Thursday, August 9, 2018

Sequence lengths from AWK one-liner


$ awk '/^>/ {if (sqlen){print sqlen}; print ;sqlen=0;next; } { sqlen = sqlen +length($0)}END{print sqlen}' db4_cdc_NDM_only.fasta | sed 's/>//g' | paste - - 

ref|NZ_CP029245.1| Escherichia_coli_strain_ECCRA-119_plasmid_pTB203,_complete_sequence 46161
ref|NZ_CP029386.1| Klebsiella_pneumoniae_subsp._pneumoniae_strain_SCKP040074_plasmid_pNDM6_040074,_complete_sequence 52989
ref|NZ_CP029731.1| Citrobacter_sp._CRE-46_strain_AR_0157_plasmid_unnamed3,_complete_sequence 108148
ref|NZ_CP029737.1| Providencia_rettgeri_strain_AR_0082_plasmid_unnamed,_complete_sequence 144970
ref|NZ_CP029978.1| Escherichia_coli_strain_51008369SK1_plasmid_p51008369SK1_E,_complete_sequence 99465
ref|NZ_KM923969.1| Acinetobacter_dijkshoorniae_strain_JVAP01_plasmid_pNDM-JVAP01,_complete_sequence 47268

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