional MTI 21115742
MIRT005945 mmu-miR-200b-3p Mus musculus Flt1 14254 Mus musculus Luciferase reporter assay Functional MTI 21115742
MIRT005946 mmu-miR-200c-3p Mus musculus Flt1 14254 Mus musculus Luciferase reporter assay Functional MTI 21115742
MIRT001696 mmu-miR-141-3p Mus musculus Klf5 12224 Mus musculus Reporter assay Non-Functional MTI 15131085
MIRT006425 mmu-miR-141-3p Mus musculus Mapk14 26416 Mus musculus Luciferase reporter assay//Microarray//qRT-PCR//Western blot Functional MTI 22101765
MIRT006426 mmu-miR-200c-3p Mus musculus Mapk14 26416 Mus musculus Microarray//qRT-PCR Non-Functional MTI (Weak) 22101765
MIRT006427 mmu-miR-200b-3p Mus musculus Mapk14 26416 Mus musculus Microarray//qRT-PCR Non-Functional MTI (Weak) 22101765
MIRT006425 mmu-miR-141-3p Mus musculus Mapk14 26416 Mus musculus Luciferase reporter assay//Microarray//qRT-PCR//Western blot Functional MTI 22101765
MIRT006426 mmu-miR-200c-3p Mus musculus Mapk14 26416 Mus musculus Microarray//qRT-PCR Non-Functional MTI (Weak) 22101765
MIRT006427 mmu-miR-200b-3p Mus musculus Mapk14 26416 Mus musculus Microarray//qRT-PCR Non-Functional MTI (Weak) 22101765
MIRT001696 mmu-miR-141-3p Mus musculus Klf5 12224 Mus musculus Reporter assay Non-Functional MTI 15131085
MIRT001696 mmu-miR-141-3p Mus musculus Klf5 12224 Mus musculus Reporter assay Non-Functional MTI 15131085
MIRT006425 mmu-miR-141-3p Mus musculus Mapk14 26416 Mus musculus Luciferase reporter assay//Microarray//qRT-PCR//Western blot Functional MTI 22101765
MIRT006426 mmu-miR-200c-3p Mus musculus Mapk14 26416 Mus musculus Microarray//qRT-PCR Non-Functional MTI (Weak) 22101765
MIRT006427 mmu-miR-200b-3p Mus musculus Mapk14 26416 Mus musculus Microarray//qRT-PCR Non-Functional MTI (Weak) 22101765
MIRT006425 mmu-miR-141-3p Mus musculus Mapk14 26416 Mus musculus Luciferase reporter assay//Microarray//qRT-PCR//Western blot Functional MTI 22101765
MIRT006426 mmu-miR-200c-3p Mus musculus Mapk14 26416 Mus musculus Microarray//qRT-PCR Non-Functional MTI (Weak) 22101765
MIRT006427 mmu-miR-200b-3p Mus musculus Mapk14 26416 Mus musculus Microarray//qRT-PCR Non-Functional MTI (Weak) 22101765
MIRT001677 mmu-miR-200b-3p Mus musculus Zeb1 21417 Mus musculus qRT-PCR//Luciferase reporter assay Functional MTI 19787069
MIRT001680 mmu-miR-200a-3p Mus musculus Zeb1 21417 Mus musculus Reporter assay Functional MTI 21049046
MIRT002336 mmu-miR-200c-3p Mus musculus Zeb1 21417 Mus musculus qRT-PCR//Luciferase reporter assay Functional MTI 19787069
MIRT001664 mmu-miR-429-3p Mus musculus Zeb1 21417 Mus musculus Reporter assay Functional MTI 21049046
MIRT001694 mmu-miR-141-3p Mus musculus Zeb1 21417 Mus musculus Reporter assay Functional MTI 18411277
MIRT001696 mmu-miR-141-3p Mus musculus Klf5 12224 Mus musculus Reporter assay Non-Functional MTI 15131085
MIRT006427 mmu-miR-200b-3p Mus musculus Mapk14 26416 Mus musculus Microarray//qRT-PCR Non-Functional MTI (Weak) 22101765
MIRT006425 mmu-miR-141-3p Mus musculus Mapk14 26416 Mus musculus Luciferase reporter assay//Microarray//qRT-PCR//Western blot Functional MTI 22101765
MIRT006427 mmu-miR-200b-3p Mus musculus Mapk14 26416 Mus musculus Microarray//qRT-PCR Non-Functional MTI (Weak) 22101765
MIRT006426 mmu-miR-200c-3p Mus musculus Mapk14 26416 Mus musculus Microarray//qRT-PCR Non-Functional MTI (Weak) 22101765
MIRT006425 mmu-miR-141-3p Mus musculus Mapk14 26416 Mus musculus Luciferase reporter assay//Microarray//qRT-PCR//Western blot Functional MTI 22101765
MIRT006426 mmu-miR-200c-3p Mus musculus Mapk14 26416 Mus musculus Microarray//qRT-PCR Non-Functional MTI (Weak) 22101765
MIRT005946 mmu-miR-200c-3p Mus musculus Flt1 14254 Mus musculus Luciferase reporter assay Functional MTI 21115742
MIRT005948 mmu-miR-429-3p Mus musculus Flt1 14254 Mus musculus Luciferase reporter assay Non-Functional MTI 21115742
MIRT005948 mmu-miR-429-3p Mus musculus Flt1 14254 Mus musculus Luciferase reporter assay Non-Functional MTI 21115742
MIRT005947 mmu-miR-200a-3p Mus musculus Flt1 14254 Mus musculus Luciferase reporter assay Non-Functional MTI 21115742
MIRT005945 mmu-miR-200b-3p Mus musculus Flt1 14254 Mus musculus Luciferase reporter assay Functional MTI 21115742
MIRT005945 mmu-miR-200b-3p Mus musculus Flt1 14254 Mus musculus Luciferase reporter assay Functional MTI 21115742
MIRT005946 mmu-miR-200c-3p Mus musculus Flt1 14254 Mus musculus Luciferase reporter assay Functional MTI 21115742
MIRT005947 mmu-miR-200a-3p Mus musculus Flt1 14254 Mus musculus Luciferase reporter assay Non-Functional MTI 21115742
MIRT001696 mmu-miR-141-3p Mus musculus Klf5 12224 Mus musculus Reporter assay Non-Functional MTI 15131085
MIRT006426 mmu-miR-200c-3p Mus musculus Mapk14 26416 Mus musculus Microarray//qRT-PCR Non-Functional MTI (Weak) 22101765
MIRT006427 mmu-miR-200b-3p Mus musculus Mapk14 26416 Mus musculus Microarray//qRT-PCR Non-Functional MTI (Weak) 22101765
MIRT006425 mmu-miR-141-3p Mus musculus Mapk14 26416 Mus musculus Luciferase reporter assay//Microarray//qRT-PCR//Western blot Functional MTI 22101765
MIRT006427 mmu-miR-200b-3p Mus musculus Mapk14 26416 Mus musculus Microarray//qRT-PCR Non-Functional MTI (Weak) 22101765
MIRT006425 mmu-miR-141-3p Mus musculus Mapk14 26416 Mus musculus Luciferase reporter assay//Microarray//qRT-PCR//Western blot Functional MTI 22101765
MIRT006426 mmu-miR-200c-3p Mus musculus Mapk14 26416 Mus musculus Microarray//qRT-PCR Non-Functional MTI (Weak) 22101765