Has anyone here worked with CNCI before? EXHAUSTED

Question

[27atcggcta27]

Has anyone here worked with CNCI before? I'm just about exhausted trying to figure out what I'm doing wrong.

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 have tried different versions of python, changing my path, etc and nothing is working. Any help at all is appreciated!! Or if someone could find a protocol or something that demonstrates CNCIs usage. I have found nothing so far

[rizoic]

Do you have twoBitToFa in your path. Taking a quick look at the source code here and the error it seems since twoBitToFa is not in the path the required fasta file creation failed.

[Kevin Blighe]

The user edited the other question to say that twoBitToFa is in the PATH variable ( Error from CNCI usage (coding non coding index) What to do? )

[27atcggcta27]

Thank you. Yes, twoBitToFa is in my path.

[Jean-Karim Heriche]

This a duplicate of this question.

[27atcggcta27]

Yes, I wanted to ask a formal question and this was more of just a forum post to just connect with others who have also used CNCI. I apologize if this violated etiquette.

[Kevin Blighe]

Is this the absolute minimum example that you are trying to run?, i.e., you have followed some tutorial line by line and are running the commands exactly as per the tutorial?

Be wary of, e.,g., character encodings. For example, there are a few different encodings of the hyphen, which can often affect command line parameter parsing. Also, if you work between a Windows and Mac/Linux system, be wary of end-line character encodings in your files.

I had a look at the GitHub landing page ( https://github.com/www-bioinfo-org/CNCI ), in fact, and I am not sure that you are running it correctly (?). Please try:

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

[27atcggcta27]

Thank you Kevin for the advice, I was unable to find a CNCI tutorial so this is based purly off the github page. I am a newbie/beginner so if anyone knows of a tutorial I would appreciate the guidance.

Answer 1

[i.sudbery]

CNCI is trying to open your files as a Fasta file, becauase the first thing the program does if you provide GTF files is convert them to fasta. Almost certainly this conversion is failing and CNCI is therefore unable to open the FASTA file it thinks it should have created.

Looking at the CNCI source code, the conversion is done in two steps. The first uses a perl script from CNCI's own directory to convert the GTF file to a bed file. The second uses twoBitToFa to convert said bed file to a FASTA file. The failure could be either one of these two steps.

Thus I would try to the following commands to see which fail:

perl PATH_TO_CNCI//gtf2Bed.pl candidate_lncs.gtf >  candidate_lncs.gtf.bed
twoBitToFa -bed=candidate_lncs.gtf.bed ~/dataBase/GRCm38.2bit candidate_lncs.gtf.fa

[27atcggcta27]

oh man oh man oh man oh man you have given a beginner hope. Thank you! there was a problem with my twoBitToFa. Everything is working now after fixing.

[anisha]

twoBittofasta is not working this is the code given Is this code given inner of the CNCI.py file?