CODEWITHSUNDEEP
linuxcsv
dang
dang

Reputation: 2412

Fasta file - line issues

I have a FASTA file test.fasta which has the following information:

>QWE2J2_DEFR00000200123 DEFR00000560077.11 DEFR00000100333.7 3:444563-33443(-
)
acccaaagggagggagagagggctattatcatggaaaactaatttttcccagagaatttcctttcaaacctcccagtatc
tatgatcactcccaacgggaggtttaagtgcaacaccaggctgtgtctttctatcacggatttccacccggacacgtgga
acccggcctggtctgtctccaccatcctgactgggctcctgagcttcatggtggagaagggccccaccctgggcagtata
gagacgtcggacttcacgaaaagacaactggcagtgcagagaaaaggggggggggggggggataaagtcttttgtgaatt
atttcctgaagtcgtggaggagattaaacaaaaacagaaagcacaagacgaactcagtagcagaccccagactctcccct
tgccagacgtggttccagaaaaaaaaaaaaacctcgtccagaacgggattcagctgctcaacgggcatgcgccgggggcc
gtcccaaacctcgcagggctccagcaggccaaccggcaccacggactcctgggtggcgccctggcgaacttgtttgtgat
agttgggtttgcagcctttgcttacacggtcaagtaggggggggggggggcgcaggagtg

I need to convert it to CSV in the following format:

>QWE2J2_DEFR00000200123,DEFR00000560077.11,DEFR00000100333.7,3:444563-33443(-),acccaaagggagggagagagggctattatcatggaaaactaatttttcccagagaatttcctttcaaacctcccagtatctatgatcactcccaacgggaggtttaagtgcaacaccaggctgtgtctttctatcacggatttccacccggacacgtggaacccggcctggtctgtctccaccatcctgactgggctcctgagcttcatggtggagaagggccccaccctgggcagtatagagacgtcggacttcacgaaaagacaactggcagtgcagagaaaaggggggggggggggggataaagtcttttgtgaattatttcctgaagtcgtggaggagattaaacaaaaacagaaagcacaagacgaactcagtagcagaccccagactctccccttgccagacgtggttccagaaaaaaaaaaaaacctcgtccagaacgggattcagctgctcaacgggcatgcgccgggggccgtcccaaacctcgcagggctccagcaggccaaccggcaccacggactcctgggtggcgccctggcgaacttgtttgtgatagttgggtttgcagcctttgcttacacggtcaagtaggggggggggggggcgcaggagtg

I have tried in Linux terminal:

input_file=test.fasta; vim -c '0,$s/>\(.*\)\n/>\1,/' -c '0,$s/\(.*\)\n\([^>]\)/\1\2/' -c 'w! my-tmp.fasta.csv' -c 'q!'  $input_file; mv my-tmp.fasta.csv $input_file.csv

However, it gives me wrong output:

>QWE2J2_DEFR00000200123 DEFR00000560077.11 DEFR00000100333.7 3:444563-33443(-,)acccaaagggagggagagagggctattatcatggaaaactaatttttcccagagaatttcctttcaaacctcccagtatctatgatcactcccaacgggaggtttaagtgcaacaccaggctgtgtctttctatcacggatttccacccggacacgtggaacccggcctggtctgtctccaccatcctgactgggctcctgagcttcatggtggagaagggccccaccctgggcagtatagagacgtcggacttcacgaaaagacaactggcagtgcagagaaaaggggggggggggggggataaagtcttttgtgaattatttcctgaagtcgtggaggagattaaacaaaaacagaaagcacaagacgaactcagtagcagaccccagactctccccttgccagacgtggttccagaaaaaaaaaaaaacctcgtccagaacgggattcagctgctcaacgggcatgcgccgggggccgtcccaaacctcgcagggctccagcaggccaaccggcaccacggactcctgggtggcgccctggcgaacttgtttgtgatagttgggtttgcagcctttgcttacacggtcaagtaggggggggggggggcgcaggagtg

How can I create this CSV file?

Upvotes: 0

Views: 36

Answers (1)

KamilCuk
KamilCuk

Reputation: 141190

Using awk with RS set to > is just simple:

awk -vRS='>' 'NR>1{
    gsub(/ /, ",")
    sub(/\)\n/, "),")
    gsub("\n", "")
    print RS $0
}' file

GNU sed with -z looks simple too:

sed -z '
    s/ /,/g
    s/)\n/),/g
    s/\n//g
    s/>/\n>/g
    s/^\n//
' file

The following sed script should also work:

sed -n '
    # if line does not start with >
    /^>/!{
        # append the line to hold space
        H
        # if its not the end of file, start over
        $!b
    }
    # switch pattern space with hold space
    x
    # add a comma after )
    s/)/),/
    # remove all the newlines
    s/\n//g
    # print it all, if hold space not empty
    /^$/!p
    # switch pattern space with hold space
    x
    # replace spaces with comma
    s/ /,/g
    # hold the line
    h
' file

Scripts written and tested on repl:

>QWE2J2_DEFR00000200123,DEFR00000560077.11,DEFR00000100333.7,3:444563-33443(-),acccaaagggagggagagagggctattatcatggaaaactaatttttcccagagaatttcctttcaaacctcccagtatcacccggcctggtctgtctccaccatcctgactgggctcctgagcttcatggtggagaagggccccaccctgggcagtataatttcctgaagtcgtggaggagattaaacaaaaacagaaagcacaagacgaactcagtagcagaccccagactctcccctgtcccaaacctcgcagggctccagcaggccaaccggcaccacggactcctgggtggcgccctggcgaacttgtttgtgat

Prefer sed instead of vim.

Upvotes: 1

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