Remove fasta sequence on the basis of header name · Biostar

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Remove fasta sequence on the basis of header name

>exon18_ENST00000194900|exon19_ENST00000194900
GCTATCAAGAGACTGCAGCAAGCACAACTTTACCCCATTGCCATTTTCATCAAGCCCAAGTCCATTGAAGCCCTTATTACTACCCGGCCTCGACGTGATAATGAGGTGGATGGACAAGACTACCACTTTGTGGTGTCCCGAGAACAAATG
>exon18_ENST00000194900|exon21_ENST00000194900
TCTAACAGAGGAAGAACTGTATTATCAAACCTTATGGTCTACCCATGAATAAATAAAATATTTGTTCAAGCACAAATACTACCCGGCCTCGACGTGATAATGAGGTGGATGGACAAGACTACCACTTTGTGGTGTCCCGAGAACAAATGG
>exon18_ENST00000194900|exon20_ENST00000194900
CAGACATATGAACAAGCAAATAAGATCTATGACAAAGCCATGAAACTGGAGCAGGAATTTGGAGAGTACTTTACAGTACTACCCGGCCTCGACGTGATAATGAGGTGGATGGACAAGACTACCACTTTGTGGTGTCCCGAGAACAAATGG
>exon18_ENST00000194900|exon21_ENST00000194900
CTCTAACAGAGGAAGAACTGTATTATCAAACCTTATGGTCTACCCATGAATAAATAAAATATTTGTTCAAGCACAAATACTACCCGGCCTCGACGTGATAATGAGGTGGATGGACAAGACTACCACTTTGTGGTGTCCCGAGAACAAATG
>exon17_ENST00000194900|>exon17_ENST00000194900
ATGATGACCTGATCTCCGAATTTCCACATAAATTTGGATCCTGTGTGCCACTCACTATGCAAGGCCTGTGATCATCCTGGGCCCAATGAAGGACCGAGTCA
>exon19_ENST00000194900|exon21_ENST00000194900
TCTAACAGAGGAAGAACTGTATTATCAAACCTTATGGTCTACCCATGAATAAATAAAATATTTGTTCAAGCACAAAGCAAGCACTGCATCTTAGATGTTTCCGGCAATGCTATCAAGAGACTGCAGCAAGCACAACTTTACCCCATTGCC
>exon19_ENST00000194900|exon20_ENST00000194900
CAGACATATGAACAAGCAAATAAGATCTATGACAAAGCCATGAAACTGGAGCAGGAATTTGGAGAGTACTTTACAGGCAAGCACTGCATCTTAGATGTTTCCGGCAATGCTATCAAGAGACTGCAGCAAGCACAACTTTACCCCATTGCC
>exon19_ENST00000194900|exon21_ENST00000194900
CTCTAACAGAGGAAGAACTGTATTATCAAACCTTATGGTCTACCCATGAATAAATAAAATATTTGTTCAAGCACAAAGCAAGCACTGCATCTTAGATGTTTCCGGCAATGCTATCAAGAGACTGCAGCAAGCACAACTTTACCCCATTGC

In this example of fasta sequence, you see there is some repeat of fasta sequence many times.for example- exon19_ENST00000194900|exon21_ENST00000194900 , exon18_ENST00000194900|exon21_ENST00000194900 So I want to remove all fasta sequence which has the same header in the fasta file and keep only 1 fasta sequnece. I want to remove fasta sequence on the basis of header not the sequence. Thanks in advance

fasta header

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updated 5.4 years ago by 5heikki

• written 5.4 years ago by harry •

Try seqkit rmdup.

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written 5.4 years ago by cpad0112

1 answer

paste -d $'\t' - - <fastaFileWithNoLinebreaksInSeq | sort -t $'\t' -uk1,1 | awk 'BEGIN{FS="\t";OFS="\n"}{print $1,$2}'

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written 5.4 years ago by 5heikki

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