search

AuReMe / padmet

Python library for hAndling metaData of METabolism.
https://padmet.readthedocs.io/en/latest/
GNU General Public License v3.0
4 stars 2 forks source link

Bug in `--enhance` functionality from pgdb_to_padmet #12

Open cfrioux opened 1 month ago

cfrioux commented 1 month ago

Observation

Running padmet report_network from a padmet "enhanced" with the content of metabolic-reactions.xml raised the following error:

padmet report_network --padmetSpec /home/jaudemar/m2m/community_padmet/PMC1354_22/PMC1354_22_Bin_2.padmet --output_dir report_54 --padmetRef Installation/metacyc_27.0.padmet
Traceback (most recent call last):
  File "/home/jaudemar/.local/bin/padmet", line 8, in <module>
    sys.exit(main())
  File "/home/jaudemar/.local/lib/python3.10/site-packages/padmet/__main__.py", line 121, in main
    getattr(command_import, command + '_cli')(command_args)
  File "/home/jaudemar/.local/lib/python3.10/site-packages/padmet/utils/exploration/report_network.py", line 45, in report_network_cli
    padmetSpec.network_report(output_dir, padmetRef_file, verbose)  
  File "/home/jaudemar/.local/lib/python3.10/site-packages/padmet/classes/padmetSpec.py", line 1215, in network_report
    if "REVERSIBLE" in [
  File "/home/jaudemar/.local/lib/python3.10/site-packages/padmet/classes/padmetSpec.py", line 1216, in <listcomp>
    self.dicOfNode[rxn_id].misc["DIRECTION"][0]
KeyError: 'ENOYL-ACP-REDUCT-NADH-RXN-POLYMER-INST-Saturated-Fatty-Acyl-ACPs-C16-H32/NAD//POLYMER-INST-TRANS-D2-ENOYL-ACP-C16-H32/NADH/PROTON.104.'

Nonetheless, it did not prevent report files to be generated, so tricky error that might be loss in logs if not checking.

Problem

I noticed that reactions from metabolic-reactions.xml in the enhanced padmet were incorrect in the padmet file: missing reaction node, although relations are there.

Doing grep on the reaction id in the padmet gives the following:

ENOYL-ACP-REDUCT-NADH-RXN-POLYMER-INST-Saturated-Fatty-Acyl-ACPs-C16-H32/NAD//POLYMER-INST-TRANS-D2-ENOYL-ACP-C16-H32/NADH/PROTON.104.  consumes    POLYMER-INST-TRANS-D2-ENOYL-ACP-C16-H32 STOICHIOMETRY   1.0 COMPARTMENT c
ENOYL-ACP-REDUCT-NADH-RXN-POLYMER-INST-Saturated-Fatty-Acyl-ACPs-C16-H32/NAD//POLYMER-INST-TRANS-D2-ENOYL-ACP-C16-H32/NADH/PROTON.104.  produces    NAD STOICHIOMETRY   1.0 COMPARTMENT c
ENOYL-ACP-REDUCT-NADH-RXN-POLYMER-INST-Saturated-Fatty-Acyl-ACPs-C16-H32/NAD//POLYMER-INST-TRANS-D2-ENOYL-ACP-C16-H32/NADH/PROTON.104.  produces    POLYMER-INST-Saturated-Fatty-Acyl-ACPs-C16-H32  STOICHIOMETRY   1.0 COMPARTMENT c
ENOYL-ACP-REDUCT-NADH-RXN-POLYMER-INST-Saturated-Fatty-Acyl-ACPs-C16-H32/NAD//POLYMER-INST-TRANS-D2-ENOYL-ACP-C16-H32/NADH/PROTON.104.  consumes    NADH    STOICHIOMETRY   1.0 COMPARTMENT c
ENOYL-ACP-REDUCT-NADH-RXN-POLYMER-INST-Saturated-Fatty-Acyl-ACPs-C16-H32/NAD//POLYMER-INST-TRANS-D2-ENOYL-ACP-C16-H32/NADH/PROTON.104.  consumes    PROTON  STOICHIOMETRY   1.0 COMPARTMENT c

I went back to pgdb_to_padmet which raised no error during its creation.

Turns out there is an error in the code: wrong variable assigned as key when updating dicOfNode. padmet.dicOfNode[reaction_id] = reactant_node should be padmet.dicOfNode[reactant_id] = reactant_node

https://github.com/AuReMe/padmet/blob/5c829d57fd93ddc54b765fada6fb1256cbd78957/padmet/utils/connection/pgdb_to_padmet.py#L1358

Fixing this and doing grep again on the reaction id in the padmet after correction:

reaction    ENOYL-ACP-REDUCT-NADH-RXN-POLYMER-INST-Saturated-Fatty-Acyl-ACPs-C16-H32/NAD//POLYMER-INST-TRANS-D2-ENOYL-ACP-C16-H32/NADH/PROTON.104.  DIRECTION   LEFT-TO-RIGHT
ENOYL-ACP-REDUCT-NADH-RXN-POLYMER-INST-Saturated-Fatty-Acyl-ACPs-C16-H32/NAD//POLYMER-INST-TRANS-D2-ENOYL-ACP-C16-H32/NADH/PROTON.104.  consumes    POLYMER-INST-TRANS-D2-ENOYL-ACP-C16-H32 STOICHIOMETRY   1.0 COMPARTMENT c
ENOYL-ACP-REDUCT-NADH-RXN-POLYMER-INST-Saturated-Fatty-Acyl-ACPs-C16-H32/NAD//POLYMER-INST-TRANS-D2-ENOYL-ACP-C16-H32/NADH/PROTON.104.  produces    POLYMER-INST-Saturated-Fatty-Acyl-ACPs-C16-H32  STOICHIOMETRY   1.0 COMPARTMENT c
ENOYL-ACP-REDUCT-NADH-RXN-POLYMER-INST-Saturated-Fatty-Acyl-ACPs-C16-H32/NAD//POLYMER-INST-TRANS-D2-ENOYL-ACP-C16-H32/NADH/PROTON.104.  consumes    NADH    STOICHIOMETRY   1.0 COMPARTMENT c
ENOYL-ACP-REDUCT-NADH-RXN-POLYMER-INST-Saturated-Fatty-Acyl-ACPs-C16-H32/NAD//POLYMER-INST-TRANS-D2-ENOYL-ACP-C16-H32/NADH/PROTON.104.  consumes    PROTON  STOICHIOMETRY   1.0 COMPARTMENT c
ENOYL-ACP-REDUCT-NADH-RXN-POLYMER-INST-Saturated-Fatty-Acyl-ACPs-C16-H32/NAD//POLYMER-INST-TRANS-D2-ENOYL-ACP-C16-H32/NADH/PROTON.104.  produces    NAD STOICHIOMETRY   1.0 COMPARTMENT c

Fix

padmet.dicOfNode[reaction_id] = reactant_node should be padmet.dicOfNode[reactant_id] = reactant_node

in

https://github.com/AuReMe/padmet/blob/5c829d57fd93ddc54b765fada6fb1256cbd78957/padmet/utils/connection/pgdb_to_padmet.py#L1358

cfrioux commented 1 month ago

@jeannegot @PaulineGHG @ArnaudBelcour you might want to take a look and assess whether you've been affected by this bug if you use pgdb_to_padmet --enhance.