[Biojava-l] Parsing embl format with biojava4

[Dario Beraldi]

Ok thank you, I'll consider Biojava 1.9 if embl files are not supported in
later versions.

By the way, I tried to compile biojava-legacy-1.9.2 and I got some tests
failing:

----------------------
cd biojava-legacy-biojava-legacy-1.9.2
mvn package
....
....

Results :


Failed tests:

  GenbankRichSequenceDBTest.testeFetch:24 Unexpected Bioexception:
org.biojava.bio.BioException: Failed to read Genbank sequence

  GenpeptRichSequenceDBTest.testeFetch:24 Unexpected BioException:
org.biojava.bio.BioException: Failed to read Genbank sequence


Tests run: 883, Failures: 2, Errors: 0, Skipped: 0


[INFO]
------------------------------------------------------------------------

[INFO] Reactor Summary:

[INFO]

[INFO] biojava-legacy ..................................... SUCCESS [
0.725 s]

[INFO] bytecode ........................................... SUCCESS [
1.505 s]

[INFO] core ............................................... FAILURE [
10.232 s]

[INFO] alignment .......................................... SKIPPED

[INFO] biosql ............................................. SKIPPED

[INFO] blast .............................................. SKIPPED

[INFO] sequencing ......................................... SKIPPED

[INFO] gui ................................................ SKIPPED

[INFO] phylo .............................................. SKIPPED

[INFO]
------------------------------------------------------------------------

[INFO] BUILD FAILURE

[INFO]
------------------------------------------------------------------------

[INFO] Total time: 12.692 s

[INFO] Finished at: 2016-12-28T16:38:18+00:00

[INFO] Final Memory: 11M/220M

[INFO]
------------------------------------------------------------------------

[ERROR] Failed to execute goal
org.apache.maven.plugins:maven-surefire-plugin:2.17:test (default-test) on
project core: There are test failures.

[ERROR]

[ERROR] Please refer to
/Users/berald01/Downloads/biojava-legacy-biojava-legacy-1.9.2/core/target/surefire-reports
for the individual test results.

[ERROR] -> [Help 1]

[ERROR]

[ERROR] To see the full stack trace of the errors, re-run Maven with the -e
switch.

[ERROR] Re-run Maven using the -X switch to enable full debug logging.

[ERROR]

[ERROR] For more information about the errors and possible solutions,
please read the following articles:

[ERROR] [Help 1]
http://cwiki.apache.org/confluence/display/MAVEN/MojoFailureException

[ERROR]

[ERROR] After correcting the problems, you can resume the build with the
command

[ERROR]   mvn <goals> -rf :core

On 28 December 2016 at 15:45, Michael Heuer <heuermh at gmail.com> wrote:

> On Wed, Dec 28, 2016 at 3:30 AM, Dario Beraldi <dario.beraldi at gmail.com>
> wrote:
>
>> Hello,
>>
>> First, thanks for the great Biojava project!
>>
>> Is it possible to parse embl files using (Bio)Java?
>>
>> By Googling "biojava  embl format" I get some hits for the legacy Biojava
>> 1.9 but I'm wondering weather I could (should?) use the more recent Biojava
>> 4?
>>
>
> If biojava-legacy works fine for you, feel confident using it.  It is
> actively maintained; there just won't be any new features.
>
>
>
>> A more general question... Which is the primary source of documentation
>> for Biojava 4? Is it the tutorial at https://github.com/biojava/bio
>> java-tutorial together with the Javadocs (http://biojava.org/docs/api4.
>> 2.1/)?
>>
>> I find the home page Biojava.org a little confusing... The tutorial page
>> http://biojava.org/wiki/BioJava:CookBook4.0/ gives me a 404 error. The
>> wiki pages http://biojava.org/wiki.html seem a mixture of various topics.
>>
>
> The biojava.org website didn't survive a wiki migration to github without
> running into some problems.  If you find any, please file them as issues at
>
> https://github.com/biojava/biojava.github.io
>
>    michael
>
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