Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Simon Anders
    replied
    Plans, yes -- but I'm so overwhelmed with other things that it might take a while till I get to that. Sorry.

    Leave a comment:


  • GenoMax
    replied
    Hi Simon,

    We have been encountering an error with htseq-count (v. 0.6.1p1) on alignment files that have SAM v.1.4 tags.

    The specific error is

    Code:
    Unknown CIGAR code 'X' encountered
    I found an old request about this error which does not appear to have been implemented in htseq-count yet : http://sourceforge.net/p/htseq/support-requests/22/

    Are there plans to add support for SAM v.1.4 tags to htseq-count? For now we have been working around this by generating SAM v.1.3 tags.

    Thanks.

    Leave a comment:


  • gringer
    replied
    From the looks of it, the read locations are zero-based and open-ended on the right, so don't include the "end" location in the list of base locations. For an end location of -2, that's a bit more concerning, otherwise it's just business as usual for how these things are done.

    Leave a comment:


  • patchper
    replied
    I don't know where to report bugs so I posted here.
    I think the start_d and end_d feature of GenomicIntervals have bugs.
    With a SAM file below as sample.sam:
    read1 0 chr 1 40 7M * 0 0 ATGGCGT AAAAAAA
    read2 16 chr 1 40 7M * 0 0 ATGGCGT AAAAAAA

    and:
    >>> read1,read2 = list(itertools.islice(HTSeq.SAM_Reader('sample.sam'),2))

    >>> read1
    <SAM_Alignment object: Read 'read' aligned to chr:[0,7)/+>

    >>> read2
    <SAM_Alignment object: Read 'read2' aligned to chr:[0,7)/->

    >>> read1.iv.start,read1.iv.end,read1.iv.start_d,read1.iv.end_d
    (0, 7, 0, 7)

    >>> read2.iv.start,read2.iv.end,read2.iv.start_d,read2.iv.end_d
    (0, 7, 6, -1)

    the end_d of read2 ended with a negative coordinate! This behavior is mentioned in document, but I think it is a bug rather than a feature.

    Leave a comment:


  • zjrouc
    replied
    i just got a result from ht-seq. It showed that my interesting gene has 7 counts in the alignment. However, from the view of IGV, i could easily identify much more counts than 7 on this gene. My alignment is from STAR, and i used more stringent parameters to control the multiple alignment, which means there should not be any multiple aligned reads in the output. I am really confused about this.

    Any suggestion?
    Attached Files

    Leave a comment:


  • cdias
    replied
    Hi,
    I'm having trouble installing HTSeq.
    I pretty much followed the instructions, but when I try to run it, I get the following error:

    .local/lib/python2.7/site-packages/HTSeq-0.6.1-py2.7-linux-x86_64.egg/HTSeq/_HTSeq.so: undefined symbol: PyUnicodeUCS2_DecodeUTF8

    Any help is appreciated!

    Leave a comment:


  • Simon Anders
    replied
    Originally posted by superpyrin View Post
    Multiprocessing can work only with objects that can be pickled. SAM_Alignment cannot be pickled. I suspect this may be the reason it does not work.
    I suppose you are right. makes perfect sense.

    Objects must implement __getstate__ and __setstate__ functions in order to be pickled/unpickled. Would it be difficult to implement these functions?
    I don't think so. I would just need to find the time to do it.

    All one needs to do is take all the slots defined for the class in _HTSeq.SAM_Alignment, pack them into a tuple for __getstate__ and write them back for __setstate__.

    Leave a comment:


  • superpyrin
    replied
    Originally posted by Simon Anders View Post
    Yes, the C code is machine generated, but if you look at the pyx files which it is generated from, it should be clearer. Have a look at:
    http://www-huber.embl.de/users/ander...c/contrib.html
    Multiprocessing can work only with objects that can be pickled. SAM_Alignment cannot be pickled. I suspect this may be the reason it does not work.

    Objects must implement __getstate__ and __setstate__ functions in order to be pickled/unpickled. Would it be difficult to implement these functions?

    Leave a comment:


  • Simon Anders
    replied
    Yes, the C code is machine generated, but if you look at the pyx files which it is generated from, it should be clearer. Have a look at:

    Leave a comment:


  • superpyrin
    replied
    Originally posted by Simon Anders View Post
    You asked me this before, but Ididn't reply, right? Sorry about that, I was a bit overwhelmed with mails.

    The bad news is: I have no clue why it does not work; I have never worked with the multiprocessing package. But I agree that it would be nice if this worked.

    Maybe somebody else here has some idea?
    my guess is that it is something trivial, perhaps missing implementation of some part of dictionary/list interface in on of HTSeq data structures. I tried to look into HTSeq source, but it seems to be machine generated code, so I quickly gave up.

    Leave a comment:


  • Simon Anders
    replied
    You asked me this before, but Ididn't reply, right? Sorry about that, I was a bit overwhelmed with mails.

