Replace spaces in linux for sequence file fasta

Question

I have an output file and I want to convert it to I file where I can extract whole sequences.

The output is like this: (but then without the " in front of the > and after each line there is an enter

">comp2_c0_seq1 len=265 path=[1:0-264]
GTTTGAATGGTTTGTGGTTCTGCCTTTGACAAACTGATCATAGTGGAATAATAAGGGAAC
ATGAAGAAATTCCAAGCCCATTGATTTTCTCTTGAGACCAATTAGGTAAAGTCACTCAAA
ATTTTTGAGAGTGGATGCTCAGAGGTAACACTTTGGCATAGAATTGTTAAATAGCATGCA
CTTTAATGGAAGAATAGAATCATTAAAGATTGGTTGATAACAAGTCACAGTGTATTTAAC
CATCATCACAGCAGATGTAGACAGA

">comp2_c1_seq1 len=203 path=[2794:0-202]
CAGCAGATGTAGACAGAAATGGCACCACTGCTTATGAAGGAAACTGGAACCCAGAAGCAC
ACCCTCCCCTCATTCACCATGAGCATCATGAGGAAGAAGAGACCCCACATTCTACAAGCA
CAAGTAAGCAAGATGGCGGTCGGCAGTTCTGGGTTAGATGAATTAGTAAAGACATTCCAG
CAATAGGGAAGATTTTGTTTAGA

">comp6_c0_seq1 len=424 path=[1744:0-423]
CCAGCTCCTACTCACCAGTCTCTCCGCATGGAGAAGTGGCCGTCATGGTCGACCTGTTCC
CAAGGGTGGCCTTGTGAGTGCAGGCTCTCCTCACCAGAGCTGAGGGCTTTGTGAACCTCT
GATGTCAATAGATGCCCCTCATCTTCCAGGAGGACAAAACAGGGCAAAGCAAGACATGGG
GTGAGAACAGGAGTGCATCAGTGGGGTTCCCCAAGCCTGTGTCAGGTCCGGATCTGGGTG
GGAGTTCCCTTCTGCGTCATCCAGGCCAGGCGAGTGGGCATCCTCCCTGAGCACCTGTGC
TTGGGGCTTTGCCTGTGTCAGTCAGGAAGACAGAGTACACGGAAGAGTTACCATTGCTTT
CAGAGCAAACCTTCCTTTGACATGCATTTAACACAGCACGGAGTGATTGACATGTGTCCT
TGTG

">comp7_c0_seq1 len=208 path=[22:0-207]
GGAAGGACAGCATGTTTTCCATCTCAAAGACAGGAAAGAGTTATCTCTTCCTCTGGGATC
CATCAGCATCCTGCCTACTCCTGCGTCACAGCACAGATCCTAACTGGCAAAATTATTAAT
CTCTCTTCCACTGAAATAGATACATCAGACAGATTCCTTTCTGACTGAAACTGTTCTGCT
GTGAAAGACTAACAACAAAGCAGATGCT

">comp8_c0_seq1 len=537 path=[1925:0-536]
TTAATAATTTAATTTTACTTTGAATATGTGTATATAAAATGCCTAATGTGATAAAAGTAG
AATATGCCTGGTTGAAGGAAACATAGAAAATTGAATTGCCACTGATTTGGCCTTTCCTTC
ATCTTTCATGGGGAGCCAGAGAGAATCTGGTTCAGAAGACAGACTCTAGAGTCAAGCAGC
TGGGGTTCAAATCTTGGCAACATTTCAGGGTGATTTTAAAAATATTTAACAGCTGGTAAT
GCTAGATGTCGACTTGTCAGAATGGATAAAGCCTGACATGACGTATATAGCCACACCAGC
ATATAATCAGCCCTGTCTCCACCACTTACTAGTAGTGTCTTTATCTGTAAGATAAAGATA
GCAATAGGCATTATCTCATAGGGGTTTTATGAGGATTAGGTGTAATAATATATATAAAGC
ACTTATGACAATGTTTGGAAGAAAGTGTCATTCAACATTAGATATCATCATCATTGTCAT
CATCGTGACTAATACTTGAGGAATTCCAGAATGTTATGGTTAGAATGGTAAAGTTCT

What I would like the have is this:

