transcript/cog

Scripts and steps for making a consolidated COG database file for tools like DIAMOND.

cog's Issues

Code update request to merge COG2020 files

Hi Sam,
thanks for sharing your code on GitHub. Your scripts work smoothly. I was just wondering if you were planing to update your merge.py script to process the updated COG2020 database file formats.

Reference
https://academic.oup.com/nar/article/49/D1/D274/5964069
ftp://ftp.ncbi.nih.gov/pub/COG/COG2020/data

Fail try to run DIAMOND_COG_analysis_counter.py

Hi MR. SAM,

when i am runing DIAMOND_COG_analysis_counter.py, error encountered:

(base) [wfangab@login-0 annotation]$ python DIAMOND_COG_analysis_counter.py -I test.cogs -O result.cogs -D merged_cogs.fa

Analysis of test.cogs complete.
Number of total lines: 4863
Number of unique sequences: 250
Time elapsed: 0.01116103120148182 seconds.

Starting database analysis now.
Traceback (most recent call last):
  File "/home/wfangab/COG/annotation/DIAMOND_COG_analysis_counter.py", line 125, in <module>
    db_id = str(splitline[0] + "|" + splitline[1] + "|" + splitline[2] + "|" + splitline[3] + "|")[1:]
IndexError: list index out of range

Then I found out that the head of 'merged_cogs.fa' is not the same as it shows in github.
Here is an example of my head:

ABK77980.1 glutamate-1-semialdehyde aminotransferase [Cenarchaeum symbiosum A] | COG0001 | H

Could you please help with it?

Best,
Ben

Error trying to run merger.py

Hi Mr Sam,

Thank you for your contribution!

I have some issue when running the merger.py file.

On my terminal, I face a index error. Unfortunately I am just a beginner in Linux and just trying to annotate my data using KOG database. I have already unzipped the pro2003-2014.fa and the other two were left as it. All 4 files, including merger.py is in the same directory/

Thank you for your time!

My error in Terminal :-

ray@rain:/Downloads/COG-master$ source /home/ray/anaconda2/bin/activate
(base) ray@rain:/Downloads/COG-master$ python merger.py prot2003-2014.fa cog2003-2014.csv cognames2003-2014.tab
Traceback (most recent call last):
File "merger.py", line 16, in
cog_db[split[0]] = split[6] # GI ID == COG ID
IndexError: list index out of range

My error in Spyder (Python 2.7) Console :-

runfile('/home/ray/Downloads/COG-master/merger.py', wdir='/home/ray/Downloads/COG-master')
Traceback (most recent call last):

File "", line 1, in
runfile('/home/ray/Downloads/COG-master/merger.py', wdir='/home/ray/Downloads/COG-master')

File "/home/ray/anaconda2/lib/python2.7/site-packages/spyder_kernels/customize/spydercustomize.py", line 827, in runfile
execfile(filename, namespace)

File "/home/ray/anaconda2/lib/python2.7/site-packages/spyder_kernels/customize/spydercustomize.py", line 102, in execfile
builtins.execfile(filename, *where)

File "/home/ray/Downloads/COG-master/merger.py", line 5, in
prot_file = open(sys.argv[1], "r") # prot2003-2014.fa (note: unzipped)

IndexError: list index out of range