Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • HTSeq - NameError: name 're' is not defined

    I'm trying to use HTSeq but getting "NameError: name 're' is not defined" after import HTSeq command. As I'm a novice, I don't know how to resolve the issue. It would be nice if someone could help me in getting through.
    >>> import HTSeq

    Traceback (most recent call last):
    File "<pyshell#11>", line 1, in <module>
    import HTSeq
    File "C:\Python27\lib\site-packages\HTSeq\__init__.py", line 144, in <module>
    _re_attr_main = re.compile( "\s*([^\s\=]+)[\s=]+(.*)" )
    NameError: name 're' is not defined

  • #2
    Does this work for you?

    Code:
    import re
    Did you follow the installation instructions for Windows?

    Comment


    • #3
      Yes, I followed all instructions.
      No, "import re" doesn't work. See below,


      >>> import re
      >>> import HTSeq

      Traceback (most recent call last):
      File "<pyshell#1>", line 1, in <module>
      import HTSeq
      File "C:\Python27\lib\site-packages\HTSeq\__init__.py", line 9, in <module>
      from _HTSeq import *
      File "numpy.pxd", line 155, in init HTSeq._HTSeq (src/_HTSeq.c:34392)
      ValueError: numpy.dtype has the wrong size, try recompiling
      >>> import HTSeq

      Traceback (most recent call last):
      File "<pyshell#2>", line 1, in <module>
      import HTSeq
      File "C:\Python27\lib\site-packages\HTSeq\__init__.py", line 144, in <module>
      _re_attr_main = re.compile( "\s*([^\s\=]+)[\s=]+(.*)" )
      NameError: name 're' is not defined

      Comment


      • #4
        Probably should try recompiling numpy:

        I just installed pandas and statsmodels package on my python 2.7 When I tried "import pandas as pd", this error message comes out. Can anyone help? Thanks!!! numpy.dtype has the wrong size, try

        Comment


        • #5
          How did you install HTSeq and NumPy?

          My guess is you have a mis-match between the version of NumPy installed, and the version that HTSeq expects (i.e. what it was compiled against).

          Comment


          • #6
            Thanks fanli!
            I'll recompile and check whether the same error comes again or not.
            Is R / Bioconductor useful in high throughput sequence analysis?

            Comment


            • #7
              Yes, R is pretty handy for all sorts of statistical things. For example, differential expression testing using edgeR, DESeq2, etc.

              Comment


              • #8
                Thanks fanli!

                Comment

                Latest Articles

                Collapse

                • 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
                • seqadmin
                  Techniques and Challenges in Conservation Genomics
                  by seqadmin



                  The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

                  Avian Conservation
                  Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
                  03-08-2024, 10:41 AM

                ad_right_rmr

                Collapse

                News

                Collapse

                Topics Statistics Last Post
                Started by seqadmin, 03-27-2024, 06:37 PM
                0 responses
                12 views
                0 likes
                Last Post seqadmin  
                Started by seqadmin, 03-27-2024, 06:07 PM
                0 responses
                11 views
                0 likes
                Last Post seqadmin  
                Started by seqadmin, 03-22-2024, 10:03 AM
                0 responses
                53 views
                0 likes
                Last Post seqadmin  
                Started by seqadmin, 03-21-2024, 07:32 AM
                0 responses
                68 views
                0 likes
                Last Post seqadmin  
                Working...
                X