#**The gene IDs BP0101A and BP0101B were both listed as open reading frame (ORF) genes in the .xml file as opposed to ordered locus names. This presented a new category of gene IDs that the custom ''Bordetella pertussis'' species profile was not designed to export.

#**The gene IDs BP0101A and BP0101B were both listed as open reading frame (ORF) genes in the .xml file as opposed to ordered locus names. This presented a new category of gene IDs that the custom ''Bordetella pertussis'' species profile was not designed to export.

#*ORF investigation

#*ORF investigation

#**To see if there were other ORF genes with the pattern BP####A or BP####B, we ran a query to retrieve such IDs from the original PostgreSQL: ''bpertussis_cw20151119_gmb3build5''.

#**To see if there were other ORF genes with the pattern BP####A or BP####B, we ran a query to retrieve such IDs from the original PostgreSQL database: ''bpertussis_cw20151119_gmb3build5''.

#***[[File: ORFissue_cw20151119.png]]

#***[[File: ORFissue_cw20151119.png]]

#****This query retrieved a list of 11 ORF genes. Seven of these genes exhibited numerical sequences (####) that were cross-listed as ordered locus names, whereas four of the genes exhibited unique numerical sequences that were only listed as ORF genes. Therefore, only four of the ORF IDs should been discrepant during our comparative analysis between .gdb and .xml IDs. Of these four, two were BP0101A and BP0101B.

#****This query retrieved a list of 11 ORF genes. Seven of these genes exhibited numerical sequences (####) that were cross-listed as ordered locus names, whereas four of the genes exhibited unique numerical sequences that were only listed as ORF genes. Therefore, only four of the ORF IDs should been discrepant during our comparative analysis between .gdb and .xml IDs. Of these four, two were BP0101A and BP0101B.

#*This was the third ORF gene with a unique numerical sequence. The gene was listed as BP0684A in the original .xml file.

#*This was the third ORF gene with a unique numerical sequence. The gene was listed as BP0684A in the original .xml file.

Conclusion: The custom ''Bordetella pertussis'' species profile in GenMAPP Builder needs to be customized to export the 11 ORF genes. The gene BP3167.1 was already being exported and, therefore, does not warrant coding changes. Instead, this unique pattern should be incorporated into the regex used to count ''Bordetella pertussis'' gene IDs when running future gene database testing reports.

'''Conclusion:''' The custom ''Bordetella pertussis'' species profile in GenMAPP Builder needs to be customized to export the 11 ORF genes. The gene BP3167.1 was already being exported and, therefore, does not warrant coding changes. Instead, this unique pattern should be incorporated into the regex used to count ''Bordetella pertussis'' gene IDs when running future gene database testing reports.

===Changes to the Code===

===Changes to the Code===