I have to find out the size of the protein sequence, but even using the codes below, I couldn't. This first code was to find how many proteins there are in total and to find the size of the sequences.
The attached image is just to show what I want the code to search for. I don't know what is missing in the code
arq = open("genoma9.faa")
conteudo = arq.read()
print(conteudo)
fh = open("genoma9.faa")
n= 0
for line in fh:
if line.startswith(">"):
n+= 1
print(line)
proteins = line.count(">")
print("Total of Proteins: " + str(proteins))
Trying to find this middles characters above the >WP:
Example:
>WP_013277001.1 DNA polymerase III subunit beta [Acetohalobium arabaticum]
MQIKIDRKNFYDGIQTVRKAISSKSTLPILSGILIETQEKKLKLVGTDLELGIECRVDANIIKDGAIVLPANHLANIVRE
LPNKELELELKKDNKIEISCGLSQFKIHGSPADEYPLLPEVGSGIEYTLSQEKFQAMINRIKFATSDDESRPFLTGGLLS
•
written
by
Maria Eduarda •
1 answer
I think you are reinventing the wheel. There is no need to write separate code for handling biological sequences when it all exists in BioPython and can be accessed in several lines of code. What I show below could be optimized, so it is only for illustration. I suggest you save it into a file fasta_len_and_number.py or something like that.
import sys
from Bio import SeqIO
# open the file specified after script name
FastaFile = open(sys.argv[1], 'r')
counter = 0 # initialize sequence counter
for rec in SeqIO.parse(FastaFile, 'fasta'):
counter = counter + 1 # increase sequence counter
name = rec.id # sequence header
seq = rec.seq # protein/DNA sequence
seqLen = len(rec) # determine sequence length
print(seqLen, name) # print the length + header
print('\n A total of %d sequences' % counter)
FastaFile.close()
Running this line:
python fasta_len_and_number.py genoma9.faa
will make hopefully a desired output. On one of my files when I tested, the last 10 lines look like this:
130 2HY5_A
114 2Q68_A
141 4CDL_A
47 6O3S_A
12 4AKT_C
37 4Z80_C
145 1Y23_A
215 6S5A_L
A total of 112217 sequences
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you said. FAA File Sequence
please, do so now.
Answer of the other post:
Have you tried running this piece of code? It looks like it has an indentation error?
this post is the same of your previous one Print the size of a protein . Stop asking new questions and update your original post.
I reposted because I deleted the other one since I didn't post the code in the old post.
The
editbutton is for edits, no need to delete.