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Thread | Thread Starter | Forum | Replies | Last Post |
Cuffdiff: Importance Sampling and Variance Calculation | jk1124 | RNA Sequencing | 0 | 10-25-2012 02:43 PM |
PubMed: RNA-seq : technical variability and sampling. | Newsbot! | Literature Watch | 0 | 06-08-2011 03:00 AM |
PubMed: Sampling and pyrosequencing methods for characterizing bacterial communities | Newsbot! | Literature Watch | 0 | 08-03-2010 05:40 AM |
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#1 |
Junior Member
Location: Ithaca NY Join Date: Apr 2013
Posts: 5
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Hi, warning that this is a noob question.
I am running into problems importing HTSeq. The context is that I am trying to sample randomly from a fastq file (not paired reads). After trying a few methods and always running out of memory I think I need to use the script Simon Anders posted here that relies on HTSeq: http://seqanswers.com/forums/showthread.php?t=12070 I navigate to the directory where my script and the fastq file of interest are saved, then call the script as follows in order to randomly subsample a tenth of the reads: python subsamplewithHTSeq.py 0.10 SRR12345.fastq out_tenth_SRR12345.fastq However, I always get a message that HTSeq can't be imported. I have installed HTSeq (version HTSeq-0.5.4p1.win32-py2.7.exe), along with Numpy and I am using 32 bit python 2.7 on Windows 7. I have read the tour through HTSeq, but I still can't figure this out. I am a newbie to computational work and any help would be greatly appreciated. The error is below: C:\Users\kak\Desktop\ShortReads\fastqformatted>python subsamplewithHTSeq.py 0 .1 fastq_SRR12345.fastq tenth_SRR12345.fastq Traceback (most recent call last): File "subsamplewithHTSeq.py", line 15, in <module> import HTSeq File "C:\Python27\lib\site-packages\HTSeq\__init__.py", line 9, in <module> from _HTSeq import * File "_HTSeq.pyx", line 14, in init HTSeq._HTSeq (src/_HTSeq.c:31058) File "C:\Python27\lib\site-packages\HTSeq\StepVector.py", line 26, in <module> _StepVector = swig_import_helper() File "C:\Python27\lib\site-packages\HTSeq\StepVector.py", line 22, in swig_imp ort_helper _mod = imp.load_module('_StepVector', fp, pathname, description) ImportError: DLL load failed: The specified module could not be found. HTSeq-0.5.4p1.win32-py2.7.exe |
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#2 |
Senior Member
Location: East Coast USA Join Date: Feb 2008
Posts: 7,087
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#3 |
Junior Member
Location: Ithaca NY Join Date: Apr 2013
Posts: 5
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hi,
Thank you so much for taking a few minutes to help me. When I type import HTSeq after typing python it gives me nearly the same error message as above. But, if I type import HTSeq again it doesn't give me an error message. I tried reinstalling HTSeq to no avail. |
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#4 |
Senior Member
Location: East Coast USA Join Date: Feb 2008
Posts: 7,087
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I have sent some email to Simon Anders (not sure if he is on this forum). It appears that the current version of HTseq for windows is not working (for me either).
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#6 |
Junior Member
Location: Ithaca NY Join Date: Apr 2013
Posts: 5
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hi,
Thanks for your help. For now I guess I'll run HTSeq on a mac instead and look into seqtk for future use. |
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#7 |
Junior Member
Location: North Carolina Join Date: Sep 2012
Posts: 3
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I'm having the same issue with HTSeq on my PC. Made sure I was using Python 2.7, reinstalled numpy, reinstalled HTSeq, also without success.