    The bad news is: I have no clue why it does not work; I have never worked with the multiprocessing package. But I agree that it would be nice if this worked.

    Maybe somebody else here has some idea?

    Leave a comment:


  • superpyrin
    replied
    Running HTSeq in parallel

    Hello,

    I am trying to process mapped reads in parallel. However, when using pool of workers (multiprocessing package), I get following error:

    Traceback (most recent call last):
    File "testmp.py", line 15, in <module>
    out = pool.map(repr, iter(sa), chunksize=1)
    File "/usr/lib/python2.7/multiprocessing/pool.py", line 228, in map
    return self.map_async(func, iterable, chunksize).get()
    File "/usr/lib/python2.7/multiprocessing/pool.py", line 531, in get
    raise self._value
    AttributeError: 'NoneType' object has no attribute 'name'


    Running in serial fashion (using just built-in 'map' function) works fine.

    Do you know what can be wrong here?

    Thank you.

    ---

    Here is a simple script to reproduce the error. I am using HTSeq ver 0.6.1, Python 2.7.3, 64bit ubuntu 12.04

    import HTSeq
    from multiprocessing import Pool
    # this works for me
    map(repr, sa)

    # this does not work
    pool = Pool(processes=1)
    sa = HTSeq.SAM_Reader('test.sam')
    out = pool.map(repr, sa, chunksize=1)
    print list(out)

    Leave a comment:


  • emolinari
    replied
    Originally posted by fanli View Post
    Yep, that output looks good.

    samtools sort -n gives the same result as Unix sort -k 1,1 on the SAM file.
    That's reassuring!!!
    thanks indeed

    Manu

    Leave a comment:


  • fanli
    replied
    Yep, that output looks good.

    samtools sort -n gives the same result as Unix sort -k 1,1 on the SAM file.

    Leave a comment:


  • emolinari
    replied
    Originally posted by fanli View Post
    This sorts your alignment by genomic position. You want to sort by read name:
    Hi fanli,

    thanks for your reply! Meanwhile I had done samtools sort -n on my .bam file, samtools view -h to create a .sam file and run HTSeq again.
    I guess it worked, as the sterror file created was way way smaller, and contains this:
    100000 sam line pairs processed.
    200000 sam line pairs processed.
    300000 sam line pairs processed.
    500000 sam line pairs processed.
    600000 sam line pairs processed.
    700000 sam line pairs processed.
    800000 sam line pairs processed.
    900000 sam line pairs processed.
    1000000 sam line pairs processed.
    1100000 sam line pairs processed.
    1200000 sam line pairs processed.
    1300000 sam line pairs processed.
    1400000 sam line pairs processed.
    1500000 sam line pairs processed.
    1600000 sam line pairs processed.
    1700000 sam line pairs processed.
    1800000 sam line pairs processed.
    1900000 sam line pairs processed.
    2000000 sam line pairs processed.
    2100000 sam line pairs processed.
    2200000 sam line pairs processed.
    2300000 sam line pairs processed.
    2500000 sam line pairs processed.
    [...]
    31936941 sam line pairs processed.

    So I guess this is correct, right?
    So I guess my question is: does it make any difference practically if you sort the .bam and then make it .sam or if you sort a .sam file with the command you suggested? I am too ignorant to appreciate the difference!

    Thanks again!!!

    Leave a comment:

Latest Articles

Collapse

  • seqadmin
    Latest Developments in Precision Medicine
    by seqadmin



    Technological advances have led to drastic improvements in the field of precision medicine, enabling more personalized approaches to treatment. This article explores four leading groups that are overcoming many of the challenges of genomic profiling and precision medicine through their innovative platforms and technologies.

    Somatic Genomics
    “We have such a tremendous amount of genetic diversity that exists within each of us, and not just between us as individuals,”...
    05-24-2024, 01:16 PM
  • seqadmin
    Recent Advances in Sequencing Analysis Tools
    by seqadmin


    The sequencing world is rapidly changing due to declining costs, enhanced accuracies, and the advent of newer, cutting-edge instruments. Equally important to these developments are improvements in sequencing analysis, a process that converts vast amounts of raw data into a comprehensible and meaningful form. This complex task requires expertise and the right analysis tools. In this article, we highlight the progress and innovation in sequencing analysis by reviewing several of the...
    05-06-2024, 07:48 AM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, 05-24-2024, 07:15 AM
0 responses
15 views
0 likes
Last Post seqadmin  
Started by seqadmin, 05-23-2024, 10:28 AM
0 responses
18 views
0 likes
Last Post seqadmin  
Started by seqadmin, 05-23-2024, 07:35 AM
0 responses
21 views
0 likes
Last Post seqadmin  
Started by seqadmin, 05-22-2024, 02:06 PM
0 responses
10 views
0 likes
Last Post seqadmin  
Working...
X