re = /^.*:\s+([A-Z].*)_(\D+)_(\d+).*/m
str = 'dog-Cf-Nox1: Porites_lobata_1381 49.126 572 275 8 1 564 1 564 0.0 563
dog-Cf-Nox1: Porites_australiensis_5912 48.776 572 277 8 1 564 1 564 0.0 560
dog-Cf-Nox1: Astreopora_sp_20372 48.776 572 276 9 1 564 1 563 0.0 555
dog-Cf-Nox1: Montastraea_cavernosa_106939 48.148 567 279 7 5 564 6 564 0.0 555
dog-Cf-Nox1: Seriatopora_hystrix_66126 50.000 554 262 7 18 564 19 564 0.0 553
dog-Cf-Nox1: Porites_australiensis_4812 46.946 573 287 6 1 564 1 565 0.0 553
dog-Cf-Nox1: Stylophora_pistillata_7748 49.009 555 268 7 17 564 18 564 0.0 550
dog-Cf-Nox1: Porites_lobata_724 46.435 575 289 7 1 564 1 567 0.0 548
dog-Cf-Nox1: Acropora_digitifera_16260 46.935 571 288 7 1 564 1 563 0.0 538'
subst = '\\1,\\2,\\3'
result = str.gsub(re, subst)
# Print the result of the substitution
puts result
Please keep in mind that these code samples are automatically generated and are not guaranteed to work. If you find any syntax errors, feel free to submit a bug report. For a full regex reference for Ruby, please visit: http://ruby-doc.org/core-2.2.0/Regexp.html