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mkutmon / regin-creator

Scripts to create RegINs (Regulatory Interaction Networks) from several different databases
Apache License 2.0
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error Creating RINs file #1

Open Rimsk opened 10 years ago

Rimsk commented 10 years ago

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 commented 10 years ago

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 commented 10 years ago

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 commented 10 years ago

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 < notifications@github.com> 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/mkutmon/regin-creator/issues/1#issuecomment-38038039 .

mkutmon commented 10 years ago

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

Rimsk commented 10 years ago

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 commented 10 years ago

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 < notifications@github.com> 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/mkutmon/regin-creator/issues/1#issuecomment-38040127 .

mkutmon commented 10 years ago

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 commented 10 years ago

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 < notifications@github.com> wrote:

Reopened #1 https://github.com/mkutmon/regin-creator/issues/1.

Reply to this email directly or view it on GitHubhttps://github.com/mkutmon/regin-creator/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 commented 10 years ago

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 commented 10 years ago

On Wed, Mar 19, 2014 at 3:12 PM, Martina Summer-Kutmon < notifications@github.com> 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/mkutmon/regin-creator/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