pysam: a python wrapper of samtools

[TGBelgard]

Dear NGS community:

We announce the first release of pysam, a free/open-source lightweight wrapper of SAMtools with a pythonic interface.

The code and documentation can be found at the Pysam website:

http://code.google.com/p/pysam/

The python module wraps most functionality of Heng Li's C implementation of SAMtools (http://samtools.sourceforge.net). We would like to thank Heng Li for his assistance and, of course, all the samtools developers for providing samtools in the first place.

We hope you find it useful and we welcome feedback and comments.

Best wishes,

The pysam developers

[ffinkernagel]

I've used pysam for a couple of days now and greatly appreciate your effort!

[quinlana]

This is very welcome news, thanks for taking the time to create it. Does it use SWIG?

[TGBelgard]

Pysam uses pyrex to wrap the samtools code. Also, note there has been a bugfix release.

Originally Posted by quinlana

This is very welcome news, thanks for taking the time to create it. Does it use SWIG?

[choy]

I tried pysam today and found that it is not compatible with python <2.6.

The reason is because it uses the 'namedtuple' object which is new is python 2.6

I downloaded the following namedtuple implementation and am now able to use pysam with python 2.5 --

http://code.activestate.com/recipes/500261/

Pysam developers -- you might consider making a python2.5 version available too!

Thanks a lot for your sharing this great tool!

[nilshomer]

Any chance of supporting python 3.1 or greater?

[TGBelgard]

We intend to support python 3 in the near future (this requires moving to cython from pyrex). For older versions of python 2 (<2.6), we would suggest using choy's work-around (using the namedtuple available from ActiveState code).

[Mr Mutundes]

Yes, thanks for making this available.

Unfortunately I have not been able to install it and get the compilation errors below. If anyone can help I'd be grateful.

Using:
pysam-0.1.1
Python 2.6.4
Pyrex-0.9.8.5
gcc (GCC) 4.3.2 20081105 (Red Hat 4.3.2-7)
Linux 2.6.27.5-117.fc10.x86_64

pysam-0.1.1: python2.6 setup.py build
running build
running build_py
running build_ext
building 'pysam/csamtools' extension
gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Isamtools -I/c/matthew/include/py
thon2.6 -c pysam/csamtools.c -o build/temp.linux-x86_64-2.6/pysam/csamtools.o
In file included from pysam/csamtools.c:35:
samtools/bam.h:341: warning: function declaration isnât a prototype
samtools/bam.h:351: warning: function declaration isnât a prototype
pysam/csamtools.c: In function â:
pysam/csamtools.c:1740: warning: passing argument 7 of â from incompatible pointer type
pysam/csamtools.c: In function â:
pysam/csamtools.c:2020: warning: passing argument 1 of â from incompatible pointer type
pysam/csamtools.c:2023: warning: passing argument 7 of â from incompatible pointer type
pysam/csamtools.c: In function â:
pysam/csamtools.c:4042: warning: assignment from incompatible pointer type
pysam/csamtools.c: In function â:
pysam/csamtools.c:7162: error: â undeclared (first use in this function)
pysam/csamtools.c:7162: error: (Each undeclared identifier is reported only once
pysam/csamtools.c:7162: error: for each function it appears in.)
pysam/csamtools.c:7163: error: â undeclared (first use in this function)
pysam/csamtools.c:7168: error: â undeclared (first use in this function)
pysam/csamtools.c:7191: error: â undeclared (first use in this function)
error: command 'gcc' failed with exit status 1

[Mr Mutundes]

for the record - this was caused by not cleaning up an earlier unsuccessful installation attempt with an older version of pyrex

[cswarth]

I apologize if this is not an appropriate forum for this type of thing, but it is the only forum I can find that mentions pysam.

I'm trying to compile the latest version of pysam (0.1.2) under Windows Vista 64-bit (and that is not by choice).

I started using gcc from the cygwin tools, but gcc.exe would not run on this 64-bit system (odd). I switched to MinGW toolchain and got pysam to compile, but it won't link.

