NameError: global name '...' is not defined

Question

[mdgn]

Hello, I am trying to use a script for the software Transdecoder. But I am getting this error. I created a new conda environment with all necessary prerequisites.

$ python transdecoder_wrapper.py Trinity_lactea.largest_cluster_transcripts.fa 2 stranded ./
TransDecoder.LongOrfs -t /home/papaya/anaconda2/envs/transdecoder/Trinity_lactea.largest_cluster_transcripts.fa -S
* Running CMD: /home/papaya/anaconda2/envs/transdecoder/opt/transdecoder/util/compute_base_probs.pl /home/papaya/anaconda2/envs/transdecoder/Trinity_lactea.largest_cluster_transcripts.fa 1 > /home/papaya/anaconda2/envs/transdecoder/Trinity_lactea.largest_cluster_transcripts.fa.transdecoder_dir/base_freqs.dat


-first extracting base frequencies, we'll need them later.


- extracting ORFs from transcripts.
-total transcripts to examine: 1849
[1800/1849] = 97.35% done    CMD: touch /home/papaya/anaconda2/envs/transdecoder/Trinity_lactea.largest_cluster_transcripts.fa.transdecoder_dir.__checkpoints_longorfs/TD.longorfs.ok


#################################
### Done preparing long ORFs.  ###
##################################

    Use file: /home/papaya/anaconda2/envs/transdecoder/Trinity_lactea.largest_cluster_transcripts.fa.transdecoder_dir/longest_orfs.pep  for Pfam and/or BlastP searches to enable homology-based coding region identification.

    Then, run TransDecoder.Predict for your final coding region predictions.


Traceback (most recent call last):
  File "transdecoder_wrapper.py", line 250, in <module>
    run_transdecoder_blastp(transcripts,num_cores,strand,DIR)
  File "transdecoder_wrapper.py", line 106, in run_transdecoder_blastp
    assert fasta_ok(DIR+allpep), DIR+allpep+" small in size"    
  File "transdecoder_wrapper.py", line 30, in fasta_ok
    for i in seq.read_fasta_file(fasta):
NameError: global name 'seq' is not defined

I couldn't find the attachment link so the pipeline I am using is this . Transdecoder_wrapper.py step is where my problem is happening. Thank you in advance.

Mert

[Joe]

What does the output of python transcoder_wrapper.py look like?

It seems its not finding your fasta/sequences. I'm not familiar with the tool, but I'm guessing you could be missing some -f or -i like flags, since you're currently providing them as positionals, which typically come at the end of a command.

[h.mon]

You are trying to use a third-party wrapper to run TransDecoder, honestly I think it is better to just run TransDecoder directly. It has good documentation.

[mdgn]

The output should contain pep and cds files for downstream analyses with some descriptive outputs as well.

@Joe, I will look into this, from my search it might be a problem about Biopython.

@h.mon, Yes I used it before, but since I was following this pipeline this time I tried to stick with it. But if i can't find a solution I will do as you suggest.

Thank you for answers.

[Joe]

Sorry, typo on my part, I meant what does the output of python transcoder_wrapper.py --help look like? (not the result output)

It does seem strange to me to use a python wrapper around a perl script...

[mdgn]

Usage: python transdecoder_wrapper.py transcripts num_cores strand(stranded or non-stranded) output_dir

This is the --help output.

To be honest the pipeline is outdated despite of an update on the scripts. The softwares have compatibility issues with outdated versions and so on. I thought giving a last shot asking here hoping someone had an idea.