Error with Manual data

[JoergDoellinger]

Hi,

I am trying to run ClassiCOL (version_1_0_2) with "manual" input data (derived from FragPipe). I use the command:

python ClassiCOL.py -d C:/Users/ZBS6-Proteomik/Desktop/ClassiCOL_1.0.2 -l C:/Users/ZBS6-Proteomik/Desktop/ClassiCOL/Input -s Manual -m P,15.994915/P,31.989829/M,31.989829/P,47.984744/N,0.984016/Q,0.984016 -t Mammalia -c 20

Unfortunately, I receive the following error:

Traceback (most recent call last):
File "C:\Users\ZBS6-Proteomik\Desktop\ClassiCOL_1.0.2\ClassiCOL.py", line 2378, in
fixed_mod = [(el[0],float(el[1])) for el in fixed_mod]
File "C:\Users\ZBS6-Proteomik\Desktop\ClassiCOL_1.0.2\ClassiCOL.py", line 2378, in
fixed_mod = [(el[0],float(el[1])) for el in fixed_mod]
ValueError: could not convert string to float: '15.994915/P'

Could you please help me?

Best regards

Joerg

[EngelsI]

Hello,

It might be a bit difficult to see but the separation character should be '|' and not '/', that should fix the error. If the modifications are variable (so it is possible that an amino acid residue can be both unmodified and modified), you best not use the '-m' command. Otherwise you will only consider peptides that have those fixed modifications. For the manual file it is enough to state in the modification column where the mod is located and what the type of modification is, e.g. 1|Oxidation when your first residue has an oxidation. ClassiCOL automatically takes into account all of the variable modifications listed in your manual input - this is why you only need to use the '-m' command for specifying the fixed modifications.

I hope this helps :)

Best wishes,
Ian

[JoergDoellinger]

Thank you for your quick response.
I run into an error with my input file:

(base) C:\Users\ZBS6-Proteomik\Desktop\ClassiCOL_1.0.2>python ClassiCOL.py -d C:/Users/ZBS6-Proteomik/Desktop/ClassiCOL_1.0.2 -l Input -s Manual -t Mammalia -c 20
making database
240718_FishboneDB.fasta
240719_BirdboneDB.fasta
240806_MammalBoneDB.fasta
240813_AmphibianBoneDB.fasta
240813_ReptileBoneDB.fasta
Addition_to_ClassiCOL_DB_version1_0_1.txt
open file Input/Peptides.csv
Traceback (most recent call last):
File "C:\Users\ZBS6-Proteomik\Desktop\ClassiCOL_1.0.2\ClassiCOL.py", line 2426, in
df, df2, unimod_db, protein, ids, adj_pep = load_manual_files(path,test_file)
File "C:\Users\ZBS6-Proteomik\Desktop\ClassiCOL_1.0.2\ClassiCOL.py", line 2281, in load_manual_files
new_pvm[int(pvm[i])]=pvm[i+1]
IndexError: list index out of range

The first lines of the file look like this:

seq,modifications
EGAPGAEGSPGRDGSPGAKGDR,10|Oxidation|16|Oxidation
GSPGPAGPKGSPGEAGR,12|Oxidation|3|Oxidation
GAPGPQGPRGDKGETGER,3|Oxidation|6|Deamidation
GPAGPSGPAGKDGR,
GDAGAPGAPGGKGDAGAPGER,18|Oxidation|6|Oxidation|9|Oxidation
GPPGPPGKNGDDGEAGKPGR,3|Oxidation|6|Oxidation|9|Deamidation
GPTGDPGKNGDKGHAGLAGAR,6|Oxidation|9|Deamidation
GPPGPPGKNGDDGEAGKPGR,2|Oxidation|6|Oxidation|9|Deamidation
GPPGPPGKNGDDGEAGKPGR,3|Oxidation|5|Oxidation|9|Deamidation
GAAGEPGRDGVPGGPGMR,12|Oxidation|15|dihydroxy|6|Oxidation
GAAGEPGRDGVPGGPGMR,12|Oxidation|17|dihydroxy|6|dihydroxy
GPAGPQGPRGDKGETGEQGDR,6|Deamidation|8|Oxidation
GAAGEPGRDGVPGGPGMR,12|Oxidation|15|cysteine oxidation to cysteic acid|6|Oxidation

Do you have an clue what might cause the problem?

Best regards

Joerg

[EngelsI]

Hi,

When I try it with the lines of your data you sent, it works. Could it be that somewhere in your datafile there is an extra '|', for example at the start of one of the modification column cells (before the location)? Could be at the beginning or at the end of one of your modifications. The program splits the modifications at locations where there is an '|' so if there is a '|' where there should not be one, then it can run into problems.
Your modifications should all be in the same cell - I would also check for any rogue commas in that column that could cause some of the data to fall outside of the index range.

[JoergDoellinger]

Hi,

there was indeed one '|' missing in the data. The script is now running.

thanks

Joerg