search

xpolak37 / COGtools

A computational tools for improving the functional annotation of bacterial genomes and the classification of CDSs into cllusters of orthologous groups (COGs). It allows summarizing annotations from different resources to provide a more accurate annotation of genes regarding their assignment into COGs and their categories.
MIT License
3 stars 0 forks source link

AttributeError: 'em.processor' #3

Closed Ujomo closed 8 months ago

Ujomo commented 8 months ago

Hello, First of, I am very new to python coding so my question may seem very elementary. When I try to run my python script following the usage example in the COGtools documentation I get an AttributeError: module 'cogtools' has no attribute 'em_processor'. Find below the script. Please what have I missed out?

import cogtools organism_name = "pseudomonas" eggnog_file = "inputs/pseudomonas_eggnog.gff" operon_file_gff = "inputs/pseudomonas_orf_operon.txt" operon_file_cog = "inputs/pseudomonas_cog_operon.txt" batch_file = "inputs/pseudomonas_batch.txt"

fasta_file = "inputs/pseudomonas.fasta" CDS_file = "inputs/pseudomonas_cds.txt" gff_file = "inputs/pseudomonas.gff3" cogtools.em_processor(organism_name, em_file=eggnog_file, cds_file=CDS_file, output_dir = "outputs") cogtools.om_processor(organism_name, operon_file_gff, operon_file_cog, output_dir = "outputs") cogtools.batch_processor(organism_name, batch_file, output_dir = "outputs") cogtools.consensus(organism_name, outputdir + "/em" + organism_name + ".gff", outputdir + "/om" + organism_name + ".gff", outputdir + "/batch" + organism_name + ".gff", fasta_file=fasta_file, get_pseudo=True, gff_file=gff_file, get_ncrna=True, cat_choice=1, output_dir = "outputs")

xpolak37 commented 8 months ago

Hi,

thank you for trying the tool. I see the problem now. After cloning the repository, you should be working inside (in folder, where documentation and other files are located). Then, you should import COGtools, not "cogtools", because "COGtools" is the folder where source code is located. I will fix this also in the documentation. Sorry for the inconvenience.

Ujomo commented 8 months ago

Thanks a lot! it worked. It imported the COGtools.

If I may ask a follow up question. While running the script I get a ValueError: substring not found, and it points to the line of COGtools.em_processor in my script and the line 32 in em_processor, seq_id = record [0: record.index(" [")]

xpolak37 commented 8 months ago

Thank you for reporting the problem. The code should be fixed now, soon I will add changes to the documentation.