[GenoMax]

Yes, and it didnt work, then i installed something else (i dont remember right now, i did to many trial) but now it works!

I have another problem with pysam (samtools). could you many help me?

this is the problem:

C:\Users\Desktop\pysam-0.7.4>python setup.py install
running install
running bdist_egg
running egg_info
writing requirements to pysam.egg-info\requires.txt
writing pysam.egg-info\PKG-INFO
writing top-level names to pysam.egg-info\top_level.txt
writing dependency_links to pysam.egg-info\dependency_links.txt
reading manifest file 'pysam.egg-info\SOURCES.txt'
reading manifest template 'MANIFEST.in'
writing manifest file 'pysam.egg-info\SOURCES.txt'
installing library code to build\bdist.win32\egg
running install_lib
running build_py
running build_ext
skipping 'pysam\csamtools.c' Cython extension (up-to-date)
building 'pysam.csamtools' extension
c:\mingw\bin\gcc.exe -mno-cygwin -mdll -O -Wall -D_FILE_OFFSET_BITS=64 -D_USE_KN
ETFILE= -Isamtools -Ipysam -Iwin32 -IC:\Python27\include -IC:\Python27\PC -c pysam\csamtools.c -o build\temp.win32
2.7\Release\pysam\csamtools.o
In file included from pysam\csamtools.c:241:
samtools/razf.h:38:18: error: zlib.h: No such file or directory
In file included from pysam\csamtools.c:241:
samtools/razf.h:91: error: expected specifier-qualifier-list before 'z_stream'
pysam\csamtools.c: In function '__pyx_pf_9csamtools_7Samfile_10fetch':
pysam\csamtools.c:9814: warning: passing argument 7 of 'bam_fetch' from incompatible pointer type
pysam\csamtools.c: In function '__pyx_pf_9csamtools_7Samfile_11mate':
pysam\csamtools.c:10254: warning: passing argument 7 of 'bam_fetch' from incompatible pointer type
pysam\csamtools.c: In function '__pyx_pf_9csamtools_7Samfile_12count':
pysam\csamtools.c:10730: warning: passing argument 7 of 'bam_fetch' from incompatible pointer type
pysam\csamtools.c: In function '__pyx_pf_9csamtools_7Samfile_13pileup':
pysam\csamtools.c:11148: warning: passing argument 7 of 'bam_fetch' from incompatible pointer type
pysam\csamtools.c: In function '__pyx_f_9csamtools___advance_snpcalls':
pysam\csamtools.c:17424: warning: implicit declaration of function 'bam_prob_realn'
pysam\csamtools.c:17452: warning: implicit declaration of function 'bam_cap_mapQ'
pysam\csamtools.c: In function'__pyx_pf_9csamtools_20IteratorColumnRegion_1__next__':
pysam\csamtools.c:18907: warning: passing argument 1 of '__pyx_f_9csamtools_make
PileupProxy' from incompatible pointer type
pysam\csamtools.c: In function '__pyx_pf_9csamtools_21IteratorColumnAllRefs_1__next__':
pysam\csamtools.c:19134: warning: passing argument 1 of '__pyx_f_9csamtools_make
PileupProxy' from incompatible pointer type
pysam\csamtools.c: In function '__Pyx_InitGlobals':
pysam\csamtools.c:38587: warning: this decimal constant is unsigned only in ISO
C90
error: command 'gcc' failed with exit status 1

Thank you

You should create a new thread for this problem since it is unrelated to the original one (if the following does not help).

You appear to be missing the "zlib" library. Since you are using windows this may be is what you need: http://www.winimage.com/zLibDll/index.html

A previous post on SeqAnswers seems to indicate that pysam may not work on windows (http://seqanswers.com/forums/showthread.php?t=2870)

[GenoMax]

Hi guys!
I followed all the instructions reported on the official web site for HTseq and i read all your posts.
I cannot import HTSeq. There is the error explained here.

I'm working on windows 7, with python 2.7.5 and HTSeq 0.5.4p3.
I really need help!

Cheers!

Did you install the redistributable package mentioned in post #28?