> ">comp2_c0_seq1 len=265 path=[1:0-264] GTTTGAATGGTTTGTGGTTCTGCCTTTGACAAACTGATCATAGTGGAATAATAAGGGAACATGAAGAAATTCCAAGCCCATTGATTTTCTCTTGAGACCAATTAGGTAAAGTCACTCAAAATTTTTGAGAGTGGATGCTCAGAGGTAACACTTTGGCATAGAATTGTTAAATAGCATGCACTTTAATGGAAGAATAGAATCATTAAAGATTGGTTGATAACAAGTCACAGTGTATTTAACCATCATCACAGCAGATGTAGACAGA

That every sequence is on the same line so I can easily extract sequences via grep. Hope this is possible.

thanks

Answer 1

This awk should do:

awk '{printf (/comp/&&NR>1?"\n":"")"%s",$0}' file
">comp2_c1_seq1 len=203 path=[2794:0-202]CAGCAGATGTAGACAGAAATGGCACCACTGCTTATGAAGGAAACTGGAACCCAGAAGCACACCCTCCCCTCATTCACCATGAGCATCATGAGGAAGAAGAGACCCCACATTCTACAAGCACAAGTAAGCAAGATGGCGGTCGGCAGTTCTGGGTTAGATGAATTAGTAAAGACATTCCAGCAATAGGGAAGATTTTGTTTAGA
">comp6_c0_seq1 len=424 path=[1744:0-423]CCAGCTCCTACTCACCAGTCTCTCCGCATGGAGAAGTGGCCGTCATGGTCGACCTGTTCCCAAGGGTGGCCTTGTGAGTGCAGGCTCTCCTCACCAGAGCTGAGGGCTTTGTGAACCTCTGATGTCAATAGATGCCCCTCATCTTCCAGGAGGACAAAACAGGGCAAAGCAAGACATGGGGTGAGAACAGGAGTGCATCAGTGGGGTTCCCCAAGCCTGTGTCAGGTCCGGATCTGGGTGGGAGTTCCCTTCTGCGTCATCCAGGCCAGGCGAGTGGGCATCCTCCCTGAGCACCTGTGCTTGGGGCTTTGCCTGTGTCAGTCAGGAAGACAGAGTACACGGAAGAGTTACCATTGCTTTCAGAGCAAACCTTCCTTTGACATGCATTTAACACAGCACGGAGTGATTGACATGTGTCCTTGTG
">comp7_c0_seq1 len=208 path=[22:0-207]GGAAGGACAGCATGTTTTCCATCTCAAAGACAGGAAAGAGTTATCTCTTCCTCTGGGATCCATCAGCATCCTGCCTACTCCTGCGTCACAGCACAGATCCTAACTGGCAAAATTATTAATCTCTCTTCCACTGAAATAGATACATCAGACAGATTCCTTTCTGACTGAAACTGTTCTGCTGTGAAAGACTAACAACAAAGCAGATGCT
">comp8_c0_seq1 len=537 path=[1925:0-536]TTAATAATTTAATTTTACTTTGAATATGTGTATATAAAATGCCTAATGTGATAAAAGTAGAATATGCCTGGTTGAAGGAAACATAGAAAATTGAATTGCCACTGATTTGGCCTTTCCTTCATCTTTCATGGGGAGCCAGAGAGAATCTGGTTCAGAAGACAGACTCTAGAGTCAAGCAGCTGGGGTTCAAATCTTGGCAACATTTCAGGGTGATTTTAAAAATATTTAACAGCTGGTAATGCTAGATGTCGACTTGTCAGAATGGATAAAGCCTGACATGACGTATATAGCCACACCAGCATATAATCAGCCCTGTCTCCACCACTTACTAGTAGTGTCTTTATCTGTAAGATAAAGATAGCAATAGGCATTATCTCATAGGGGTTTTATGAGGATTAGGTGTAATAATATATATAAAGCACTTATGACAATGTTTGGAAGAAAGTGTCATTCAACATTAGATATCATCATCATTGTCATCATCGTGACTAATACTTGAGGAATTCCAGAATGTTATGGTTAGAATGGTAAAGTTCT

Answer 2

You can try this sed,

sed '/">comp/{:loop; N; /\n">comp/{P;D}; s/\n//g; b loop;}' yourfile.txt