How to find shortest lenth or longest length from fasta file
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12 weeks ago
Neel ▴ 20

Hi, I am trying to sort shortest length and longest length fasta seq of amino acids from fasta file. If anyone know anything about it please let me know.

GNNVVIGAGAKVLGSFKVGDNVKIGAGSVVNKVVPSDTTVVGIPGRIVLHNGVPIKDPDL
RHDELPDPVNEMLKCLMQRVEYLEERLNDEESRYNVFEIIQHHDTSKRGVPPKGERESCD
VRVRSNDL
>tr|A0A3D3WF91|A0A3D3WF91_9PROT
MRGFIDELRSIRERDPAAGGLLGLMFLTPSVHVMLAYRLGHRLWRWRMRFLARFTMQLAR
WFTGIEIHPAARIGKRFFIDHGMGVVIGETAVIGDDVTFYHGVTLGGLLPSVDSDGQRQK
KRHPTIRNNVIVGAGAQILGAITVNECARVGANSVVVKDVPQGTTVTGIPARPVSARRVT
DETTFQPYGTPSDLSSDARDKAIKGLLREVDILHNKLKMLEDLQGEAKQSESSFQPEATS
LSASDRN
>tr|Q2JWT3|Q2JWT3_SYNJA
MLTESSRVSGTKSLPSAVESPETGGSDSPSSAKPEPKLGFWQQFWEDIDCVFERDPAARN
RWEVLLTYPGVHALFLHRIAHWLWKRRCFFLARLLSFISRSFTLIEIHPAARIGRRFFID
HGCGVVIGETAEIGDDVTLYHGVTLGGTSWTKGKRHPTLEDGVIVGTGAKILGPVRIGAR
ARIGANAVVIQDVAPGMTVVGIPGRAVIPPHQRRIPAHGIDLDHHLMPDPVGRAIEQLLH
RIQELEAQVARLNQEREQDRQDQVRCE
>sp|P0A9D5|CYSE_ECOL6
MSCEELEIVWNNIKAEARTLADCEPMLASFYHATLLKHENLGSALSYMLANKLSSPIMPA
IAIREVVEEAYAADPEMIASAACDIQAVRTRDPAVDKYSTPLLYLKGFHALQAYRIGHWL
WNQGRRALAIFLQNQVSVTFQVDIHPAAKIGRGIMLDHATGIVVGETAVIENDVSILQSV
TLGGTGKSGGDRHPKIREGVMIGAGAKILGNIEVGRGAKIGAGSVVLQPVPPHTTAAGVP
ARIVGKPDSDKPSMDMDQHFNGINHTFEYGDGI

Thank you!

fasta • 435 views
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this looks suspiciously like homework ...

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0
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use seqkit sort sequences by length

$ seqkit -w 0 --quiet sort -l test.fa
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Hi, i used this script, which result is given below but i want to find the seq which is shortest and longest in all seq of fasta file.

"awk '/^>/{if (l!="") print l; print; l=0; next}{l+=length($0)}END{print l}' file.fasta"

>tr|A0A0B4WZN6|A0A0B4WZN6_9HYPH Serine acetyltransferase OS=Rhizobium gallicum bv. gallicum R602sp OX=1041138 GN=cysE PE=3 SV=1
276
>tr|A0A2A5GE89|A0A2A5GE89_9GAMM Serine acetyltransferase OS=Porticoccaceae bacterium OX=2026782 GN=cysE PE=3 SV=1
280
>tr|A0A5F0DFU6|A0A5F0DFU6_9MICO Serine acetyltransferase OS=Cryobacterium sp. HLT2-28 OX=1259146 GN=cysE PE=3 SV=1
192

Thank you|

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Thank you so much to all for your reply

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11 weeks ago
Jesse ▴ 170

seqmagick has a feature for summarizing sequence files that gives minimum and maximum length:

$ seqmagick info file.fasta 
name       alignment    min_len   max_len   avg_len  num_seqs
file.fasta FALSE            128       273    228.75         4
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