odt export error

odt export error

[Kevin Emerson]

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Hello all,
I am relatively new to org-mode, but I am certainly a convert - a
great piece of work!  I usually export things as html, but my employer
always wants updates in doc format.  I was hoping to use the new odt
export functionality and then I can save the odt as a doc file.  This
works for me sometimes - but not always.

I can not pinpoint exactly what yields the error, but it reads "Format
error discovered in the file in sub-document styles.xml at
415,108(row,col) when the file attempts to open in openoffice 3.2.  I
am using org-mode 7.6.

I have attached my org file and the resulting odt file.

Any thoughts would be greatly appreciated.

Cheers,
Kevin

-- 
------
------
Kevin J. Emerson, Ph.D.
Post-Doctoral Researcher, Bradshaw-Holzapfel Lab
Institute of Ecology and Evolution
335 Pacific Hall
5289 University of Oregon
Eugene, OR 97403
web: http://www.uoregon.edu/~kemerson
email: kemerson@uoregon.edu, kevin.j.emerson@gmail.com
--

[-- Attachment #2: 2011-12-13-periodAnnotationTranscriptome2.odt --]
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[-- Attachment #3: 2011-12-13-periodAnnotationTranscriptome2.org --]
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# 2011-12-13-periodAnnotationTranscriptome2.org
#+TITLE:     Period annotation (Assembly 2)
#+AUTHOR:    Kevin Emerson
#+OPTIONS:   H:2 num:t toc:t \n:nil @:t ::t |:t ^:t -:t f:t *:t <:t
#+OPTIONS:   TeX:t LaTeX:t skip:nil d:nil todo:nil pri:nil tags:not-in-toc
#+STYLE: <link rel="stylesheet" type="text/css" href="org.css" />

* Locate sequences that are associated with /period/
  Using OrthoDB ID: [[http://cegg.unige.ch/orthodb4/results?searchtext=EOG4V41PZ&level=Aa_Ag_Am_Ap_Bm_Cq_Da_De_Dg_Dme_Dmo_Dpe_Dps_Dpu_Dse_Dsi_Dv_Dw_Dy_Is_Lh_Nvi_Pb_Ph_Tc&tree=Arth&swaptree=][EOG4V41PZ]]
** contig15855
*** Sequence
    >contig15855  length=258  numreads=17  gene=isogroup02170  status=isotig
    ACATTATCCAGCCATGGTGGATtAGGACGACgTTTtACGCGGCTCGCGCTGTCCCAGTCG
    CCATCGTTGACTATCCgTTTCAACGGATCGTCACTATCGGACGAGTTATCCGTCTTCAGG 
    AAGCTTGAGTAGAAaCTAgaCAAACTtGAAATATCCATGTCGTCGTTGATtCCcGGTGGA
    GGATAGATGGTTCTACGGCTGGCTGGTTTATCGGTATCTTCTAGCTGGAAGCCTCCGCcG
    ACGTTcAATACTtGTGTC    
** contig24967
*** Sequence
    >contig24967  length=80  numreads=793  gene=isogroup00699  status=isotig
    GAACTTGTTGCGGTTGGTATTGCGGCTGATATTGCCGAGCTACCTGCTGCTGTTGGGGCT
    GCTGGAATTGTCGTTGAATC

** F5BTJ3O01A331S 
*** Sequence
    >F5BTJ3O01A331S rank=0100662 x=339.0 y=3054.0 length=527 trimmed=11-527
    GAGGCGCCGCTGGGAAATGGCGAATTCGAAACGAACAGCGTTCGAACCATTCTGTTGATA
    GTTTCTGCTACTCCAATCAAGAGTGTCTTCAAAGTTCCCAACGAACAGTTCAGCGATAAC
    GCAATGAAATTCACTACCAGACACACGACGTGCGGAGTGTTGAGTTACGTCGATGGGAAT
    TCGGCAGAGTTGATCGGGTATCTACCGCAGGACATCCTGGGACGCTCGGTAATGGAGTTC
    TATCACCCAGAGGACATGACCATTTTGAAAAACGTTTACGAGACAGTTATGGTGAAAGGA
    CAGACGGCTGGAGCATCGTTCGTCAGTCAACCATATCGCTTTTTGATCAACAATGGATGT
    TTTATAGTGTTGCAAACGGAATGGACCAGTTTCGTTAACCCGTGGTCCAGAGGGCTTGAG
    TTTGTAATAGGACATCACCAGATATTGGAAGGACCCGTGATTCCGGATGTGTTTGCTTCG
    AATGAAAACTCGCGCACATTTTCCAATGAGCTAATGG

