* odt export error
@ 2011-12-14 3:03 Kevin Emerson
2011-12-14 8:38 ` Christian Moe
` (2 more replies)
0 siblings, 3 replies; 4+ messages in thread
From: Kevin Emerson @ 2011-12-14 3:03 UTC (permalink / raw
To: emacs-orgmode
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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]]
^ permalink raw reply [flat|nested] 4+ messages in thread
* Re: odt export error
2011-12-14 3:03 odt export error Kevin Emerson
@ 2011-12-14 8:38 ` Christian Moe
2011-12-14 9:09 ` Eric S Fraga
2011-12-15 7:45 ` Jambunathan K
2 siblings, 0 replies; 4+ messages in thread
From: Christian Moe @ 2011-12-14 8:38 UTC (permalink / raw
To: Kevin Emerson; +Cc: emacs-orgmode
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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 --]
[-- Type: application/vnd.oasis.opendocument.text, Size: 11078 bytes --]
^ permalink raw reply [flat|nested] 4+ messages in thread
* Re: odt export error
2011-12-14 3:03 odt export error Kevin Emerson
2011-12-14 8:38 ` Christian Moe
@ 2011-12-14 9:09 ` Eric S Fraga
2011-12-15 7:45 ` Jambunathan K
2 siblings, 0 replies; 4+ messages in thread
From: Eric S Fraga @ 2011-12-14 9:09 UTC (permalink / raw
To: Kevin Emerson; +Cc: emacs-orgmode
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)
^ permalink raw reply [flat|nested] 4+ messages in thread
* Re: odt export error
2011-12-14 3:03 odt export error Kevin Emerson
2011-12-14 8:38 ` Christian Moe
2011-12-14 9:09 ` Eric S Fraga
@ 2011-12-15 7:45 ` Jambunathan K
2 siblings, 0 replies; 4+ messages in thread
From: Jambunathan K @ 2011-12-15 7:45 UTC (permalink / raw
To: Kevin Emerson; +Cc: emacs-orgmode
> 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.
--
^ permalink raw reply [flat|nested] 4+ messages in thread
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2011-12-14 3:03 odt export error Kevin Emerson
2011-12-14 8:38 ` Christian Moe
2011-12-14 9:09 ` Eric S Fraga
2011-12-15 7:45 ` Jambunathan K
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