how to fatch fasta sequences if header line match from another fileGetting matched fasta fileRemove line...
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how to fatch fasta sequences if header line match from another file
Getting matched fasta fileRemove line breaks in a FASTA fileExtracting subset from fasta fileExtract sequences from a fasta fileOnly one line break in fasta filehow to remove newline characters in fasta sequenceHow to match a pattern in lines before another pattern matchextract fasta entries from list using while readHow to match a column from File1 to get its corresponding fasta sequences in File 2?replace header in a file with list of lines in another file
.everyoneloves__top-leaderboard:empty,.everyoneloves__mid-leaderboard:empty,.everyoneloves__bot-mid-leaderboard:empty{ margin-bottom:0;
}
I have a file of lines of headers (file 1) and another file is sequences in fasta format (file 2). I want grep fasta sequences if header line from file 1 match from file 2.
Example:
File 1:
>sp|B7UM99|TIR_ECO27
>sp|P06616|ERA_ECOLI
File 2:
>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
............
linux text-processing bioinformatics
edited 3 hours ago
Kusalananda♦
145k18274454
asked 3 hours ago
Manoj KumarManoj Kumar
12
add a comment |
I have a file of lines of headers (file 1) and another file is sequences in fasta format (file 2). I want grep fasta sequences if header line from file 1 match from file 2.
Example:
File 1:
>sp|B7UM99|TIR_ECO27
>sp|P06616|ERA_ECOLI
File 2:
>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
............
linux text-processing bioinformatics
edited 3 hours ago
Kusalananda♦
145k18274454
asked 3 hours ago
Manoj KumarManoj Kumar
12
add a comment |
I have a file of lines of headers (file 1) and another file is sequences in fasta format (file 2). I want grep fasta sequences if header line from file 1 match from file 2.
Example:
File 1:
>sp|B7UM99|TIR_ECO27
>sp|P06616|ERA_ECOLI
File 2:
>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
............
linux text-processing bioinformatics
edited 3 hours ago
Kusalananda♦
145k18274454
asked 3 hours ago
Manoj KumarManoj Kumar
12
I have a file of lines of headers (file 1) and another file is sequences in fasta format (file 2). I want grep fasta sequences if header line from file 1 match from file 2.
Example:
File 1:
>sp|B7UM99|TIR_ECO27
>sp|P06616|ERA_ECOLI
File 2:
>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
............
linux text-processing bioinformatics
linux text-processing bioinformatics
edited 3 hours ago
Kusalananda♦
145k18274454
asked 3 hours ago
Manoj KumarManoj Kumar
12
edited 3 hours ago
Kusalananda♦
145k18274454
asked 3 hours ago
Manoj KumarManoj Kumar
12
edited 3 hours ago
Kusalananda♦
145k18274454
edited 3 hours ago
Kusalananda♦
145k18274454
edited 3 hours ago
Kusalananda♦
145k18274454
145k18274454
asked 3 hours ago
Manoj KumarManoj Kumar
12
asked 3 hours ago
Manoj KumarManoj Kumar
12
asked 3 hours ago
Manoj KumarManoj Kumar
12
12
add a comment |
add a comment |
1 Answer
1
active
oldest
votes
grep has -f flag which allows using patterns from file, and in your case we also need 5 lines agtee the matching header. Thus what we can do is
grep -A5 -f file1.txt file2.txt
Note that files are assumed to be in current working directory. If they are not, use cd command to navigate there or provide full paths to each file
answered 46 mins ago
Sergiy KolodyazhnyySergiy Kolodyazhnyy
10.8k42765
it has still following error ........... grep: final-out.txt:23097: Invalid range end
– Manoj Kumar
19 mins ago
Moreover, I tried with the command... grep -F -A10 -f final-out.txt output.fasta >database.fasta But, it is showing sequences which are not in file 1.
– Manoj Kumar
7 mins ago
add a comment |
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1 Answer
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active
oldest
votes
1 Answer
1
active
oldest
votes
active
oldest
votes
active
oldest
votes
grep has -f flag which allows using patterns from file, and in your case we also need 5 lines agtee the matching header. Thus what we can do is
grep -A5 -f file1.txt file2.txt
Note that files are assumed to be in current working directory. If they are not, use cd command to navigate there or provide full paths to each file
answered 46 mins ago
Sergiy KolodyazhnyySergiy Kolodyazhnyy
10.8k42765
it has still following error ........... grep: final-out.txt:23097: Invalid range end
– Manoj Kumar
19 mins ago
Moreover, I tried with the command... grep -F -A10 -f final-out.txt output.fasta >database.fasta But, it is showing sequences which are not in file 1.
– Manoj Kumar
7 mins ago
add a comment |
grep has -f flag which allows using patterns from file, and in your case we also need 5 lines agtee the matching header. Thus what we can do is
grep -A5 -f file1.txt file2.txt
Note that files are assumed to be in current working directory. If they are not, use cd command to navigate there or provide full paths to each file
answered 46 mins ago
Sergiy KolodyazhnyySergiy Kolodyazhnyy
10.8k42765
it has still following error ........... grep: final-out.txt:23097: Invalid range end
– Manoj Kumar
19 mins ago
Moreover, I tried with the command... grep -F -A10 -f final-out.txt output.fasta >database.fasta But, it is showing sequences which are not in file 1.
– Manoj Kumar
7 mins ago
add a comment |
grep has -f flag which allows using patterns from file, and in your case we also need 5 lines agtee the matching header. Thus what we can do is
grep -A5 -f file1.txt file2.txt
Note that files are assumed to be in current working directory. If they are not, use cd command to navigate there or provide full paths to each file
answered 46 mins ago
Sergiy KolodyazhnyySergiy Kolodyazhnyy
10.8k42765
grep has -f flag which allows using patterns from file, and in your case we also need 5 lines agtee the matching header. Thus what we can do is
grep -A5 -f file1.txt file2.txt
Note that files are assumed to be in current working directory. If they are not, use cd command to navigate there or provide full paths to each file
answered 46 mins ago
Sergiy KolodyazhnyySergiy Kolodyazhnyy
10.8k42765
answered 46 mins ago
Sergiy KolodyazhnyySergiy Kolodyazhnyy
10.8k42765
answered 46 mins ago
Sergiy KolodyazhnyySergiy Kolodyazhnyy
10.8k42765
answered 46 mins ago
Sergiy KolodyazhnyySergiy Kolodyazhnyy
10.8k42765
10.8k42765
it has still following error ........... grep: final-out.txt:23097: Invalid range end
– Manoj Kumar
19 mins ago
Moreover, I tried with the command... grep -F -A10 -f final-out.txt output.fasta >database.fasta But, it is showing sequences which are not in file 1.
– Manoj Kumar
7 mins ago
add a comment |
it has still following error ........... grep: final-out.txt:23097: Invalid range end
– Manoj Kumar
19 mins ago
Moreover, I tried with the command... grep -F -A10 -f final-out.txt output.fasta >database.fasta But, it is showing sequences which are not in file 1.
– Manoj Kumar
7 mins ago
it has still following error ........... grep: final-out.txt:23097: Invalid range end
– Manoj Kumar
19 mins ago
it has still following error ........... grep: final-out.txt:23097: Invalid range end
– Manoj Kumar
19 mins ago
Moreover, I tried with the command... grep -F -A10 -f final-out.txt output.fasta >database.fasta But, it is showing sequences which are not in file 1.
– Manoj Kumar
7 mins ago
Moreover, I tried with the command... grep -F -A10 -f final-out.txt output.fasta >database.fasta But, it is showing sequences which are not in file 1.
– Manoj Kumar
7 mins ago
add a comment |
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