How to fetch fasta sequences corresponding to header lines in another file
2
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5
answers
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I have a file of lines of headers (
file1
) and another file is sequences in fasta format (file2
). I want to grep fasta sequences if a header line from file1
is present in file2
.
Example:
* file1
:
>sp|B7UM99|TIR_ECO27
>sp|P06616|ERA_ECOLI
* file2
:
>sp|B7UM99|TIR_ECO27
MPIGNLGNNVNGNHLIPPAPPLPSQTDGAA
RGGTGHLISSTGALGSRSLFSPLRNSMADS
VDSRDIPGLPTNPSRLAAATSETCLLGGFE
VLHDKGPLDILNTQIGPSAFRVEVQADGTH
......
>sp|P06616|ERA_ECOLI
MSIDKSYCGFIAIVGRPNVGKSTLLNKLL
GQKISITSRKAQTTRHRIVGIHTEGAYQAIY
VDTPGLHMEEKRAINRLMNKAASSSIGDVE
LVIFVVEGTRWTPDDEMVLNKLREGKAPVI
............
>sp|P0AD68|HUMAN
MKAAAKTQKPKRQEEHANFISWRFALLCGC
ILLALAFLLGRVAWLQVISPDMLVKEGDMR
SLRVQQVSTSRGMITDRSGRPLAVSVPVKA
IWADPKEVHDAGGISVGDRWKALANALNIP
.............
* Desired output
>sp|B7UM99|TIR_ECO27
MPIGNLGNNVNGNHLIPPAPPLPSQTDGAA
RGGTGHLISSTGALGSRSLFSPLRNSMADS
VDSRDIPGLPTNPSRLAAATSETCLLGGFE
VLHDKGPLDILNTQIGPSAFRVEVQADGTH
......
>sp|P06616|ERA_ECOLI
MSIDKSYCGFIAIVGRPNVGKSTLLNKLL
GQKISITSRKAQTTRHRIVGIHTEGAYQAIY
VDTPGLHMEEKRAINRLMNKAASSSIGDVE
LVIFVVEGTRWTPDDEMVLNKLREGKAPVI
............
Asked by Manoj Kumar
(41 rep)
May 9, 2019, 08:25 PM
Last activity: Apr 14, 2024, 06:48 AM
Last activity: Apr 14, 2024, 06:48 AM