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adityagt15 •
Pattren counter in fasta file
I am trying to get the count of the matching pattren in the fasta file. i am having the fasta files which contains 57k sequences. i want to pull out the count of my matching pattern sequence. And required the starting position of the pattren Input file:
chr1 ATTAGCAGATGTGACGTCGATGTCAGATTG
chr2 TGAGCTGCAGATCGTAGATGATTCTGCAGGAACCT
chr3 TCTTTCAGATGCCTCTGCAGATTC
Searching pattern "CAGAT"
Output Required:
chr Count P1 P2
chr1 -- 2 -- 6 -- 25
chr2 -- 1 -- 8
chr3 -- 2 -- 6 -- 19
Thanks in advance
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cpad0112
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adityagt15 •
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adityagt15 •
3 answers
You can also try SeqKit.
$ seqkit locate -p CAGAT seqs.fa | column -t
seqID patternName pattern strand start end matched
chr1 CAGAT CAGAT + 6 10 CAGAT
chr1 CAGAT CAGAT + 24 28 CAGAT
chr2 CAGAT CAGAT + 8 12 CAGAT
chr3 CAGAT CAGAT + 6 10 CAGAT
chr3 CAGAT CAGAT + 18 22 CAGAT
$ seqkit locate -p CAGAT seqs.fa --bed
chr1 5 10 CAGAT 0 +
chr1 23 28 CAGAT 0 +
chr2 7 12 CAGAT 0 +
chr3 5 10 CAGAT 0 +
chr3 17 22 CAGAT 0 +
$ seqkit locate -p CAGAT seqs.fa --gtf
chr1 SeqKit location 6 10 0 + . gene_id "CAGAT";
chr1 SeqKit location 24 28 0 + . gene_id "CAGAT";
chr2 SeqKit location 8 12 0 + . gene_id "CAGAT";
chr3 SeqKit location 6 10 0 + . gene_id "CAGAT";
chr3 SeqKit location 18 22 0 + . gene_id "CAGAT";
Count of every sequences with help of csvtk:
$ seqkit locate -p CAGAT seqs.fa | csvtk freq -t -f seqID -k
seqID frequency
chr1 2
chr2 1
chr3 2
# multiple search patterns
$ seqkit locate -p CAGAT -p TTC seqs.fa | csvtk freq -t -f seqID,patternName -k | column -t
seqID patternName frequency
chr1 CAGAT 2
chr2 CAGAT 1
chr2 TTC 2
chr3 CAGAT 2
chr3 TTC 2
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shenwei356
If interested, I wrote a program for this kind of searches, it's here fastaRegexFinder
is this the way i have to give input
python code.py -f singleline.fasta -m 'CTGCAG'
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adityagt15 •
Thanks for your response , its working..
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adityagt15 •
for R coders:
my fasta file:
>chr1
ATTAGCAGATGTGACGTCGATGTCAGATTG
>chr2
TGAGCTGCAGATCGTAGATGATTCTGCAGGAACCT
>chr3
TCTTTCAGATGCCTCTGCAGATTC
R code
library(Biostrings)
data=readDNAStringSet("~/Desktop/test.fa", format = "fasta")
query=DNAString("CAGAT")
result=as.data.frame(vmatchPattern(query,data))
result
> result
group group_name start end width
1 1 <NA> 6 10 5
2 1 <NA> 24 28 5
3 2 <NA> 8 12 5
4 3 <NA> 6 10 5
5 3 <NA> 18 22 5
>
library(Biostrings)
data=readDNAStringSet("~/Desktop/test.fa", format = "fasta")
query=DNAString("CAGAT")
result=cbind(pattern=as.character(query),as.data.frame(vmatchPattern(query,data)))
> result
pattern group group_name start end width
1 CAGAT 1 <NA> 6 10 5
2 CAGAT 1 <NA> 24 28 5
3 CAGAT 2 <NA> 8 12 5
4 CAGAT 3 <NA> 6 10 5
5 CAGAT 3 <NA> 18 22 5
*Still doesn't work multiple patterns.
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