WELCOME TO BIOINFO DATA BLOQ CODEQUEST

 A. Treatment of Sequences

No. 1

#Extract FASTA Sequences from another file using sequence IDs in another file

#Write two separate scripts with file names FastaToTbl and TblToFasta with the following content:

FastaToTbl:

#!/usr/bin/awk -f
{
        if (substr($1,1,1)==">")
        if (NR>1)
                    printf "\n%s\t", substr($0,2,length($0)-1)
        else 
            printf "%s\t", substr($0,2,length($0)-1)
        else 
                printf "%s", $0
}END{printf "\n"}

TblToFasta:

#! /usr/bin/awk -f

{
  sequence=$NF
  ls = length(sequence)
  is = 1
  fld  = 1
  while (fld < NF)
  {
     if (fld == 1){printf ">"}
     printf "%s " , $fld
     if (fld == NF-1)
      {
        printf "\n"
      }
      fld = fld+1
  }
  while (is <= ls)
  {
    printf "%s\n", substr(sequence,is,60)
    is=is+60
  }
}

#Further explainations check the reference below.

Ref: https://askubuntu.com/questions/832478/how-to-compare-2-files-and-extract-the-particular-sequence-using-id-in-first-fil

No. 2.

#Convert Multi FASTA line to a single FASTA line

$ cat input_file.fasta | awk '{if (substr($0,1,1)==">"){if (p){print "\n";} print $0} else printf("%s",$0);p++;}END{print "\n"}' > singleline.fasta

OR used awk program:

% awk '!/^>/ { printf "%s", $0; n = "\n" } 

/^>/ { print n $0; n = "" }

END { printf "%s", n }

' input_file.fasta > singleline.fasta

Ref: https://stackoverflow.com/questions/15857088/remove-line-breaks-in-a-fasta-file

No. 3

# Randommly select sets of FASTA sequences Using python script:

from Bio import SeqIO

from random import sample

v = open(r"/Users/User pc/Desktop/pythonEx/viralRandom.txt", "w")
with open(r"/Users/User pc/Desktop/pythonEx/viralNinput.txt") as f:
seqs = SeqIO.parse(f, "fasta")
samps = ((seq.name, seq.seq) for seq in sample(list(seqs),10000))
for samp in samps:
v.write(''.join(">{}\n{}".format(*samp)+'\n'))
v.write("\n")
v.write("\n\n")