Polishing a CarveMe model

CarveMe version 1.5.1 leads to some irritations in the model, the scripts in polish enable for example the addition of BiGG IDs to the annotations as well as a correct formatting of the annotations.

Warning

Using lab_strain=True has the following two requirements:

1. The model already contains GeneProduct identifiers containing valid NCBI Protein/RefSeq identifiers.

   If there is no available data for the modeled organism in any database these identifiers can be added with the pipeline described in Pipeline: From genome sequence to draft model before draft model creation.

2. Input of a FASTA file containing header lines similar to:

   >lcl|CP035291.1_prot_QCY37216.1_1 [gene=dnaA] [locus_tag=EQ029_00005] [protein=chromosomal replication initiator protein DnaA] [protein_id=QCY37216.1] [location=1..1356] [gbkey=CDS] Of the description part in the header line only locus_tag, protein and protein_id are important for cv_ncbiprotein/ polish.