esaskar / coreco

Computational method for Comparative ReConstruction of genome-scale metabolic networks

CoReCo

CoReCo is a computational method for reconstructing metabolic networks of multiple species from protein sequence and phylogenetic data.

1. Software requirements
2. Data requirements

Software requirements

1. Python
2. Perl
3. InterProScan
4. NCBI Blast+ toolkit
5. R
6. Python module newick
7. libsbml

Data requirements

1. UniProt (uniprot_sprot.fasta.gz, uniprot_sport.dat)
2. EC to GO mapping (ec2go)
3. KEGG
4. GTG nrdb40

See doc/CoReCoManual.pdf for installation and usage instructions.

Cite us

• Pitkänen et al., Comparative Genome-Scale Reconstruction of Gapless Metabolic Networks for Present and Ancestral Species. PLOS Computational Biology 2014, doi:10.1371/journal.pcbi.1003465
• Castillo et al., Whole-genome metabolic model of Trichoderma reesei built by comparative reconstruction. Biotechnology for Biofuels 2016, doi:10.1186/s13068-016-0665-0

coreco's Issues

ec_files.txt named ec_files.txt:

Software doesn't work as it does not recognise "ec_files.txt:".
When renamed python has a parsing error in buildBlastResult.py L16
uid, pext, ec = s.strip().split()

bugs in codes

found lots of bugs in code:
1.
Traceback (most recent call last):
File "MetabolicReconstructionPipeline.py", line 14, in
import MetabolicReconstructionPipeline_Blast
File "/home/mibiome/CoReCo/model_reconstruction_pipeline/MetabolicReconstructionPipeline_Blast.py", line 49
self.uniprot_dust = uniprot_dust
^
TabError: inconsistent use of tabs and spaces in indentation

Traceback (most recent call last):
File "MetabolicReconstructionPipeline.py", line 10, in
import NGS_Util
File "/home/mibiome/CoReCo/model_reconstruction_pipeline/NGS_Util.py", line 87
print call

Traceback (most recent call last):
File "MetabolicReconstructionPipeline.py", line 11, in
import NGS_Blast
File "/home/mibiome/CoReCo/model_reconstruction_pipeline/NGS_Blast.py", line 40
print traceback.print_exc()