How can I extract out lines that contains 'g__' at their end along with the first two line headers? (i.e. only the genus level OTU from metaphlan output)
I want to extract the lines that contain g__something within the line but not followed by s__something.
type obese obese obese obese obese obese obese obese obese obese obese
clade_name ERR011272_profile ERR011271_profile ERR011270_profile ERR011269_profile ERR011268_profile ERR011267_profile ERR011266_profile ERR567265_profile ERR008764_profile ERR03263_profile ERR234562_profile
k__Bacteria 100 100 100 100 100 100 100 100 100 100 100
k__Bacteria|p__Actinobacteria 8.84082 9.08752 0.5741 0.89084 0.14307 0.13286 2.37624 1.45006 0.41332 0.9011 0.6917
k__Bacteria|p__Actinobacteria|c__Actinobacteria 5.17984 4.86388 0.14615 0.20425 0.05402 0.04654 1.47203 0.88991 0.2423 0.50227 0.33122
k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Actinomycetales 0.03246 0.03837 0 0 0 0 0 0 0 0 0
k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Actinomycetales|f__Actinomycetaceae 0.03246 0.03837 0 0 0 0 0 0 0 0 0
k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces 0.03246 0.03837 0 0 0 0 0 0 0 0 0
k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces_odontolyticus 0.00902 0.01206 0 0 0 0 0 0 0 0 0
k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces_sp_HMSC035G02 0.01454 0.00469 0 0 0 0 0 0 0 0 0
k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces_sp_HPA0247 0 0 0 0 0 0 0 0 0 0 0
k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces_sp_ICM47 0.0089 0.02162 0 0 0 0 0 0 0 0 0
k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces_sp_S6_Spd3 0 0 0 0 0 0 0 0 0 0 0
k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Actinomycetales|f__Actinomycetaceae|g__Actinomyces|s__Actinomyces_sp_oral_taxon_181 0 0 0 0 0 0 0 0 0 0 0
k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Bifidobacteriales 5.14507 4.80951 0.14615 0.20425 0.05402 0.04654 1.47203 0.88991 0.2423 0.50227 0.33122
k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Bifidobacteriales|f__Bifidobacteriaceae 5.14507 4.80951 0.14615 0.20425 0.05402 0.04654 1.47203 0.88991 0.2423 0.50227 0.33122
k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Aeriscardovia 0.01509 0.02915 0 0 0 0 0.01514 0.00328 0.00187 0 0.0037
k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Aeriscardovia|s__Aeriscardovia_aeriphila 0.01509 0.02915 0 0 0 0 0.01514 0.00328 0.00187 0 0.0037
k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium 5.12998 4.78036 0.14615 0.20425 0.05402 0.04654 1.45689 0.88663 0.24043 0.50227 0.32752
k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium_adolescentis 1.83735 1.8711 0.05485 0.05771 0.05402 0.04654 0.97666 0.57204 0.20912 0.42861 0.10834
k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium_angulatum 0 0 0 0 0 0 0 0 0 0 0.01811
k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium_bifidum 0 0 0 0 0 0 0 0 0 0 0
k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium_catenulatum 0 0 0 0 0 0 0 0 0 0 0.12072
k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium_dentium 0 0 0 0 0 0 0 0 0 0 0
k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium_longum 2.40681 2.17987 0.0913 0.14654 0 0 0.48024 0.31459 0.03131 0.07367 0.08035
k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium_pseudocatenulatum 0.88581 0.72939 0 0 0 0 0 0 0 0 0
k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Bifidobacterium|s__Bifidobacterium_pullorum 0 0 0 0 0 0 0 0 0 0 0
k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Bifidobacteriales|f__Bifidobacteriaceae|g__Gardnerella 0 0 0 0 0 0 0 0 0 0 0
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This should works
Sorry. I put the question wrong by mistake. Please allow me to edit and reply me if you know the answer. Thanks @Hood.
This should work then
Result
Since it is a 7 level nomenclature, genus is 6th level and each level is separated by |, you can try this: (this would print first two line headers, followed by genus information)
Thnaks cpad0112. It helps.