The build process for python extensions generates a .def file with an undefined symbol, in this case "initpysam/csamtools". I can see where this symbol name is generated but I am wondering if anyone else has run into this. It seems like it would affect anyone compiling pysam under cygwin or MinGW32.

Thanks in advance,

-csw

[cswarth]

Originally Posted by cswarth

I'm trying to compile the latest version of pysam (0.1.2) under Windows Vista 64-bit (and that is not by choice).

I spoke with one of the authors of pysam and he said they had not tried much to make it work under windows. A colleague said it worked well under linux and mac. I compiled it easily under macos, and I'll just dual boot this windows machine with linux. Problem solved.

[bioinfosm]

Installation issue:

$ which python
/usr/local/python/2.5.1/bin/python

$ python setup.py install
Traceback (most recent call last):
File "setup.py", line 56, in <module>
from Cython.Distutils import build_ext
ImportError: No module named Cython.Distutils

[maubp]

You need to install the Cython library for Python.

See http://www.cython.org/

[bioinfosm]

Originally Posted by maubp

You need to install the Cython library for Python.

See http://www.cython.org/

that solved it. Thanks!

[dror]

running build
running build_py
running build_ext
building 'csamtools' extension
gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -DFILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.6 -c pysam/csamtools.c -o build/temp.linux-i686-2.6/pysam/csamtools.o
In file included from pysam/csamtools.c:140:
samtools/razf.h:38:18: error: zlib.h: No such file or directory
In file included from pysam/csamtools.c:140:
samtools/razf.h:91: error: expected specifier-qualifier-list before ‘z_stream’
In file included from pysam/csamtools.c:142:
samtools/bam.h:354: warning: function declaration isn’t a prototype
samtools/bam.h:369: warning: function declaration isn’t a prototype
pysam/csamtools.c: In function ‘__pyx_pf_9csamtools_7Samfile_fetch’:
pysam/csamtools.c:5363: warning: passing argument 7 of ‘bam_fetch’ from incompatible pointer type
samtools/bam.h:596: note: expected ‘bam_fetch_f’ but argument is of type ‘int (*)(struct bam1_t *, void *)’
pysam/csamtools.c: In function ‘__pyx_pf_9csamtools_7Samfile_pileup’:
pysam/csamtools.c:6057: warning: passing argument 1 of ‘bam_plbuf_init’ from incompatible pointer type
samtools/bam.h:525: note: expected ‘bam_pileup_f’ but argument is of type ‘int (*)(uint32_t, uint32_t, int, struct bam_pileup1_t *, void *)’
pysam/csamtools.c:6066: warning: passing argument 7 of ‘bam_fetch’ from incompatible pointer type
samtools/bam.h:596: note: expected ‘bam_fetch_f’ but argument is of type ‘int (*)(struct bam1_t *, void *)’
pysam/csamtools.c: In function ‘__pyx_f_9csamtools_14IteratorColumn_cnext’:
pysam/csamtools.c:10974: warning: assignment discards qualifiers from pointer target type
pysam/csamtools.c: In function ‘__pyx_pf_9csamtools_11AlignedRead_5cigar___set__’:
pysam/csamtools.c:12631: warning: passing argument 4 of ‘pysam_bam_update’ from incompatible pointer type
pysam/pysam_util.h:33: note: expected ‘uint8_t *’ but argument is of type ‘uint32_t *’
pysam/csamtools.c: In function ‘__Pyx_InitGlobals’:
pysam/csamtools.c:21875: warning: this decimal constant is unsigned only in ISO C90
error: command 'gcc' failed with exit status 1

