Question

In python

Attached is a file called sequences.txt, it contains 3 sequences (one sequence per line). Also attached is a file called AccessionNumbers.txt. Write a program that reads in those files and produces 3 separate FATSA files. Each accession number in the AccessionNumbers.txt file corresponds to a sequence in the sequences.txt file. Remember a FASTA formatted sequence looks like this:

>ABCD1234

ATGCTTTACGTCTACTGTCGTATGCTTTACGTCTACTGACTGTCGTATGCTTACGTCTACTGTCG

The file name should match the accession numbers, so for 1st one it should be called ABCD1234.txt.

Note: Print out the sequences in upper case AND remove any special characters in the sequence!

sequences.txt contains the following sequence:

ATGCTTTACGTCTACTGTCGTATGCTTTACGTCTACTGACTGTCGTATGCTTACGTCTACTGTCG
atgctttacgtctactgtcgtatgctttacgtctactgactgtcgtatgcttacgtctactgtcg
atgctttacgt-tcgtatgctttacgtc---tatgcttacgt--cttacgt-----ctactgtcg

AccessionNumbers.txt contains the following:

ABCD1234
GFRT7890
HJIS5630

the output should produce 3 separate text files named "ABCD1234.txt" "GFRT7890.txt" and "HJIS5630.txt"

each text file output should look like this:

>ABCD1234

ATGCTTTACGTCTACTGTCGTATGCTTTACGTCTACTGACTGTCGTATGCTTACGTCTACTGTCG

Answer 1

#function that takes sequence
#and returns the valid sequence in upper case.
def formatSeq(seq):
   #resultant seq
   res = ""
   #for each char in seq
   for i in seq:
       #if i_th char is one of the ATCG, then add it.
       if( i.upper() in "ATCG"):
           res += i.upper()
   #return the result
   return res

#open sequences.txt and AccessionNumbers.txt
seq = open("sequences.txt")
acNum = open("AccessionNumbers.txt")

#read one line from sequence and accession txt files
sequence = seq.readline()
accession = acNum.readline()
#till the end of the files
while(sequence and accession):
   #format the sequence by calling function
   sequence = formatSeq(sequence.strip())
   accession = accession.strip()
   #create file with accession number as txt file
   out = open(accession+".txt","w")
   #write accession number
   out.write(">"+accession+"\n")
   #and sequence
   out.write(sequence)
   out.close()
   #read next sequence and accession number.
   sequence = seq.readline()
   accession = acNum.readline()

seq.close()
acNum.close()

#sequence.txt

ATGCTTTACGTCTACTGTCGTATGCTTTACGTCTACTGACTGTCGTATGCTTACGTCTACTGTCG
atgctttacgtctactgtcgtatgctttacgtctactgactgtcgtatgcttacgtctactgtcg
atgctttacgt-tcgtatgctttacgtc---tatgcttacgt--cttacgt-----ctactgtcg
#accessionnumbers.txt

ABCD1234
GFRT7890
HJIS5630

ABCD1234.txt

>ABCD1234
ATGCTTTACGTCTACTGTCGTATGCTTTACGTCTACTGACTGTCGTATGCTTACGTCTACTGTCG

GFRT7890.txt

>GFRT7890
ATGCTTTACGTCTACTGTCGTATGCTTTACGTCTACTGACTGTCGTATGCTTACGTCTACTGTCG

HJIS5630.txt

>HJIS5630
ATGCTTTACGTTCGTATGCTTTACGTCTATGCTTACGTCTTACGTCTACTGTCG