TSV: Salmonella enterica named serovar O- and H-antigens cross reference table

README.md

Steps to retrieve table of named serovars with O- and H-antigens

Downloaded "Antigenic Formulae Of The Salmonella Serovars 2007 9th edition" from:

https://www.pasteur.fr/ip/portal/action/WebdriveActionEvent/oid/01s-000036-089

Regex Steps

Remove page numbers:

• match
  • \d{3}/\d{3}\s+
• replace
  • none

Remove alphabet headers:

• match
  • ^\s*[A-Z]\s+
• replace
  • none

Remove extra whitespace:

• match
  • ^\s+
• replace
  • none

Manually fixed Senftenberg since it was broken across 2 lines

Fix z space subscript number space bracket:

• match
  • z (\d+) \]
• replace
  • z\1]

Fix z space subscript number space comma:

• match
  • z (\d+) ,
• replace
  • z\1,

Fix z space subscript number:

• match
  • z (\d+)
• replace
  • z\1

Manually removed space in:

Paratyphi A
Paratyphi B
Paratyphi C

to give:

ParatyphiA
ParatyphiB
ParatyphiC

Find all serotypes with H0:

• match
  • ^(\w+) {2,}(\S+) {2,}(\S+) {2,}(\S+) {2,}(\S+).*
• replace
  • \1\t\2\t\3\t\4\t\5

Find all serotypes without H0:

• match
  • ^(\w+) {2,}(\S+) {2,}(\S+) {2,}(\S+).*
• replace
  • \1\t\2\t\3\t\4\t

Final product should be a tab delimited table

Headers:

• Serovar
• O-antigens
• H1
• H2
• H(other)

Salmonella_enterica-named_serotype_table-pasteur_2007.csv

Salmonella_enterica-named_serotype_table-pasteur_2007.tsv