This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Python Problem In Variable Output

Hello, i'm having difficulties in a python exercice, where i need to translate a dna sequence to it's aminoacid correrspondents. I have the whole program written, but i'm having difficulties with the way in wich the output is being writen.

In sumarry, i have this final piece of code:

for x in f1:
    x = x.strip()
    if x.count("seq"):
        f2.write((x)+("_1_+\n"))
        f2.write((x)+("_2_+\n"))
        f2.write((x)+("_3_+\n"))
        f2.write((x)+("_1_-\n"))
        f2.write((x)+("_2_-\n"))
        f2.write((x)+("_3_-\n"))
    else:
        f2.write((translate1(x))+("\n"))
        f2.write((translate2(x))+("\n"))
        f2.write((translate3(x))+("\n"))
        f2.write((translate1neg(x))+("\n"))
        f2.write((translate2neg(x))+("\n"))
        f2.write((translate3neg(x))+("\n"))

that gives this output:

>seq1_1_+
>seq1_2_+
>seq1_3_+
>seq1_1_-
>seq1_2_-
>seq1_3_-
iyyslrs-las-smrlssiv-m
fiirydrs-ladrcgshrssk
llfativas-lidaalidrl
frrsmraasis-lativannkm
lddr-ephrsas-lrs-riin
-tidesridqlasydrse--m

But what i need is something like this:

>seq1_1_+
iyyslrs-las-smrlssiv-m
>seq1_2_+
fiirydrs-ladrcgshrssk
>seq1_3_+
llfativas-lidaalidrl
>seq1_1_-
frrsmraasis-lativannkm
>seq1_2_-
lddr-ephrsas-lrs-riin
>seq1_3_-
-tidesridqlasydrse--m

So, my question is, how can i resolve this?

Thanks

python
• 1,649 views • link
updated by Devon Ryan Devon Ryan • written by joaosilvaourico • joaosilvaourico

1 answer 

for x in f1:
    x = x.strip()
    if x.count("seq"):
        name = x
    else :
        f2.write((name)+("_1_+\n"))
        f2.write((translate1(x))+("\n"))
        f2.write((name)+("_2_+\n"))
        f2.write((translate2(x))+("\n"))
        f2.write((name)+("_3_+\n"))
        f2.write((translate3(x))+("\n"))
        f2.write((name)+("_1_-\n"))
        f2.write((translate1neg(x))+("\n"))
        f2.write((name)+("_2_-\n"))
        f2.write((translate2neg(x))+("\n"))
        f2.write((name)+("_3_-\n"))
        f2.write((translate3neg(x))+("\n"))
• 255 views • link
written by Devon Ryan Devon Ryan

Log in to answer this question.

More posts like this