 


** F5BTJ3O01D9IE3
*** Sequence
    >F5BTJ3O01D9IE3 rank=0059719 x=1631.0 y=1773.5 length=428 trimmed=11-417
    TGATCGGGTATCTACCGCAGGACATCCTGGGACGCTCGGTAATGGAGTTCTATCACCCAG
    AGGACATGACCATTTTGAAAAACGTTTACGAGACAGTTATGGAGAAAGGACAGACGGCTG
    GAGCATCGTTCGTCAGTCAACCATATCGCTTTTTGATCAACAATGGATGTTTCATAGTGT
    TGCAAACGGAATGGACCAGTTTCGTTAACCCGTGGTCCAGAGAGCTTGAGTTTGTAATAG
    GACATCACCAGATATTGGAAGGACCCGTGATTCCGGATGTGTTTGCTTCGAATGAAAACT
    CGCGCACATTTTCCAATGAGCTAATGGCATCCGCGAAAAGGATGGAGGAACATATTCTGC
    GTATTCTGAAGGAACCGGTAGCAAAGCCCTCGGATAAGGTTAAACAG
    
** F5BTJ3O01DOJYE
*** Sequence
    >F5BTJ3O01DOJYE rank=0475003 x=1392.5 y=2932.0 length=534 trimmed=11-534
    TTGATGATTGCCGATTCACATGCTTTCTTGAATATGGATATATCCTCGGGGTGATAAAGT
    TCCATTATCGAACGGCCGAGAATATCTTGCGGTAAATAGCCGATTGATTTGACAGAATTT
    TCATCCACATATTTTAGTATTCCACCGATCGTGTGGCGGGTGCTGAACCGCAGTTGTTTA
    TTGTCCAACGATTCATTAGGCTCTTTATAAATACTAAAAAACCGGTTGAGCGCAGATCAC
    TAGTATAATATTCGTGGCACTCTTCGAGCTCGTAAGTTCTTTGCCTTCTAAAGGTGCATT
    CCGGAACATTAAAGTCAACCTGTACGGTTGGTAGATTACGGAAGACTTGGTAATACAGAA
    ACCTACATTCCTTAATCCTCGATACTTCCGTAACATGACGTACAGAAAATTTGTTTGTTC
    TTTCTGATTAGAATCACTCAGGGCGAGCATCACGTTCGAGGTAATTTGCTTAGAAAATGT
    CGCCGATCTCTGGGATGAACGAAGTCAATGAAGGATCTGCCGAG

** F5BTJ3O02HC7W4
*** Sequence
    >F5BTJ3O02HC7W4 rank=0548528 x=2903.0 y=3526.5 length=424 trimmed=11-424
    CAGCAGCACGGATGCCTCCTCCGGCAGTATGCTTCCATCATCGTTAACCGAAGAAATACT
    CTGTCAGCACAACGAAGATATGCAGAAGGTGATGCTGAAGCGTCATCGTGAGGCAAGAAC
    ATTAGCACGTAGCACAGAGAAGAACAAAAAAGGACCTCCGGAGAAAGCGCAAGTCTGTGC
    CCACGGTGTAAAAAGNGGATCATCTCATTCCTGGGAAGGAGATATCCAAAAAACGGTTAG
    ACATCAGCACAAGCAGACTGTTGCTTCGAACATGAAGAATCAACCCCTACACGCAGTAAC
    ACCCTCGAATCCAACACCAATATCATCAGCCGTTGTCACAATGCCGTCAAGGACAGTCAT
    AACAACTGCGGCCTCTTCGGCTGCACCCCAAGGTTCAACCTTGCCGTACAGTTT

** F5BTJ3O02HOBEW
*** Sequence 
    >F5BTJ3O02HOBEW rank=0246219 x=3030.0 y=1078.0 length=493 trimmed=11-482
    TCAAATCCCGACGTATTCGCTACTGGCGTCTCGGAACTCGGAGCATTGCACAGCTTTCCG
    GAAGAGCTTCTCAAGGAGGCGAAGTCGGTGGAAGAACAAATTGTACAACTTTTGAAAAGA
    CCGATCGTTGAGTCCCCAAGTGAGAAGAAGCAAATATTTTTAAAGCAATGCAAAACGTTA
    AACGCTTTCATGGAACAAATAATCAGTGAGATGACCGGTTCCAAAACAAAATTCACACTC
    CCTAGCGATTCGGAATTTACTTCTTCTAAGCGCGACTCTATTATCATTGGAGAGGTATCT
    CCACATCATGAAGGATTGGATAGCAAAACCACATCCGACACCCTGCTAAGCTATAATCAG
    TTGAACTATAATGATAATATTCAGAGATTTTTTGTACAGTTGCCCAGTCATTAACGTATG
    TGATCCTTTAAAACCTGGCAGTTCTACGGATGTGAATCTATTTGTCTATAGG

