Include PRODIGAL FAA support in README; amend logger name

README.md

@@ -33,13 +33,22 @@ sanntis test/files/BGC0001472.fna
 conda deactivate sanntis
 ```
 
-SanntiS can be executed using preprocessed InterProScan outputs along with a GenBank (GBK) file specifying the coding sequences (CDSs). This integration facilitates a streamlined analysis pipeline for bioinformatics applications, allowing for enhanced functionality and user flexibility.
+### Support of preprocessed InterProScan outputs
+
+SanntiS can be executed using preprocessed InterProScan outputs along with a GenBank (GBK) file specifying the coding sequences (CDSs). This integration increases user flexibility.
 ```bash
 conda activate sanntis
 sanntis --ip-file test/files/BGC0001472.fna.prodigal.faa.gff3 test/files/BGC0001472.fna.prodigal.faa.gb
 conda deactivate sanntis
 ```
 
+Additionally, the --ip-file option can be provided with a protein FASTA file containing headers formatted according to Prodigal's convention. In this case, the --is_protein flag must be included to indicate that the sequence file is a proteins FASTA. 
+```bash
+conda activate sanntis
+sanntis --is_protein --ip-file test/files/BGC0001472.fna.prodigal.faa.gff3 test/files/BGC0001472.fna.prodigal.faa
+conda deactivate sanntis
+```
+
 ###  Docker:
 
 #### Get InterProsScan data:

sanntis/modules/BGCdetection.py

@@ -112,7 +112,7 @@ def transformCDSpredToCDScontigs(self, cdsPredFile, file_format):
                 header = record.description
                 prodigal_match = _prodigal_pattern.search(header)
                 if not prodigal_match:
-                    logger.warning(
+                    log.warning(
                         f"Protein {record.id} does not follow the Prodigal header format. "
                     )
                     continue