has anyone ever worked with the CNCI tool

Question

[Assa Yeroslaviz]

Hi,

Has anyone ever worked with the CNCI tool from www-bioinfo-org (github).

Iam trying to analyse my lncRNA data set with a self-made lncRNA-gtf file. but I get the following error when running the compare.py:

    $python /local/Assa/software/CNCI/compare.py -c ~/genomes/Caenorhabditis_elegans/Ensembl/WBcel235.2017/Cel.WBcel235.gtf -n Cel_NONCODEv5_lncRNA.gtf.mod.txt -i merge_outdir/merged.gtf -o cnci_out

Classification start:
Traceback (most recent call last):
  File "/local/Assa/software/CNCI/compare.py", line 187, in <module>
    combined_gtf_input, cuffcompare_outdir)
  File "/local/Assa/software/CNCI/compare.py", line 114, in fetch_gtfs
    erase_strand(coding_ref_input,coding_ref)
  File "/local/Assa/software/CNCI/compare.py", line 107, in erase_strand
    result.update_col(7,'+')
  File "/local/Assa/software/CNCI/Table.py", line 451, in update_col
    self.data[index][the_number]=new_value
IndexError: list assignment index out of range

At first I thought that this is because the chromosome names are not identical in the two files, but this is not the case.

 head Cel_NONCODEv5_lncRNA.gtf.mod.txt 
I       cufflinks       transcript      630008  630221  0       -       .       gene_id "NONCELG000005.2";  transcript_id "NONCELT000029.2";FKPM "0" exon_number1;
I       cufflinks       exon    630008  630221  0       -       .       gene_id "NONCELG000005.2";  transcript_id "NONCELT000029.2";FKPM "0" exon_number1;
I       cufflinks       transcript      3122013 3127663 0       +       .       gene_id "NONCELG000034.2";  transcript_id "NONCELT000194.2";FKPM "0" exon_number1;
I       cufflinks       exon    3122013 3127663 0       +       .       gene_id "NONCELG000034.2";  transcript_id "NONCELT000194.2";FKPM "0" exon_number1;

and

head ~/genomes/Caenorhabditis_elegans/Ensembl/WBcel235.2017/Cel.WBcel235.gtf 
#!genome-build WBcel235
#!genome-version WBcel235
#!genome-date 2012-12
#!genome-build-accession NCBI:GCA_000002985.3
#!genebuild-last-updated 2014-10
V       WormBase        gene    180     329     .       +       .       gene_id "WBGene00197333"; gene_name "cTel3X.2"; gene_source "WormBase"; gene_biotype "ncRNA";
V       WormBase        transcript      180     329     .       +       .       gene_id "WBGene00197333"; transcript_id "cTel3X.2"; gene_name "cTel3X.2"; gene_source "WormBase"; gene_biotype "ncRNA"; transcript_name "cTel3X.2"; transcript_source "WormBase"; transcript_biotype "ncRNA";
V       WormBase        exon    180     329     .       +       .       gene_id "WBGene00197333"; transcript_id "cTel3X.2"; exon_number "1"; gene_name "cTel3X.2"; gene_source "WormBase"; gene_biotype "ncRNA"; transcript_name "cTel3X.2"; transcript_source "WormBase"; transcript_biotype "ncRNA"; exon_id "cTel3X.2.e1";

If someone has encountered this problem, I would appreciate some hints about the case.

thanks Assa

[mahsa.saliani]

Hi I have the same problem as you. I download gene annotation and lnRNA annotation gft files from GENECODE. I have also a transcript.gft file as the output file of cufflinks. I got the same error when using compare.py. Could you please help me to solve the problem. Thank you in advance