"list index out of range" during Network Preparation

[Joshua Cook]

Hello,

I am running into an error when trying to run makeNetworkFiles.py:

My code is:

num_cores=1

num_network_permutations=20

num_heat_permutations=20

beta=0.5

MAKENETWORKFILES=$FUNCTIONS_DIR/makeNetworkFiles.py

python $MAKENETWORKFILES \
    -e $input_dir/STRING_edge_list \
    -i $input_dir/STRING_gene_index \
    --network_name string \
    --prefix string \
    --beta $beta \
    -o $output_dir/networks \
    -np $num_network_permutations \
    -c $num_cores

And the output is:

Creating PPR matrix for real network

--------------------------------------

Traceback (most recent call last):
  File "/n/data2/bidmc/medicine/haigis/Cook/KrasComutation/Pathway/running_HotNet2/hotnet2/makeNetworkFiles.py", line 92, in <module>

    run(get_parser().parse_args(sys.argv[1:]))

  File "/n/data2/bidmc/medicine/haigis/Cook/KrasComutation/Pathway/running_HotNet2/hotnet2/makeNetworkFiles.py", line 65, in run

    save_diffusion_to_file( HOTNET2, args.beta, args.gene_index_file, args.edgelist_file, pprfile, params=params)

  File "/n/data2/bidmc/medicine/haigis/Cook/KrasComutation/Pathway/running_HotNet2/hotnet2/hotnet2/network.py", line 51, in save_diffusion_to_file

    G = load_network_from_file( index_file, edge_file)

  File "/n/data2/bidmc/medicine/haigis/Cook/KrasComutation/Pathway/running_HotNet2/hotnet2/hotnet2/network.py", line 88, in load_network_from_file

    indexToGene = dict((int(arr[0]), arr[1]) for arr in arrs)

  File "/n/data2/bidmc/medicine/haigis/Cook/KrasComutation/Pathway/running_HotNet2/hotnet2/hotnet2/network.py", line 88, in <genexpr>

    indexToGene = dict((int(arr[0]), arr[1]) for arr in arrs)

IndexError: list index out of range

I have checked that the gene index file has unique IDs for each gene in the network. Also, the variables pointing to the input do point to the correct files. I can't think of what else would cause this error. I have previously successfully run the example paper commands and my own input before this, but now can't generate the network files.

Thank you for any help,

Josh Cook

[matthe...@brown.edu]

Hi Josh,

I would check that each line of your gene-index file has two entries.  For example, if there is only one entry for a line, then that would cause this error.

Best,

Matt

[Joshua Cook]

Hello Matt,

Thank you for getting back to me.

I check the gene index file and found no missing values. I also checked the edge list, and all of the values are >0.

I also tried running the script on 2 cores because all of my previous successful attempts were multi-core runs, but still got the same error.

Any other thoughts?

Thank you,

Josh Cook

[matthe...@brown.edu]

Hi Josh,

Please try replacing this line in hotnet2/network.py

indexToGene = dict((int(arr[0]), arr[1]) for arr in arrs)

with these lines

indexToGene = dict()

for i, arr in enumerate(arrs):

    try:

        indexToGene[int(arr[0])] = arr[1]

    except:

        print 'Error on line {}: {}'.format(i+1, arr)

This change will identify lines in your input file that may cause this error and skip them.

Best,

Matt

[Joshua Cook]

Hi Matt,

That did the trick! It was a missing value on one line of the gene index file. I'm not sure how I missed it before, but thank you for your help.

Thank you,

Josh Cook