Cistrome example

[Amir Gamliel]

Hello,

I am trying to run the cistrome example as detailed on https://github.com/ryanlayer/giggle/blob/master/examples/cistrome/README.md.

I got stuck at this step:

~/tools/giggle_v0.6.3/giggle/examples/cistrome/rename.py \

-m data/TF_human_data_information.txt \

-i data/TF_human \

-o data/named \

-n cistrome_id_to_name_map.txt

I get the following error:

Traceback (most recent call last):

  File "/mnt/home/agamliel/tools/giggle_v0.6.3/giggle/examples/cistrome/rename.py", line 31, in <module>

    if not options.metadata_file_name:

NameError: name 'options' is not defined

Any suggestions?

Thanks,

Amir

[Ryan Layer]

I think I fixed it, please give it another try

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Ryan Layer

[Amir Gamliel]

Hello again,

I tried again with the instructions on https://github.com/ryanlayer/giggle/blob/master/examples/cistrome/README.md

However, I got an error at the same step, with different error:

trying to run this script:

~/tools/giggle_v0.6.3/giggle/examples/cistrome/rename.py \

-m data/TF_human_data_information.txt \

-i data/TF_human \

-o data/named \

-n cistrome_id_to_name_map.txt

I received this error:

Traceback (most recent call last):

  File "/mnt/home/agamliel/tools/giggle_v0.6.3/giggle/examples/cistrome/rename.py", line 43, in <module>

    for l in open(metadata_file_name, 'r'):

NameError: name 'metadata_file_name' is not defined   

Thanks,

Amir

On Monday, April 9, 2018 at 2:19:18 PM UTC-7, Ryan Layer wrote:

I think I fixed it, please give it another try

On Wed, Apr 4, 2018 at 11:29 PM, Amir Gamliel <agaml...@gmail.com> wrote:

Hello,

I am trying to run the cistrome example as detailed on https://github.com/ryanlayer/giggle/blob/master/examples/cistrome/README.md.

I got stuck at this step:

~/tools/giggle_v0.6.3/giggle/examples/cistrome/rename.py \

-m data/TF_human_data_information.txt \

-i data/TF_human \

-o data/named \

-n cistrome_id_to_name_map.txt

I get the following error:

Traceback (most recent call last):

  File "/mnt/home/agamliel/tools/giggle_v0.6.3/giggle/examples/cistrome/rename.py", line 31, in <module>

    if not options.metadata_file_name:

NameError: name 'options' is not defined

Any suggestions?

Thanks,

Amir

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Ryan Layer