Want to reverse the fasta sequence

Question

[harry]

>ENST00000014935
TAGGTTTTTAATTACCTTTATTTTATTTTGCCAAACATACCTGGGAATACCTTTTATTTTTTTTTTACCTTGGGGTGATGGTTCCAAACCATAAATGTGATTATAGTTAACACATGACCCTTCTAGCGTCCCAGCCAGTGTTTTTCCTGACCTCTCTTCTTTGGAGAGGAGGATGGAAGGGAGGGGTCCGGCATGCTGCTGGCATTTTGCTGTGTCCTGCAGCCCCTTTCCGGGACACCTGGGTTCACACAGCTTTTTAGCTTACATAACTGGTGCAGATTTTCTGTGTGGAGATGTTGCCTTGACCAGCCTTGGCTGGACTTTACCAGGCATGCAGAAGCCTGTACCAACACAGACTACAGCACCCAGGAGGTGCGAGTGTGGCTGCTCAGCGGTTATAACAGGCCTGACTGCATTGTTCACCGGATTATAATGAGCCAAAATGTTTCCCGGTGTTTGCTGGTTTCAGGGAAGGAGTTTGATATAGCAGATTAACCACCCTCCTTGTAGCTATTGGGGCTTAATGGTTTCCTGGTGATTCTTACCAATCCACAATAAACATGGCCCATTGGCATATCTGCTGCACAAGTGTCCTATCTCACCAATCTGGGTTTTTGTTCTCAGTAACTTTCCTTCTTGTCATACAACATCTTCATTCCTCTTTCTGAACCCTCCCTTCCCCTACCCCAACCCAGAGCCCACTTTGTCTCCACTCCTGATACTACACTACCTGGCAGGTGGCATGAGTGCAGGGCCCCTGGCTTCCTCTCCTAATCTAGGCACAAGCCCAACCAAAGAACAAGAGCCAAATCAAACAAGGCAGGCAGGGGTGGACTACAGTCACAGGGCAACTATAGTTGAAGCCCCCCAGCCCCAGGGCTGGATGGACGGGGGAGGCTGGGGTTTAAGTCCCAAAAGGCAGCAGGCCCTGGGGGGGTAGGGGGACGCTCAGGCAGCAGGGCACAGCTGAGGGGACAGGAGTGATAGCAGCAACAGAACAGTGAGGCTGAGAGGCTGGACGCTGTGCGCCTGGCTCAGCTTCAGCTCCACCTCCACGGGGTAGTGGTCACTGATGTTGAGGGC
>ENST00000014944
TCCTCCTCGGTGAGCTGGAAGCTCGTGGGGAAGTCAAAGGCAGCCGCAGTGTGCAGCAGACTCCGGCAGCGCTCCCCGTGCAGCACGACGCGGTCATAGGTGCAGTGGGTGCTGGCCCGCACTGTGGTGTCCTCCCCATCGGCAATCACCCAGTGGAAGCCTGGCTCAGTCCGCAGCTCCAGCTTGTCCAGGCGCTTTTTGGTCAGTGAAGCGCAGTCAGCATTGAAGTCCCCAAGCAGGATCACGTC

Likewise, I have a huge fasta sequence and I want to reverse the sequence of those fasta sequences like below:-

>ENST00000014935
CGGGAGTTGTAGTCACTGGTGATGGGGCACCTCCACCTCGACTTCGACTCGGTCCGCGTGTCGCAGGTCGGAGAGTCGGAGTGACAAGACAACGACGATAGTGAGGACAGGGGAGTCGACACGGGACGACGGACTCGCAGGGGGATGGGGGGGTCCCGGACGACGGAAAACCCTGAATTTGGGGTCGGAGGGGGCAGGTAGGTCGGGACCCCGACCCCCCGAAGTTGATATCAACGGGACACTGACATCAGGTGGGGACGGACGGAACAAACTAAACCGAGAACAAGAAACCAACCCGAACACGGATCTAATCCTCTCCTTCGGTCCCCGGGACGTGAGTACGGTGGACGGTCCATCACATCATAGTCCTCACCTCTGTTTCACCCGAGACCCAACCCCATCCCCTTCCCTCCCAAGTCTTTCTCCTTACTTCTACAACATACTGTTCTTCCTTTCAATGACTCTTGTTTTTGGGTCTAACCACTCTATCCTGTGAACACGTCGTCTATACGGTTACCCGGTACAAATAACACCTAACCATTCTTAGTGGTCCTTTGGTAATTCGGGGTTATCGATGTTCCTCCCACCAATTAGACGATATAGTTTGAGGAAGGGACTTTGGTCGTTTGTGGCCCTTTGTAAAACCGAGTAATATTAGGCCACTTGTTACGTCAGTCCGGACAATATTGGCGACTCGTCGGTGTGAGCGTGGAGGACCCACGACATCAGACACAACCATGTCCGAAGACGTACGGACCATTTCAGGTCGGTTCCGACCAGTTCCGTTGTAGAGGTGTGTCTTTTAGACGTGGTCAATACATTCGATTTTTCGACACACTTGGGTCCACAGGGCCTTTCCCCGACGTCCTGTGTCGTTTTACGGTCGTCGTACGGCCTGGGGAGGGAAGGTAGGAGGAGAGGTTTCTTCTCTCCAGTCCTTTTTGTGACCGACCCTGCGATCTTCCCAGTACACAATTGATATTAGTGTAAATACCAAACCTTGGTAGTGGGGTTCCATTTTTTTTTTATTTTCCATAAGGGTCCATACAAACCGTTTTATTTTATTTCCATTAATTTTTGGAT
>ENST00000014944
CTGCACTAGGACGAACCCCTGAAGTTACGACTGACGCGAAGTGACTGGTTTTTCGCGGACCTGTTCGACCTCGACGCCTGACTCGGTCCGAAGGTGACCCACTAACGGCTACCCCTCCTGTGGTGTCACGCCCGGTCGTGGGTGACGTGGATACTGGCGCAGCACGACGTGCCCCTCGCGACGGCCTCAGACGACGTGTGACGCCGACGGAAACTGAAGGGGTGCTCGAAGGTCGAGTGGCTCCTCCT