[Stefania_IT]

Hi guys!
I followed all the instructions reported on the official web site for HTseq and i read all your posts.
I cannot import HTSeq. There is the error explained here.

I'm working on windows 7, with python 2.7.5 and HTSeq 0.5.4p3.
I really need help!

Cheers!

[Simon Anders]

Okay, then I'll change the installation instructions and ask people to install the redistributable.

[GenoMax]

Perhaps you should create a new thread and let users (Windows) know that a working version of HTSeq is now possible/available.

Thank you for your help.

[GenoMax]

The 2010 distributable did not work but I had to get 2012 32-bit redistributable from here: http://www.microsoft.com/en-us/downl....aspx?id=30679

That worked!

Python 2.7.4 (default, Apr  6 2013, 19:54:46) [MSC v.1500 32 bit (Intel)] on win
32
Type "help", "copyright", "credits" or "license" for more information.
>>> import HTSeq
>>>

PS: Had not seen your update when I wrote the above.

[Simon Anders]

Sorry, better use this one: http://www.microsoft.com/en-gb/downl....aspx?id=30679 (file vcredist_x86.exe)

[GenoMax]

Will do. Give me a few minutes.

[Simon Anders]

I think I got it. The Windows version of Python 2.7 available from the Python web site seems to have been compiled with MSVC9, as is apparent fdrom the fact that according to Dependency Walker, PYTHON27.DLL depends on MSVCR90.DLL. I used MSVC12, and hence, the missing library is MSVCR110.DLL. So, I should either include this one, or ask people to install the Microsoft Visual C++ 2010 Redistributable Package (x86), or maybe use MSVC9 to compile HTSeq.

Could you maybe quickly try to download and install VCredist and tell me if this solves the issue?

[Simon Anders]

Until version 0.5.4, I always used MinGW to compile HTSeq for Windows. Now, the new version of MinGW has changed an option and Python distutils did not follow suit, causing general annoyance, and so I switched to using MSVC with the newest version, which is what the Python people actually recommend. With MinGW, the 'build_wininst' function of distutils always included everything that was needed and I would have expected that it still does so with MSVC. Doesn't seem to work, though.

Just googled. You are right, they are not included: https://groups.google.com/forum/?fro...er/4a9Nb2zgteo

[GenoMax]

I have Visual Studio Express 2012. That's what I compiled the package with.

Aha. That was a clue I had found while searching. Let me see if I can pin down the exact DLL mentioned by going back to search.

Note: Apparently there is a "release mode" for compiling the package.

Note2: This is a list of the DLL's and Python versions that go with them. Now to install the 32-bit version or 64-bit is the question.

http://stackoverflow.com/questions/9047072/windows-python-version-and-vc-redistributable-version

[Simon Anders]

I have Visual Studio Express 2012 installed. That's what I compiled the package with.

[GenoMax]

So, you went right to the directory that contained _HTSeq.pyd (you did notice the "cd" command I put on top? I shoudl have highlighted it.), and even then, it doesn't see it? That's strange.

Yes I did(see below). Not sure what is going on.

c:\Python27\Lib\site-packages\HTSeq>cd
c:\Python27\Lib\site-packages\HTSeq

c:\Python27\Lib\site-packages\HTSeq>c:\Python27\python.exe
Python 2.7.4 (default, Apr  6 2013, 19:54:46) [MSC v.1500 32 bit (Intel)] on win
32
Type "help", "copyright", "credits" or "license" for more information.
>>> import _HTSeq
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
ImportError: DLL load failed: The specified module could not be found.
>>>

Do you have Visual Studio 2010 installed on your machine by any chance?

[Simon Anders]

So, you went right to the directory that contained _HTSeq.pyd (you did notice the "cd" command I put on top? I shoudl have highlighted it.), and even then, it doesn't see it? That's strange.

[GenoMax]

Here is what I get. May try to uninstall and reinstall everything tomorrow.

Python 2.7.4 (default, Apr  6 2013, 19:54:46) [MSC v.1500 32 bit (Intel)] on
32
Type "help", "copyright", "credits" or "license" for more information.
>>> import _HTSeq
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
ImportError: No module named _HTSeq
>>>