Python_05_answers

1. 

Write a script to do the following to Python_05.txt

Open and read the contents.
Uppercase each line
Print each line to the STDOUT


#!/usr/bin/env python3
#Python_05 question 1

file = open("../python_05.txt", "r")
contents = file.read()
print (contents)

song_upper = contents.upper()
print (song_upper)

file.close()

2.  

Modifiy the script in the previous problem to write the contents to a new file called "Python_05_uc.txt"

#!/usr/bin/env python3
#Python_05 question 2

file = open("../python_05.txt", "r")
file_write = open ("../Python_05_uc.txt", "w")

contents = file.read()
print (contents)

song_upper = contents.upper()
print (song_upper)

file_write.write(song_upper)

file.close()
file_write.close()


3.  Open and print the reverse complement of each sequence in Python_05.fasta. 
Make sure to print the output in fasta format including the sequence name and a note in the description that this is the reverse complement. 
Print to STDOUT and capture the output into a file with a command line redirect '>'.

wget --no-check-certificate https://raw.githubusercontent.com/srobb1/pfb2017/master/files/Python_05.fasta 

(check text file for full notes)

#!/usr/bin/env python3
#Python_05 question 3


fasta_read = open ("../Python_05.fasta", "r")
fasta_write = open ("../Python_05comb.fasta", "w")

combined = ""

for dna in fasta_read:
        dna = dna.rstrip()

        if dna.startswith('>'):
                if combined:
                        fasta_write.write(combined + "\n")
                combined = ""
                fasta_write.write(dna + "\n")

        else:
                combined += dna

fasta_write.write(combined + "\n")

fasta_read.close()
fasta_write.close()


 #dna = dna.rstrip()

#dna_reverse= dna.replace('T', 'a').replace('A', 't').replace('G', 'c').replace('C', 'g')

                #dna_reverse = dna_reverse.rstrip()

        #fasta_write.write(dna_reverse[::-1])

#print ("../Python_05_rc.fasta")


4.  

Open the FASTQ file Python_05.fastq and go through each line of the file. Count the number of lines and the number of characters per line. Have your program report the:

total number of lines
total number of characters
average line length

#!/usr/bin/env python3
#Python_05 question 4

linecount = 0
chrcount = 0

fastq = open ("../Python_05.fastq", "r")

for line in fastq:

        linecount+= 1
        chrcount += len(line)

print ("linecount:", linecount)
print ("chrcount:", chrcount )
print ("avglinelength:", (chrcount/linecount) )

pfb14:files admin$ python3 myscript_19.py
linecount: 120
chrcount: 7920
avglinelength: 66.0

***** FORGOT that \n is a character

#!/usr/bin/env python3
#Python_05 question 4

linecount = 0
chrcount = 0

fastq = open ("../Python_05.fastq", "r")

for line in fastq:
        line = line.rstrip("\n")
        linecount+= 1
        chrcount += len(line)

print ("linecount:", linecount)
print ("chrcount:", chrcount )
print ("avglinelength:", (chrcount/linecount) )

linecount: 120
chrcount: 7800
avglinelength: 65.0



5.  Genelists from Ensembl Biomart



pfb14:files admin$ python3 myscript_20.py 
not_sc_count: 15147

ENSVPAG00000000048
ENSVPAG00000006160
ENSVPAG00000003148
ENSVPAG00000006812
both_scandpigm_count: 5