find_alt3prime_5prime_ss.py

[brookslabucsc]

find_alt3prime_5prime_ss.py

[belgravia]

Your command is fine and your psl is in the format that the script is expecting, which is good. However my script was expecting integers for counts when float counts were given. The quantification format had changed and I hadn't changed find_alt3prime_5prime_ss.py to match. I just pushed a newer version of the script that should fix this. Let me know how this goes!
-Alison

[dorothyzh]

Traceback (most recent call last):
File "flair/flair/bin/find_alt3prime_5prime_ss.py", line 106, in
alljuncs = pslreader(psl)
File "flair/flair/bin/find_alt3prime_5prime_ss.py", line 25, in pslreader
count0, count1 = float(line[colnum]), float(line[colnum + 1])
IndexError: list index out of range

[belgravia]

I pushed an updated version of the script that takes the command line arguments as such:
python find_alt3prime_5prime_ss.py isoforms_counts.psl 21 22 accept.txt donor.txt
since I realize the way it read the column numbers in before was confusing. Let me know if that works for you. Thanks for your patience!
-Alison

[dorothyzh]

Sorry to bother you, I still find errors, I give you the output.psl file I used

output.psl.txt
python flair/bin/find_alt3prime_5prime_ss.py output.psl2 22 23 alt_acceptor.txt alt_donor.txt
Traceback (most recent call last):
File "flair/bin/find_alt3prime_5prime_ss.py", line 107, in
alljuncs = pslreader(psl)
File "flair/bin/find_alt3prime_5prime_ss.py", line 26, in pslreader
count0, count1 = float(line[colnum1]), float(line[colnum2])
IndexError: list index out of range

python flair/bin/find_alt3prime_5prime_ss.py output.psl2 22 22 alt_acceptor.txt alt_donor.txt
Traceback (most recent call last):
File "flair/bin/find_alt3prime_5prime_ss.py", line 107, in
alljuncs = pslreader(psl)
File "flair/bin/find_alt3prime_5prime_ss.py", line 33, in pslreader
for j in junctions:
TypeError: 'NoneType' object is not iterable

[dorothyzh]

That's my original file, I have changed the last columns of it to integer using R, but still cannot work. Thanks.