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Questions - fasta

Compare values present in two data frames with the usage of sliding window function in R

We have two data frames Data frame 1 sl no. Segment_name Segment 1 Segment1 AACG 2 Segment2 ACTG 3 Segment3 GTCA Data frame 2 sl no. Dinucleotides Free energy Values 1 ...
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Maharshi

r

function

fasta

sliding-window

Votes: 0

Answers: 1

Latest Answer

I used my own sample data (see bottom), since columnnames with spaces in them are a pain in the ass to work with. The [] at the end of each line are to show you the in-between-lines results. You can o...
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Wimpel

Move new line character 5 positions downstream in a text (fasta) file

I am trying to transform a text file like this (fasta format): >seq1 AAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAA ATGATGATGGAATGAGGAT TTAGGAGGGAGGAAAATTC >seq2 CCCTCCGGGAAAAAAGAGG...
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Jeni

awk

fasta

Votes: 0

Answers: 4

Latest Answer

Assuming the line that starts with > is never more than 24 chars long: $ awk '{printf "%s", (/^>/ ? sep $0 ORS : $0); sep=ORS} END{print ""}' file | fold -w24 >seq1 AAAAAA...
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Ed Morton

How do I upload a FASTA file to R if it contains multiplexed data?

I was hoping to use the seqinr method to upload FASTA files to R for analysis. However, they are multiplexed sequences. library(seqinr) dnafile <- system.file("sra_data-3.fasta", package...
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hank00000

r

fasta

dna-sequence

Votes: 0

Answers: 1

Latest Answer

Update: dodging seqinr for initial input and simply using dnafile <- "file_name" DNAfile <- read.fasta(file = dnafile, as.string = TRUE, forceDNAtolower = FALSE) length(SRAfile) wo...
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hank00000

Get ID and protein sequences in biopython

I have this code. from Bio import SeqIO for seq_record in SeqIO.parse("aminoacids.txt", "fasta"): print(seq_record.id) print(repr(seq_record.seq)) Output: NP_414584.1 Seq('MNT...
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arteagavskiy

python

sequence

biopython

fasta

Votes: 0

Answers: 1

Latest Answer

repr is not designed for doing final output. It's essentially a debug tool. What you have is a Seq object. You probably need to be doing: print(seq_record.seq) which uses the str method.
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Tim Roberts

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