something wrong with tophat-1.0.14 version, don't use it

[frankyue50]

Hi, guys, I was trying the "new" version of tophat and found that it has 3708 lines.

But in the old version, 1.0.13 it only has around 1600 lines. so I wonder WTH is going on? I open the tophat file and found that from 1857 to the end of file, basically it is the same as the first 1800 lines. they even do the "import" part twice. For example, the following lanes appeared one at line 2 and AGAIN at line 1872.

import sys
import getopt
import subprocess
import errno
import os
import tempfile
import warnings
import shutil
import copy
from datetime import datetime, date, time

Can the authors give us some explanations?

[quinlana]

At first glance, I think you might want to double-check your work. This seemed quite odd to me, so I downloaded Tophat for grins. tophat.py ends at line 1855. I suspect that you have duplicated the source yourself subsequent to downloading. Perhaps you should download the file again and retry.

[frankyue50]

I just tested it again. I cannot imagine how can I mess up the installation. All I did is: download the source file, unzip it and:

./configure --prefix=/home/myusername
make
make install

I've tried this on two servers. And it give me the same result ... can anyone else test it? Thanks!

Anyway I just edit the tophat and delete everything after 1857. Hope that's it.

At first glance, I think you might want to double-check your work. This seemed quite odd to me, so I downloaded Tophat for grins. tophat.py ends at line 1855. I suspect that you have duplicated the source yourself subsequent to downloading. Perhaps you should download the file again and retry.

[kmcarr]

At first glance, I think you might want to double-check your work. This seemed quite odd to me, so I downloaded Tophat for grins. tophat.py ends at line 1855. I suspect that you have duplicated the source yourself subsequent to downloading. Perhaps you should download the file again and retry.

You are looking at the tophat.py file in the source tree, whereas franky is referring to the tophat script that is produced after compiling. I have downloaded the pre-built 1.0.14.Linux_x86_64 distribution and can confirm franky's observation of duplicated code in the final tophat script. Apparently something in the build process is duplicating the code.

[frankyue50]

thanks, kmcarr! glad to see I am not the only one see this.