Is there an alternative for getting read counts from SAM file produced by BWA? |
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#8 |
Senior Member
Location: Heidelberg, Germany Join Date: Feb 2010
Posts: 994
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It's hard to say what's wrong if you don't post complete session logs (i.e., all commands typed plus all output and error messages)
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#9 | |
Senior Member
Location: East Coast USA Join Date: Feb 2008
Posts: 7,087
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![]() Quote:
On a windows 7 (64-bit) machine: I installed 32-bit python, NumPy (BTW: the www.scipy.org link you have in the instructions does not work any more, I downloaded NumPy from: https://pypi.python.org/pypi/numpy). Trying "import HTSeq" as recommended in your instructions is generating the following error. Googling around seems to indicate that a VS2010 DLL may be missing but I would like to get your take on what is going on. Code:
Python 2.7.4 (default, Apr 6 2013, 19:54:46) [MSC v.1500 32 bit (Intel)] on win 32 Type "help", "copyright", "credits" or "license" for more information. >>> import HTSeq Traceback (most recent call last): File "<stdin>", line 1, in <module> File "C:\Python27\lib\site-packages\HTSeq\__init__.py", line 9, in <module> from _HTSeq import * File "_HTSeq.pyx", line 14, in init HTSeq._HTSeq (src/_HTSeq.c:31058) File "C:\Python27\lib\site-packages\HTSeq\StepVector.py", line 26, in <module> _StepVector = swig_import_helper() File "C:\Python27\lib\site-packages\HTSeq\StepVector.py", line 22, in swig_imp ort_helper _mod = imp.load_module('_StepVector', fp, pathname, description) ImportError: DLL load failed: The specified module could not be found. >>> |
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#10 |
Senior Member
Location: Heidelberg, Germany Join Date: Feb 2010
Posts: 994
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Seems that "_StepVector.dll" is really missing in this binary package. I'll try to fix it.
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#11 |
Senior Member
Location: East Coast USA Join Date: Feb 2008
Posts: 7,087
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#12 |
Senior Member
Location: Heidelberg, Germany Join Date: Feb 2010
Posts: 994
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Okay, after an hour of fighting with Windows (even the easiest things are hard on an OS that one uses less than once a year), I found the mistake and fixed it.
Please try HTSeq-0.5.4p2.win32-py2.7.exe and let me know if it still fails. |
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#13 |
Senior Member
Location: East Coast USA Join Date: Feb 2008
Posts: 7,087
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Lot of people want to use this package on windows so "fighting windows" on your part is worthwhile
![]() We are not in the clear yet. This is the latest result. Code:
Python 2.7.4 (default, Apr 6 2013, 19:54:46) [MSC v.1500 32 bit (Intel)] on wi 32 Type "help", "copyright", "credits" or "license" for more information. >>> import HTSeq Traceback (most recent call last): File "<stdin>", line 1, in <module> File "C:\Python27\lib\site-packages\HTSeq\__init__.py", line 9, in <module> from _HTSeq import * ImportError: DLL load failed: The specified module could not be found. >>> |
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#14 |
Senior Member
Location: Heidelberg, Germany Join Date: Feb 2010
Posts: 994
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Could you post a list of all file in C:\Python27\lib\site-packages\HTSeq\, please? With file extensions, if possible. Or, maybe compare with my system, where the directory looks like this:
Code:
C:\Python27\Lib\site-packages\HTSeq>dir Volume in drive C has no label. Volume Serial Number is BC62-98E8 Directory of C:\Python27\Lib\site-packages\HTSeq 18/04/2013 16:22 <DIR> . 18/04/2013 16:22 <DIR> .. 18/04/2013 16:22 <DIR> scripts 18/02/2013 17:06 25,079 StepVector.py 18/04/2013 16:42 32,148 StepVector.pyc 18/04/2013 16:42 32,097 StepVector.pyo 18/04/2013 18:21 248,832 _HTSeq.pyd 20/02/2013 17:19 1,407 _HTSeq_internal.py 18/04/2013 16:42 2,011 _HTSeq_internal.pyc 18/04/2013 16:42 2,011 _HTSeq_internal.pyo 18/04/2013 18:21 83,968 _StepVector.pyd 18/04/2013 18:17 24 _version.py 18/04/2013 16:42 168 _version.pyc 18/04/2013 16:42 168 _version.pyo 18/04/2013 18:16 32,996 __init__.py 18/04/2013 16:42 36,726 __init__.pyc 18/04/2013 16:42 36,495 __init__.pyo 14 File(s) 534,130 bytes 3 Dir(s) 5,331,779,584 bytes free |
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#15 |
Senior Member
Location: East Coast USA Join Date: Feb 2008
Posts: 7,087
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Here it is. Looks the same at first glance to me.
