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

fasta.py sequences.bxtAccessionNumbers.brtABCD1234.tt | GFRT7890.brt HUIS5630.bt #function that takes sequence #and returns the valid sequence in upper case. Eder formatseq(seq) geq reg #for each char in seq for i in seq char is one of the ATCG, then add it ir 1.upper () in "ATCG"): 10 res +i.upper () #return the result return res 13 #open sequences.txt and AccessionNumbers.txt 14 seq open("equences.Ext" open ("AccessionNumbers . txt") acNum 17 #read one line from sequence and accession txt files 18 sequence seq.readiine () 21 #till the end of the files while (sequence and accession): 22 #format the sequence by calling function . strip ()) accession,strip ( ) 25 accession 26 #create file with accession number as txt file open (accession+" . txt", "w") out 29 out.write (">"+accession+"\n" ) 30 #and sequence out.write (sequence) 31 #read next sequence and accession number. sequence - 5eg.readline ( 33 34 35 acNum,readline () accession

Accession Numbers.bxt xABCD1234.bt xGFRT7890.txt x HJIS5630.txt fasta.py sequences.brt rea-" in sea or 1 in sea: #1r 1 th char is one of the ATCG, then add it. ir 1.upper in "ATCG"): pper #return the rezutt 12 return rea 13 ionNumbers,EXt acNum 16 open ("AccessionNumbers. txt") 17 ence and accession txt files #read che e accession - acNum.readline ) 20 21 #till the end of the files while (sequence and accession) 1ling function sequence formatSeg (sequence.atrip ()) accession = accession.strip) 24 25 TCreate Eile with access1on number as txt file ', ") #write acceasion number out.write (">"+accession+"\n") #and sequence 28 29 30 sequence) 32 our.close(1 #read next sequence and accession number sequence *** 33 adline () accession 36 seq.close (1 acNum.close () 37