Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • #31
    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!

    Comment


    • #32
      Originally posted by Stefania_IT View Post
      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?

      Comment


      • #33
        Originally posted by Stefania_IT
        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)

        Comment

        Latest Articles

        Collapse

        • seqadmin
          Current Approaches to Protein Sequencing
          by seqadmin


          Proteins are often described as the workhorses of the cell, and identifying their sequences is key to understanding their role in biological processes and disease. Currently, the most common technique used to determine protein sequences is mass spectrometry. While still a valuable tool, mass spectrometry faces several limitations and requires a highly experienced scientist familiar with the equipment to operate it. Additionally, other proteomic methods, like affinity assays, are constrained...
          04-04-2024, 04:25 PM
        • seqadmin
          Strategies for Sequencing Challenging Samples
          by seqadmin


          Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
          03-22-2024, 06:39 AM

        ad_right_rmr

        Collapse

        News

        Collapse

        Topics Statistics Last Post
        Started by seqadmin, 04-11-2024, 12:08 PM
        0 responses
        31 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 04-10-2024, 10:19 PM
        0 responses
        33 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 04-10-2024, 09:21 AM
        0 responses
        28 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 04-04-2024, 09:00 AM
        0 responses
        53 views
        0 likes
        Last Post seqadmin  
        Working...
        X