[dror]

running build
running build_py
running build_ext
building 'csamtools' extension
gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -DFILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.6 -c pysam/csamtools.c -o build/temp.linux-i686-2.6/pysam/csamtools.o
In file included from pysam/csamtools.c:140:
samtools/razf.h:38:18: error: zlib.h: No such file or directory
In file included from pysam/csamtools.c:140:
samtools/razf.h:91: error: expected specifier-qualifier-list before ‘z_stream’
In file included from pysam/csamtools.c:142:
samtools/bam.h:354: warning: function declaration isn’t a prototype
samtools/bam.h:369: warning: function declaration isn’t a prototype
pysam/csamtools.c: In function ‘__pyx_pf_9csamtools_7Samfile_fetch’:
pysam/csamtools.c:5363: warning: passing argument 7 of ‘bam_fetch’ from incompatible pointer type
samtools/bam.h:596: note: expected ‘bam_fetch_f’ but argument is of type ‘int (*)(struct bam1_t *, void *)’
pysam/csamtools.c: In function ‘__pyx_pf_9csamtools_7Samfile_pileup’:
pysam/csamtools.c:6057: warning: passing argument 1 of ‘bam_plbuf_init’ from incompatible pointer type
samtools/bam.h:525: note: expected ‘bam_pileup_f’ but argument is of type ‘int (*)(uint32_t, uint32_t, int, struct bam_pileup1_t *, void *)’
pysam/csamtools.c:6066: warning: passing argument 7 of ‘bam_fetch’ from incompatible pointer type
samtools/bam.h:596: note: expected ‘bam_fetch_f’ but argument is of type ‘int (*)(struct bam1_t *, void *)’
pysam/csamtools.c: In function ‘__pyx_f_9csamtools_14IteratorColumn_cnext’:
pysam/csamtools.c:10974: warning: assignment discards qualifiers from pointer target type
pysam/csamtools.c: In function ‘__pyx_pf_9csamtools_11AlignedRead_5cigar___set__’:
pysam/csamtools.c:12631: warning: passing argument 4 of ‘pysam_bam_update’ from incompatible pointer type
pysam/pysam_util.h:33: note: expected ‘uint8_t *’ but argument is of type ‘uint32_t *’
pysam/csamtools.c: In function ‘__Pyx_InitGlobals’:
pysam/csamtools.c:21875: warning: this decimal constant is unsigned only in ISO C90
error: command 'gcc' failed with exit status 1

[maubp]

Originally Posted by dror

running build
running build_py
running build_ext
building 'csamtools' extension
gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -DFILE_OFFSET_BITS=64 -D_USE_KNETFILE= -Isamtools -Ipysam -I/usr/include/python2.6 -c pysam/csamtools.c -o build/temp.linux-i686-2.6/pysam/csamtools.o
In file included from pysam/csamtools.c:140:
samtools/razf.h:38:18: error: zlib.h: No such file or directory
...

The first error is usually the most important. It appears you have not installed zlib (or at least, not installed the development header files for zlib).

[dror]

i installed zlib from the synaptic in ubuntu.
do you know which specific should i install?

after i installed another zlib it run, but with many warning..
an now the installation isn't work...

python setup.py install

running install
running build
running build_py
running build_ext
running install_lib
copying build/lib.linux-i686-2.6/ctabix.so -> /usr/local/lib/python2.6/dist-packages
error: /usr/local/lib/python2.6/dist-packages/ctabix.so: Permission denied

[maubp]

Originally Posted by dror

i installed zlib from the synaptic in ubuntu.
do you know which specific should i install?

after i installed another zlib it run, but with many warning..

Did you also install the zlib *-dev package?

(On my machine I think this means installing zlib1g and zlib1g-dev)

Originally Posted by dror

an now the installation isn't work...

python setup.py install

running install
running build
running build_py
running build_ext
running install_lib
copying build/lib.linux-i686-2.6/ctabix.so -> /usr/local/lib/python2.6/dist-packages
error: /usr/local/lib/python2.6/dist-packages/ctabix.so: Permission denied

By default it tries to install it at system level, so use sudo:

sudo python setup.py install

Alternatively you could install it under your home folder.

[dror]

thank you very much!!
now its working!!