Linearizing a FASTA sequence.

Linearize a FASTA sequence with AWK

Reading line by line

awk '/^>/ {printf("%s%s\t",(N>0?"\n":""),$0);N++;next;} {printf("%s",$0);} END {printf("\n");}' < input.fa

one can read this awk script as:

if the current line ($0) starts like a fasta header (^>). Then we print a carriage return if this is not the first sequence. (N>0?"\n":"") followed with the line itself ($0), followed with a tabulation (\t). And we look for the next line (next;)
if the current line ($0) does not start like a fasta header, this is the default awk pattern. We just print the whole line without carriage return.
At the end (END) we only print a carriage return for the last sequence.

Linearize FASTA sequences from Uniprot

download and linearize the 10 first FASTA sequences from UniProt:

$ curl -s  "ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.fasta.gz" |\
  gunzip -c |\
  awk '/^>/ {printf("%s%s\t",(N>0?"\n":""),$0);N++;next;} {printf("%s",$0);} END {printf("\n");}'  |\
  head

>sp|Q6GZX4|001R_FRG3G Putative transcription factor 001R OS=Frog virus 3 (isolate Goorha) GN=FV3-001R PE=4 SV=1    MAFSAEDVLKEYDRRRRMEALLLSLYYPNDRKLLDYKEWSPPRVQVECPKAPVEWNNPPSEKGLIVGHFSGIKYKGEKAQASEVDVNKMCCWVSKFKDAMRRYQGIQTCKIPGKVLSDLDAKIKAYNLTVEGVEGFVRYSRVTKQHVAAFLKELRHSKQYENVNLIHYILTDKRVDIQHLEKDLVKDFKALVESAHRMRQGHMINVKYILYQLLKKHGHGPDGPDILTVKTGSKGVLYDDSFRKIYTDLGWKFTPL
>sp|Q6GZX3|002L_FRG3G Uncharacterized protein 002L OS=Frog virus 3 (isolate Goorha) GN=FV3-002L PE=4 SV=1    MSIIGATRLQNDKSDTYSAGPCYAGGCSAFTPRGTCGKDWDLGEQTCASGFCTSQPLCARIKKTQVCGLRYSSKGKDPLVSAEWDSRGAPYVRCTYDADLIDTQAQVDQFVSMFGESPSLAERYCMRGVKNTAGELVSRVSSDADPAGGWCRKWYSAHRGPDQDAALGSFCIKNPGAADCKCINRASDPVYQKVKTLHAYPDQCWYVPCAADVGELKMGTQRDTPTNCPTQVCQIVFNMLDDGSVTMDDVKNTINCDFSKYVPPPPPPKPTPPTPPTPPTPPTPPTPPTPPTPRPVHNRKVMFFVAGAVLVAILISTVRW
>sp|Q197F8|002R_IIV3 Uncharacterized protein 002R OS=Invertebrate iridescent virus 3 GN=IIV3-002R PE=4 SV=1    MASNTVSAQGGSNRPVRDFSNIQDVAQFLLFDPIWNEQPGSIVPWKMNREQALAERYPELQTSEPSEDYSGPVESLELLPLEIKLDIMQYLSWEQISWCKHPWLWTRWYKDNVVRVSAITFEDFQREYAFPEKIQEIHFTDTRAEEIKAILETTPNVTRLVIRRIDDMNYNTHGDLGLDDLEFLTHLMVEDACGFTDFWAPSLTHLTIKNLDMHPRWFGPVMDGIKSMQSTLKYLYIFETYGVNKPFVQWCTDNIETFYCTNSYRYENVPRPIYVWVLFQEDEWHGYRVEDNKFHRRYMYSTILHKRDTDWVENNPLKTPAQVEMYKFLLRISQLNRDGTGYESDSDPENEHFDDESFSSGEEDSSDEDDPTWAPDSDDSDWETETEEEPSVAARILEKGKLTITNLMKSLGFKPKPKKIQSIDRYFCSLDSNYNSEDEDFEYDSDSEDDDSDSEDDC
