[dror]

running - python setup.py build, i have this error. why!??!

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]

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]

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)

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!!

[aggp11]

pysam not working from terminal

Hello,

I am a new pysam user. I installed pysam and it is running fine in the python interpreter but when I try to run a python script (*.py) from the command line it gives me the "pysam command not found error".

I am guessing this is something to do woth the installation. I can run samtools properly and like I said pysam is running fine in the interpreter. Could you help me with this?

Thanks a lot,

Praful

[ffinkernagel]

How are you trying to run the python script?
Usually you'd type 'python myscript.py', while the command not found error suggests
you're inputing 'pysam myscript.py' instead.

[aggp11]

ffinkernagel

Thanks for your reply..

Actually I am trying to run the script as ./myscript.py. Also, the error comes when python tries to import pysam: "import pysam" ...

[ffinkernagel]

Then my magic glassball says, you're missing a correct shebang at the start of your file.
It should start with "#! /usr/bin/python" (or wherever your python executable is located. "Which python" will tell you what to place there).
In effect, it tells the system with which engine to run this script.

If python couldn't import the module, you'd get an "ImportError" (and a complet traceback), not a 'command not found'.

[aggp11]

Ohh....I am sorry for the trouble...I just missed that line on top of the script...

Thanks a lot...

[ffinkernagel]

don't worry, glad to help!

[vyellapa]

Im trying to a runs simple script to print reads that align to chr1 between 100 and 120 using pysam

import pysam
samfile=pysam.Samfile("sorted309.bam", "rb")
for alignedread in samfile.fetch('chr1', 100, 120):
	print alignedread
samfile.close()

However I'm getting an error:
code

dhcp-ws-10-55-120-36:programs vyellapantula$ python sampy.py 
Traceback (most recent call last):
  File "sampy.py", line 3, in <module>
    for alignedread in samfile.fetch('chr1', 100, 120):
  File "csamtools.pyx", line 771, in csamtools.Samfile.fetch (pysam/csamtools.c:8233)
  File "csamtools.pyx", line 702, in csamtools.Samfile._parseRegion (pysam/csamtools.c:7458)
ValueError: invalid reference `chr1`

Does this something to do with Tophat alignment output or is there something Im not doing right?

[Mr Mutundes]

Are you sure that the reference sequence name in the bam file is 'chr1' and not '1'? What is shown if you add a line to your script to print samfile.references?

[vyellapa]

It is indeed '1' and not 'chr1'.

[arvid]

I just noticed that pysam.Samfile.pileup() only gives me primary read alignments that overlap a given position, no secondary alignments. Is there a reason for this behaviour?

I do get all the read alignments in a certain region with pysam.Samfile.fetch(), but for my application I find the pileup engine more convenient.

Did I miss anything here, or is this an undocumented "feature"?