Polishing a CarveMe model

The newer version of CarveMe 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.