[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!

[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?

[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)