>sp|Q197F7|003L_IIV3 Uncharacterized protein 003L OS=Invertebrate iridescent virus 3 GN=IIV3-003L PE=4 SV=1    MYQAINPCPQSWYGSPQLEREIVCKMSGAPHYPNYYPVHPNALGGAWFDTSLNARSLTTTPSLTTCTPPSLAACTPPTSLGMVDSPPHINPPRRIGTLCFDFGSAKSPQRCECVASDRPSTTSNTAPDTYRLLITNSKTRKNNYGTCRLEPLTYGI
>sp|Q6GZX2|003R_FRG3G Uncharacterized protein 3R OS=Frog virus 3 (isolate Goorha) GN=FV3-003R PE=3 SV=1    MARPLLGKTSSVRRRLESLSACSIFFFLRKFCQKMASLVFLNSPVYQMSNILLTERRQVDRAMGGSDDDGVMVVALSPSDFKTVLGSALLAVERDMVHVVPKYLQTPGILHDMLVLLTPIFGEALSVDMSGATDVMVQQIATAGFVDVDPLHSSVSWKDNVSCPVALLAVSNAVRTMMGQPCQVTLIIDVGTQNILRDLVNLPVEMSGDLQVMAYTKDPLGKVPAVGVSVFDSGSVQKGDAHSVGAPDGLVSFHTHPVSSAVELNYHAGWPSNVDMSSLLTMKNLMHVVVAEEGLWTMARTLSMQRLTKVLTDAEKDVMRAAAFNLFLPLNELRVMGTKDSNNKSLKTYFEVFETFTIGALMKHSGVTPTAFVDRRWLDNTIYHMGFIPWGRDMRFVVEYDLDGTNPFLNTVPTLMSVKRKAKIQEMFDNMVSRMVTS
>sp|Q6GZX1|004R_FRG3G Uncharacterized protein 004R OS=Frog virus 3 (isolate Goorha) GN=FV3-004R PE=4 SV=1    MNAKYDTDQGVGRMLFLGTIGLAVVVGGLMAYGYYYDGKTPSSGTSFHTASPSFSSRYRY
>sp|Q197F5|005L_IIV3 Uncharacterized protein 005L OS=Invertebrate iridescent virus 3 GN=IIV3-005L PE=3 SV=1    MRYTVLIALQGALLLLLLIDDGQGQSPYPYPGMPCNSSRQCGLGTCVHSRCAHCSSDGTLCSPEDPTMVWPCCPESSCQLVVGLPSLVNHYNCLPNQCTDSSQCPGGFGCMTRRSKCELCKADGEACNSPYLDWRKDKECCSGYCHTEARGLEGVCIDPKKIFCTPKNPWQLAPYPPSYHQPTTLRPPTSLYDSWLMSGFLVKSTTAPSTQEEEDDY
>sp|Q6GZX0|005R_FRG3G Uncharacterized protein 005R OS=Frog virus 3 (isolate Goorha) GN=FV3-005R PE=4 SV=1    MQNPLPEVMSPEHDKRTTTPMSKEANKFIRELDKKPGDLAVVSDFVKRNTGKRLPIGKRSNLYVRICDLSGTIYMGETFILESWEELYLPEPTKMEVLGTLESCCGIPPFPEWIVMVGEDQCVYAYGDEEILLFAYSVKQLVEEGIQETGISYKYPDDISDVDEEVLQQDEEIQKIRKKTREFVDKDAQEFQDFLNSLDASLLS
>sp|Q91G88|006L_IIV6 Putative KilA-N domain-containing protein 006L OS=Invertebrate iridescent virus 6 GN=IIV6-006L PE=3 SV=1    MDSLNEVCYEQIKGTFYKGLFGDFPLIVDKKTGCFNATKLCVLGGKRFVDWNKTLRSKKLIQYYETRCDIKTESLLYEIKGDNNDEITKQITGTYLPKEFILDIASWISVEFYDKCNNIIINYFVNEYKTMDKKTLQSKINEVEEKMQKLLNEKEEELQEKNDKIDELILFSKRMEEDRKKDREMMIKQEKMLRELGIHLEDVSSQNNELIEKVDEQVEQNAVLNFKIDNIQNKLEIAVEDRAPQPKQNLKRERFILLKRNDDYYPYYTIRAQDINARSALKRQKNLYNEVSVLLDLTCHPNSKTLYVRVKDELKQKGVVFNLCKVSISNSKINEEELIKAMETINDEKRDV
>sp|Q6GZW9|006R_FRG3G Uncharacterized protein 006R OS=Frog virus 3 (isolate Goorha) GN=FV3-006R PE=4 SV=1    MYKMYFLKDQKFSLSGTIRINDKTQSEYGSVWCPGLSITGLHHDAIDHNMFEEMETEIIEYLGPWVQAEYRRIKG