Can anyone tell me how can I do this. Thanks in advance.

[cpad0112]

you can try (for flattened fasta):

$ paste  <(grep ">" test.fa) <(grep -v ">" test.fa|rev) | awk -v OFS="\n" '{print $1,$2}'

or use revseq -nocomplement from EMBOSS.

[MSRS]

fasta - reverse complement sequence previously answed. Please have a look.

[harry]

I don't want reverse complementary sequence, I just want to only reverse the sequence.

[GenoMax]

If you only want to reverse then change @Pierre's solution to:

cat input.fa | while read L; do  echo $L; read L; echo "$L" | rev ; done

[GenoMax]

harry : Don't forget to follow up on your past threads.

If an answer/comment was helpful, you should upvote it; if the answer resolved your question, you should mark it as accepted. You can accept more than one if they work.

[harry]

Can anyone help me if I have the fasta file in tab separated format which I got from bedtools get fasta. Then is there a way to get the reverse sequence of that fasta sequence.

Thanks in advance

[ATpoint]

bedtools getfasta returns a normal fasta, not tab. Please be more precise what the problem is.

[harry]

bedtools getfasta option see below, so as i used -tab option then how i reverse the sequence of the output fasta sequence.

-fi     Input FASTA file
        -fo     Output file (opt., default is STDOUT
        -bed    BED/GFF/VCF file of ranges to extract from -fi
        -name   Use the name field for the FASTA header
        -name+  Use the name field and coordinates for the FASTA header
        -split  given BED12 fmt., extract and concatenate the sequences
                from the BED "blocks" (e.g., exons)
        -tab    Write output in TAB delimited format.
                - Default is FASTA format.

        -s      Force strandedness. If the feature occupies the antisense,
                strand, the sequence will be reverse complemented.
                - By default, strand information is ignored.

        -fullHeader     Use full fasta header.
                - By default, only the word before the first space or tab
                is used.

Thanks in advance for helping me to sort this issue.

[ATpoint]

Don't use tab ¯_(ツ)_/¯

If you need the reversed fasta (output of the bioawk command) as tab-separated file then you can do:

(...) | bioawk-command | tr "\n" "\t"

That will replace the newline character \n by tab so you should have the name of the sequence in column1 and the sequence itself in column2.

So 1) get fasta with bedtools, 2) reverse it with bioawk, 3) get tabdelimited file with tr.

Does that make sense in your case?

[harry]

Hi, I tried it but again I didn't get the reverse sequence. I don't know why is it happen. this command is done fine with pipe command or not. Thanks in advance

[ATpoint]

I cannot see your screen or your data, cannot comment unfortunately.

Answer 1

[ATpoint]

awk '$1 ~ /^>/ {print $0;next} {print $0 | "rev"}' test.fa

Edit: Forget about cumbersome awk, and just use bioawk (bioawk Github):

cat test.fa 
>foo
AATTGGC
GGAT
TGATCGATCGATCGAC
>bar
GGT
TTTTTT
>gee
TATCGACTGACTTTTTTTTTTT

bioawk -c fastx '{print ">"$name;print reverse($seq)}' test.fa 
>foo
CAGCTAGCTAGCTAGTTAGGCGGTTAA
>bar
TTTTTTTGG
>gee
TTTTTTTTTTTCAGTCAGCTAT

[MutationalMeltdown]

This will not handle multi-line fasta (which is pretty common) correctly since each line is reversed individually

[ATpoint]

Correct! Edited it.

Answer 2

[predeus]

If you sequence is unfolded (two lines per sequence), you can do

perl -ne 'if (/^>/) {print} else {chomp; $rev = reverse($_); print "$rev\n"}' file.fa > rev.fa

If it's folded, you can unfold it first:

seqtk seq -l 0 file.fa | perl -ne 'if (/^>/) {print} else {chomp; $rev = reverse($_); print "$rev\n"}' > rev.fa

(If you don't have seqtk, you can get it via conda, or just download the binary from GitHub)

[cpad0112]

Better to use seqtk seq -r file.fa for revcomp.

[predeus]

The original poster wanted reverse, not revcomp.

[cpad0112]

You are right. I misread the OP.