** F5BTJ3O02HSKYJ
*** Sequence 
    >F5BTJ3O02HSKYJ rank=0659698 x=3078.0 y=3465.0 length=192 trimmed=11-192
    AACGGAGTGGCAGTTCCAAATCCCAACACAGTGGTAGTAATTCATCCGGCAGCAGCGGCT
    ATGGCGGCAAAAGCAACAGTCAGCCATCCACAGCCGGAAGTACCTTCCACCCACCAGGCA
    AACATGCCAAGGAAAAAGCCGCAAAAAGAAGGACAAGGAAGCGAAAACTTTAATCGATTC
    CT


* PERIOD alignments
  Alignments were all performed using Geneious aligner.  Alignments
  were done on amino acid sequences.  Initially, for each sequence,
  all six translations were made and an amino acid alignment was used
  to determine the correct reading frame.  Then, when the correct
  reading frame was known for each sequence, a final alignment was
  made.  Note that there are a few annotations along with two of the
  sequences. F5BTJ3O01DOJYE shows a 'half-good' alignment with the
  second portion of hte sequence aligning perfectly in the PAS domain,
  and the rest of the sequence not aligning at all with the other
  mosquito sequences (which are conserved).  Also, the alignemnt for
  F5BTJ3O02HOBEW is not very strong.

#  [[./images/per_alignments.png]]

Re: odt export error

[Christian Moe]

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Hi,

Looking into your styles.xml, it seems openoffice is choking on the 
representation of the bullet character.

Exporting your org document with the default stylesheet in Org 7.8 
works (result attached), with a valid unicode bullet character in the 
styles.xml.

It is likely that you are running an old bleeding-edge development 
version of the ODT exporter.

If you can update to Org 7.8, you should do that; as of this week, the 
ODT exporter is part of core Org. (And when you update, clean out old 
versions of org-odt from your load-path and your .emacs.)

hope this helps,
Christian



On 12/14/11 4:03 AM, Kevin Emerson wrote:
> Hello all,
> I am relatively new to org-mode, but I am certainly a convert - a
> great piece of work!  I usually export things as html, but my employer
> always wants updates in doc format.  I was hoping to use the new odt
> export functionality and then I can save the odt as a doc file.  This
> works for me sometimes - but not always.
>
> I can not pinpoint exactly what yields the error, but it reads "Format
> error discovered in the file in sub-document styles.xml at
> 415,108(row,col) when the file attempts to open in openoffice 3.2.  I
> am using org-mode 7.6.
>
> I have attached my org file and the resulting odt file.
>
> Any thoughts would be greatly appreciated.
>
> Cheers,
> Kevin
>


[-- Attachment #2: 2011-12-13-periodAnnotationTranscriptome2.odt --]
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Re: odt export error

[Eric S Fraga]

Kevin Emerson <kemerson@uoregon.edu> writes:

> Hello all,
> I am relatively new to org-mode, but I am certainly a convert - a
> great piece of work!  I usually export things as html, but my employer
> always wants updates in doc format.  I was hoping to use the new odt
> export functionality and then I can save the odt as a doc file.  This
> works for me sometimes - but not always.
>
> I can not pinpoint exactly what yields the error, but it reads "Format
> error discovered in the file in sub-document styles.xml at
> 415,108(row,col) when the file attempts to open in openoffice 3.2.  I
> am using org-mode 7.6.

I had this error when I first tried the odt exporter.  I think you may
wish to upgrade to a more recent version of org; 7.6 is quite old,
especially for ODT export.

The file you attached exports fine for me in org 7.8.02.

-- 
: Eric S Fraga (GnuPG: 0xC89193D8FFFCF67D) in Emacs 24.0.90.1
: using Org-mode version 7.8.02 (release_7.8.02.2.g490d6a)

Re: odt export error

[Jambunathan K]

> I can not pinpoint exactly what yields the error, but it reads "Format
> error discovered in the file in sub-document styles.xml at
> 415,108(row,col) when the file attempts to open in openoffice 3.2.  I
> am using org-mode 7.6.

What is your default coding system. As christian points out, the bullet
char is not representable in the specific coding system that you use. As
a consequence, the file is clobbered.

If you are averse to upgrading to latest org -- odt exporter is not
available in the standard GNU ELPA packages -- you can switch your org
file to utf-8 encoding. That could help a bit.

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