juncBASE python script

Question

[priyankamaripuri]

Hello,

I'm using "juncBASE".when I tried to run the sample files given in the manual, I'm encountering a problem. When I'm running the python script run_preProcess_by_chr_step1.py, I'm encountering an error. The command I used is:

python softwares/juncBASE_v0.6/run_preProcess_by_chr_step1.py \
  -i data/human/juncBASE/IlluminaHBM_2.0_samp2test_bam.txt \
  -o data/human/juncBASE/juncBASE_input_files/ \
  --preProcess_options "-unique -j Homo_sapiens_assembly19_introns.txt -c 1.1" \
  -p 2 \
  --check
# (as per the manual)

The text file IlluminaHBM_2.0_samp2test_bam.txt contains the location of the BAM files.

data/human/juncBASE/BAM/kidney.bam
data/human/juncBASE/BAM/breast.bam

The error I'm encountering is:

Traceback (most recent call last):
  File "softwares/juncBASE_v0.6/run_preProcess_by_chr_step1.py", line 243, in <module>
    if __name__ == "__main__": main()
  File "softwares/juncBASE_v0.6/run_preProcess_by_chr_step1.py", line 136, in main
    samp, bam = line.split("\t")
ValueError: need more than 1 value to unpack

I really hope that you can help me out. Is that an error in the script or its an error in my command? I'll be more than thankful if you can give me a detailed description on the error.

[GouthamAtla]

Paste a few lines from data/human/juncBASE/IlluminaHBM_2.0_samp2test_bam.txt

Answer 1

[GouthamAtla]

From source:

opt_parser.add_option("-i",
                      dest="input_file",
                      type="string",
                      help="""File containing sample name with bam file
                              location.""",
                      default=None)​

And Line 133-136

for line in input_file:
    line = formatLine(line)

    samp, bam = line.split("\t")

So there is something wrong with your data/human/juncBASE/IlluminaHBM_2.0_samp2test_bam.txt

[priyankamaripuri]

Sorry, I'm new to python. Can you please explain to me in detail?

[GouthamAtla]

According to the program, the file data/human/juncBASE/IlluminaHBM_2.0_samp2test_bam.tx should have sample names and the path to bam files separate by a tab. Can you copy paste few lines from that file?

[priyankamaripuri]

You can find the lines in my post.

[GouthamAtla]

So it should be Sample Name and BAM location. I recommend to use full path to avoid any further errors.

Kidney    data/human/juncBASE/BAM/kidney.bam
breast    data/human/juncBASE/BAM/breast.bam

[priyankamaripuri]

Thanks. I'll look into it.