parse out gff3 - no modules named pandas

[seboles]

Hello!

I have hit another bump in the dammit pipeline and am having an issue parsing the dammit output. Thank you for any suggestions.

Sara

Here is my code: cd /home/seboles/annotation/developmental_annotation source ~/.bashrc python3 import pandas as pd from dammit.fileio.gff3 import GFF3Parser gff_file = "Trinitydevelopment.fasta.dammit.gff3" annotations = GFF3Parser(filename=gff_file).read() names = annotations.sort_values(by=['seqid', 'score'], ascending=True).query('score < 1e-05').drop_duplicates(subset='seqid')[['seqid', 'Name']] new_file = names.dropna(axis=0,how='all') new_file.head() new_file.to_csv("abalone_development_gene_name_id.csv") exit()

Here is the error message I receive.

Python 3.6.4 |Anaconda, Inc.| (default, Jan 16 2018, 18:10:19) [GCC 7.2.0] on linux Type "help", "copyright", "credits" or "license" for more information.

import pandas as pd Traceback (most recent call last): File "", line 1, in ModuleNotFoundError: No module named 'pandas'

[bluegenes]

Hi @seboles, you likely need to install pandas into your environment. If you have a dammit environment (e.g. dammit-env from before), you should conda activate dammit-env to enter into that conda environment, where pandas should already be available. Alternatively, you can use conda install pandas to install pandas into your current environment.

[seboles]

Hi Tessa,

I'll give that a shot and let you know how it goes. As always, thank you for your help.

Sara

On Wed, Jul 10, 2019 at 11:56 AM Tessa Pierce notifications@github.com wrote:

Hi @seboles https://github.com/seboles, you likely need to install pandas into your environment. If you have a dammit environment (e.g. dammit-env from before), you should conda activate dammit-env to enter into that conda environment, where pandas should already be available. Alternatively, you can use conda install pandas to install pandas into your current environment.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/dib-lab/dammit/issues/149?email_source=notifications&email_token=AEHDXAFZOMMFOOITQFHUTXDP6YWGZA5CNFSM4H7IDL4KYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODZUNDJA#issuecomment-510185892, or mute the thread https://github.com/notifications/unsubscribe-auth/AEHDXAG4FGJW5FBGCREYNGDP6YWGZANCNFSM4H7IDL4A .

-- Sara E. Boles, MS PhD Candidate | Whitehead Lab Pharmacology and Toxicology Graduate Group Department of Environmental Toxicology University of California, Davis, CA 95616 http://whiteheadresearch.wordpress.com/ https://sites.google.com/a/ucdavis.edu/sara-e-boles/

[seboles]

That worked. Thanks a bunch!

On Mon, Jul 15, 2019 at 12:50 PM Sara Boles seboles@ucdavis.edu wrote:

Hi Tessa,

I'll give that a shot and let you know how it goes. As always, thank you for your help.

Sara

On Wed, Jul 10, 2019 at 11:56 AM Tessa Pierce notifications@github.com wrote:

Hi @seboles https://github.com/seboles, you likely need to install pandas into your environment. If you have a dammit environment (e.g. dammit-env from before), you should conda activate dammit-env to enter into that conda environment, where pandas should already be available. Alternatively, you can use conda install pandas to install pandas into your current environment.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/dib-lab/dammit/issues/149?email_source=notifications&email_token=AEHDXAFZOMMFOOITQFHUTXDP6YWGZA5CNFSM4H7IDL4KYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODZUNDJA#issuecomment-510185892, or mute the thread https://github.com/notifications/unsubscribe-auth/AEHDXAG4FGJW5FBGCREYNGDP6YWGZANCNFSM4H7IDL4A .

-- Sara E. Boles, MS PhD Candidate | Whitehead Lab Pharmacology and Toxicology Graduate Group Department of Environmental Toxicology University of California, Davis, CA 95616 http://whiteheadresearch.wordpress.com/ https://sites.google.com/a/ucdavis.edu/sara-e-boles/

-- Sara E. Boles, MS PhD Candidate | Whitehead Lab Pharmacology and Toxicology Graduate Group Department of Environmental Toxicology University of California, Davis, CA 95616 http://whiteheadresearch.wordpress.com/ https://sites.google.com/a/ucdavis.edu/sara-e-boles/