Code:
Directory of c:\Python27\Lib\site-packages\HTSeq 04/18/2013 11:29 AM <DIR> . 04/18/2013 11:29 AM <DIR> .. 04/18/2013 11:29 AM <DIR> scripts 02/18/2013 11:06 AM 25,079 StepVector.py 04/18/2013 11:29 AM 32,148 StepVector.pyc 04/18/2013 11:29 AM 32,097 StepVector.pyo 04/18/2013 12:21 PM 248,832 _HTSeq.pyd 02/20/2013 11:19 AM 1,407 _HTSeq_internal.py 04/18/2013 11:29 AM 2,011 _HTSeq_internal.pyc 04/18/2013 11:29 AM 2,011 _HTSeq_internal.pyo 04/18/2013 12:21 PM 83,968 _StepVector.pyd 04/18/2013 12:17 PM 24 _version.py 04/18/2013 11:29 AM 168 _version.pyc 04/18/2013 11:29 AM 168 _version.pyo 04/18/2013 12:16 PM 32,996 __init__.py 04/18/2013 11:29 AM 36,726 __init__.pyc 04/18/2013 11:29 AM 36,495 __init__.pyo 14 File(s) 534,130 bytes |
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#16 |
Senior Member
Location: East Coast USA Join Date: Feb 2008
Posts: 7,087
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When I checked _HTseq.pyd with "dependency walker" it is complaining that "IESHIMS.DLL" can't be found. I will try to see if I can diagnose this further.
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#17 |
Senior Member
Location: Heidelberg, Germany Join Date: Feb 2010
Posts: 994
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Interesting. Just ran "dependency walker" on my system, and I don't have IESHIMS.DLL either, although everything is working for me. Also, it's a "delayed dependency", so it wouldn't cause an issue right at loading.
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#18 |
Senior Member
Location: Heidelberg, Germany Join Date: Feb 2010
Posts: 994
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1. Could somebody else who ha a Windows system maybe try? Just to know if its a general problem or something specific to GenoMax's system.
2. GenoMax, could you try to load "_HTSeq" (with the underscore) directly, as follows? Code:
C:\>cd \Python27\Lib\site-packages\HTSeq C:\Python27\Lib\site-packages\HTSeq>c:\Python27\python.exe Python 2.7.4 (default, Apr 6 2013, 19:54:46) [MSC v.1500 32 bit (Intel)] on win32 Type "help", "copyright", "credits" or "license" for more information. >>> import _HTSeq Last edited by Simon Anders; 04-18-2013 at 01:45 PM. Reason: added full path |
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#19 |
Senior Member
Location: East Coast USA Join Date: Feb 2008
Posts: 7,087
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Here is what I get. May try to uninstall and reinstall everything tomorrow.
Code:
Python 2.7.4 (default, Apr 6 2013, 19:54:46) [MSC v.1500 32 bit (Intel)] on 32 Type "help", "copyright", "credits" or "license" for more information. >>> import _HTSeq Traceback (most recent call last): File "<stdin>", line 1, in <module> ImportError: No module named _HTSeq >>> |
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#20 |
Senior Member
Location: Heidelberg, Germany Join Date: Feb 2010
Posts: 994
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So, you went right to the directory that contained _HTSeq.pyd (you did notice the "cd" command I put on top? I shoudl have highlighted it.), and even then, it doesn't see it? That's strange.
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