Thank you sir! This worked perfectly.
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How do I add ">" symbol to FASTA headers?
Dear community,
How do I add the ">" symbol to FASTA headers? I searched for other similar posts but none of them worked for me. Can I add the symbol with sed or awk? What would be the command? I want to add ">" to all the headers. Thanks in advance!
Input file (example):
Proteus_mirabilis_ARLG2970_2781
atggagacaggtacagtaaagtggttcaataatgctaagggctttggttttattaccccagcaaacggtg
gcgaagatatttttgcccactattcaacaattagaatggaaggctaccgcacacttaaagcggggcagaa
agttaattatagcacgataaaagggcctaaaggtgaccatactgaccttatcattcctatcattgaatag
Proteus_mirabilis_ARLG2970_0131
atgtctgacaaaatgaaaggtcaagttaagtggttcaacgagtctaaaggctttggttttattactccag
cagacggaagcaaagacgtattcgttcacttttctgccattcaaggtaacggtttcaaaactctggctga
aggtcagaacgtagaattcacaattgaaaacggtgcaaaaggtccagcagcagctaacgtaacagctctg
taa
Proteus_penneri_ATCC35198_1543
ttacagagcagttacgttagcagctgctggaccttttgcaccgttttcaattgtgaattctacgttctga
ccttcagccagagttttgaaaccgttaccttgaatggcagaaaagtgaacgaatacgtctttgcttccgt
ctgctggagtaataaaaccaaagcctttagactcgttgaaccacttaacttgacctttcattttgtcaga
cat
Proteus_vulgaris_FDAARGOS366_2819
ttagagagccaccacgttgcctgctgctgggcctttcataccattttccatggtgaatgaaacttgttgc
ccttcagctaatgttttgaagctatcactttggattgcagagaaatgtacgaatacatctttgctgccat
cagctggagtaataaaaccaaaacctttaccttcatcgaaccattttactgtaccagtcattgtattaga
cat
Proteus_mirabilis_ARLG2970_2695
ttacagagcgattacgttcgctgctgcagggcctttagcgccattttcaatagaaaatgaaacttcttgg
ccttctttcagtgacttgaagctttcactttggatcgctgaaaagtgtacgaatacgtctttgctaccgt
ctttaggagtgataaaaccgaagcctttatcatcgttaaaccattttactgtaccagtcattgtattaga
cat
Desired output: before each Proteus_.....................................etc, I want to add the ">" symbol.
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GenoMax
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Alec Watanabe
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Alec Watanabe
3 answers
$ awk '{ if ($0 ~ /_/) { printf ">"; } print $0; }' in.fa > out.fa
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Alex Reynolds
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Can you confirm if the sequences (Proteus word) is on a new line each time? It did not look like that before a mod possibly edited the post.
If they are on a separate lines then a simple
sed 's/Proteus/\>Proteus/g' your_file > new_filewill work.Thank you for your preoccupation kind sir! The headers are indeed on a new line as should be for a FASTA file. It's just that I'm new to Biostars and don't really know how to edit the text I post.