help with file processing

Hi all,

I have a fasta file with sequences as below

>ATGATCTATCGTGTATCACGGTCA(1) TGACCGTGATACACGATAGATCAT
>TACGGTTCTGAAACGGAGAGTTCG(1) CGAACTCTCCGTTTCAGAACCGTA
>GCTTGCGACGACTGAGTTGGAG(1) GCTTGCGACGACTGAGTTGGAG
>ATTACTTGTTGTGATTGTTGGCCT(1) ATTACTTGTTGTGATTGTTGGCCT
>ATGCCGTCGGAAATAATGAGTTTA(1) ATGCCGTCGGAAATAATGAGTTTA
>AACAGATCCGCTGTAGCACATCGG(1) CCGATGTGCTACAGCGGATCTGTT
>TTGGCACGAGTGACTCCTTAGAC(1) GTCTAAGGAGTCACTCGTGCCAA
>TTAAGCATGACTTAGACTATC(2) TTAAGCATGACTTAGACTATC
>CAAAGGAACCGTGAGCTCAACT(1) CAAAGGAACCGTGAGCTCAACT

i need an output as below

>AAGTATGATTGATAATTCGTGATT(1) 
    AATCACGAATTATCAATCATACTT
>ATGGATGAAATGACATGGAATACAC(2) 
    GTGTATTCCATGTCATTTCATCCAT
>CATGGATAAGAGAGAAAAGGACACAAGAAGCCA(1) 
    CATGGATAAGAGAGAAAAGGACACAAGAAGCCA
>ATCGGTTGCAGGTAGACCGAGCTT(1) 
    AAGCTCGGTCTACCTGCAACCGAT

can you please suggest me an easiest way to do this or any code in ubuntu

sequence ubuntu

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updated 6.1 years ago by cpad0112

• written 6.1 years ago by ravi.eshwari •

Please use the formatting bar (especially the code option) to present your post better.
code_formatting

Thank you!

With the code button your input will look like this.

>ATGATCTATCGTGTATCACGGTCA(1) TGACCGTGATACACGATAGATCAT
>TACGGTTCTGAAACGGAGAGTTCG(1) CGAACTCTCCGTTTCAGAACCGTA
>GCTTGCGACGACTGAGTTGGAG(1) GCTTGCGACGACTGAGTTGGAG
>ATTACTTGTTGTGATTGTTGGCCT(1) ATTACTTGTTGTGATTGTTGGCCT
>ATGCCGTCGGAAATAATGAGTTTA(1) ATGCCGTCGGAAATAATGAGTTTA
>AACAGATCCGCTGTAGCACATCGG(1) CCGATGTGCTACAGCGGATCTGTT
>TTGGCACGAGTGACTCCTTAGAC(1) GTCTAAGGAGTCACTCGTGCCAA
>TTAAGCATGACTTAGACTATC(2) TTAAGCATGACTTAGACTATC
>CAAAGGAACCGTGAGCTCAACT(1) CAAAGGAACCGTGAGCTCAACT

• 0 views • link

written 6.1 years ago by GenoMax

try

$ sed 's/\s\+/\n/' test.txt or $awk '{print $1"\n"$2}' test.txt

>ATGATCTATCGTGTATCACGGTCA(1)
TGACCGTGATACACGATAGATCAT
>TACGGTTCTGAAACGGAGAGTTCG(1)
CGAACTCTCCGTTTCAGAACCGTA
>GCTTGCGACGACTGAGTTGGAG(1)
GCTTGCGACGACTGAGTTGGAG
>ATTACTTGTTGTGATTGTTGGCCT(1)
ATTACTTGTTGTGATTGTTGGCCT
>ATGCCGTCGGAAATAATGAGTTTA(1)
ATGCCGTCGGAAATAATGAGTTTA
>AACAGATCCGCTGTAGCACATCGG(1)
CCGATGTGCTACAGCGGATCTGTT
>TTGGCACGAGTGACTCCTTAGAC(1)
GTCTAAGGAGTCACTCGTGCCAA
>TTAAGCATGACTTAGACTATC(2)
TTAAGCATGACTTAGACTATC
>CAAAGGAACCGTGAGCTCAACT(1)
CAAAGGAACCGTGAGCTCAACT

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written 6.1 years ago by cpad0112

1 answer

It could be as simple as:

$ cat your_file | tr " " "\n"
>ATGATCTATCGTGTATCACGGTCA(1)
TGACCGTGATACACGATAGATCAT
>TACGGTTCTGAAACGGAGAGTTCG(1)
CGAACTCTCCGTTTCAGAACCGTA
>GCTTGCGACGACTGAGTTGGAG(1)
GCTTGCGACGACTGAGTTGGAG
>ATTACTTGTTGTGATTGTTGGCCT(1)
ATTACTTGTTGTGATTGTTGGCCT
>ATGCCGTCGGAAATAATGAGTTTA(1)
ATGCCGTCGGAAATAATGAGTTTA
>AACAGATCCGCTGTAGCACATCGG(1)
CCGATGTGCTACAGCGGATCTGTT
>TTGGCACGAGTGACTCCTTAGAC(1)
GTCTAAGGAGTCACTCGTGCCAA
>TTAAGCATGACTTAGACTATC(2)
TTAAGCATGACTTAGACTATC
>CAAAGGAACCGTGAGCTCAACT(1)
CAAAGGAACCGTGAGCTCAACT

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written 6.1 years ago by GenoMax