Hi
I am new in python and want to see how this can be done in python (I can do this in R). I have a text file myfile.txt with one column and thousands of rows as shown below. I want to convert this to fasta result.fasta format as shown below. How can I do this in python?
myfile.txt
ATGTGTGGTTTTCCCCC
ATTGGCGGGGTTTTTCAGGGG
ATGGGGGGGCCCCCCCCAAAAAA
TTGGTGGGGGGGGGGGGAA
result.fasta
>1
ATGTGTGGTTTTCCCCC
>2
ATTGGCGGGGTTTTTCAGGGG
>3
ATGGGGGGGCCCCCCCCAAAAAA
>4
TTGGTGGGGGGGGGGGGAA
•
written
by
MAPK
Create a new script called ConvertFASTA.py:
import sys
#File input
fileInput = open(sys.argv[1], "r")
#File output
fileOutput = open(sys.argv[2], "w")
#Seq count
count = 1 ;
#Loop through each line in the input file
print "Converting to FASTA..."
for strLine in fileInput:
#Strip the endline character from each input line
strLine = strLine.rstrip("\n")
#Output the header
fileOutput.write(">" + str(count) + "\n")
fileOutput.write(strLine + "\n")
count = count + 1
print ("Done.")
#Close the input and output file
fileInput.close()
fileOutput.close()
Then, run it with:
python ConvertFASTA.py myfile.txt result.fasta
For the OP, Kevin did a good job showing the pseudocode, and each step.This will run in the same fashion.
#!/usr/bin/env python
import sys
n = 0
with open(sys.argv[1], 'r') as f:
with open(sys.argv[2], 'w') as out:
for line in f:
n += 1
out.write('>' + str(n) + '\n' + line.strip())
I also have the similar query but I want to use the names of sequences to be used after the '>' symbol.
for example:
Zebrafish ESLLRFGLRSDLDFR
Fugu ETVLSVGLSAETEIS
Chicken RALLAWGYSSDT
and I want:
result.fasta
>Zebrafish
ESLLRFGLRSDLDFR
>Fugu
ETVLSVGLSAETEIS
>Chicken
RALLAWGYSSDT
Can I get some guidelines?
Sometimes if you try and search for this type of information you would not need to wait to get an answer. Here is one solution.
I am really thankful for your support. I would want to discuss that I receive an error,
fileInput = open(sys.argv[1], "r")
IndexError: list index out of range
when I try using this solution (code) on windows OS and I do not use linux. Since according to my knowledge, argv is the built-in array of linux and so I guess it does not work when I run the script in python IDLE (3.6.4).
Something a bit simpler and should work in Python 2 and 3:
#!/usr/bin/env python
import sys
c = 1
for l in sys.stdin:
sys.stdout.write(">%d\n%s\n" % (c, l))
c += 1
Usage:
$ convert.py < in.txt > out.fa
Or even simpler:
import sys
for c, l in enumerate(sys.stdin, start=1):
sys.stdout.write(">%d\n%s\n" % (c, l))
I think you want sys.stdout.write
You're write, thanks. Fixed!
I agree, is that feature not available? It would help users to see various ways of doing it. Apologies, I was composing my solution whilst the other guy had posted!
FOUR! 🏌⛳️
$ python -c "import sys; [sys.stdout.write('>'+str(i)+'\n'+seq) for i, seq in enumerate(sys.stdin)]"
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