joining multi-line file into single lines

Shell Programming and Scripting
1

Hi,

I have a file like mentioned below..For each specific id starting with > I want to join the sequence in multiple lines to a single line..Is there a simple way in awk or sed to do this

>ENST00000558922 cdna:KNOWN
TCCAGGATCCAGCCTCCCGATCACCGCGCTAGTCCTCGCCCTGCCTGGGCTTCCCCAGAG
ACGGGAGCTTGGGTGGGGGACCCTGGACCCGAAGCCAAGGCTGAACTGGTGTGCCAAGCC
CAGGGAGCAACCAAGTCCCCAACTCTTTCCCTGCCCTTCCCGCAGGCTGAGCAGAAAACC
AGGAAATGGATGGACTCCACCTCCGCAGCCACGCCTGCCCGTTTGCGCTTACTGAACAGA
GGTCCTCAGGAACGTGAAAATGAAGGGAGGGTTACTAACTTTATGCCATCTTCAAACCAG
AAGATCTTAGATTAGTAAGATCATGTTGGCCATGGCATGGAGAATGGGCTGGAGGTGGAG
AGACTGGAGGTTGGAAGTCCAGTTAGGAGATTGCTCCTGCGCTGGGGAGTTGGTGTTAGG
ACAGAAGATCCAAGACGCGTTTCAGAGAGCCCCTCTTCTTGGGCCTGCGATTCCTCACCT
GGAAGGGAGAAGAGTGGACTTCCTGCCTAGAGAACACCTTGGTAAACTCTTTGTGGTTCC
>ENST00088352 cdna:UNKNOWN
TGTCATGAGAAGGTGTGCAGCTTAGGGAAAAAGCCTGTGAGCTCTGGAATCAGATGGAAC
TGGATATGAATTTCCATTTAAACTGCCTTGGGGTTCATGTTGCAGCATCAAACAGGGATG
GAAGATGCATCTTGCTTTAGCAGCAGGAGCCTGGAAAGCAGCTGAAGCCCTGGAGGGTGC
CTGGCACACAGAATCTTGTGCTGAGCCCGGAGCACAATGGGAGCGGGCTGGCGGGGTGGG
TTCACAGCTGGACTGGGAGCAGCAGACATACAGGCCGTAGGCACAGACATATAAAGACAG
TCATGCAGATTGCAGGATGCCTGAGAGCACAGACTCTCACATGCACAAATACGTGCATGA
TCGCCAGTGTGCATCCAGACAGCCCCACATGCATGCACACGCATGCACACATGTGATGTG
TACATAGATGGACACATGTCTATGCCCACAAACACTGCAGAGACACAG

Thanks,

2

Try:

awk ' /^>/ {if (FNF>1){ printf("\n")}} {printf("%s", $0) }' infile > newfile
3

Not sure if you want all in one single line as jim_mcnamara's proposal does or in one line per id. This is a bit ugly but it does it the second way:

sed -n '/^>/{x;s/\n//g;1!p;d}; /^[^>]/H; ${x;s/\n//g;p}' infile

If you want the id in an extra line, this will do:

sed -n '/^>/{x;s/\n//g;1!p;s/.*//g;x;p}; /^[^>]/H; ${x;s/\n//g;p}' infile