Hello!

I'm having trouble getting CNCI to work. I have a gtf file of some novel transcripts and some annotated trasncripts from the mouse genome. I would like to determine if the transcripts are coding or noncoding. So, I am using CNCI. I see the following from CNCI github page:

CNCI.py: A classification tool for identify coding or non-coding transcripts (fasta files and gtf files)

Parameters:

-f or --file : input files

-o or --out : assign your output file in current directory (this parameter will produce a Temp sub-folder in current directory, and will remove it automatically at the end of programming), and the result is stored in xxx.index

-p or --parallel : assign the running CUP numbers

-m or --model : assign the classification models ("ve" for vertebrate species, "pl" for plat species)

-g or --gtf : if you input files is gtf format please use this parameter

-d or --directory : if you use the -g or --gtf this parameter must be assigned, within this parameter please assign the path of your reference genome.

EXAMPLE

you can use CNCI subroutines like our example:

python CNCI_package/CNCI.py -f unannotation.gtf -g -o test -m ve -p 8 -d hg19.2bit

So, I tried the following:

python CNCI.py candidate_lncs.gtf -g -o test -m ve -p 16 -d ./dbase GRCm38.primary_assembly.genome.fa

and I recieved the following error:

name@server %57> CNCI.py -f candidate_lncs.gtf -g -o test -m ve -p 16 -d ~/dataBase/GRCm38.2bit
/home/pgian1/src/CNCI
sh: 1: twoBitToFa: not found
Traceback (most recent call last):
  File "CNCI.py", line 533, in <module>
    GtfInFiles = open(fastaFiles)
IOError: [Errno 2] No such file or directory: 'candidate_lncs.gtf.fa'

It looks to me that CNCI is trying to read my GTF file as a fasta file. I'm not sure why though. I thought CNCI will take a gtf file and the relevant genome and determine the probability of coding/noncoding using nucleotide triplates.

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So my question is: Am I implementing CNCI correctly? If not, what am I missing?

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Thank you all in advance!

EDIT: for clarity - The twoBitToFa script is in my path so I'm not sure about that error either...