Join paired ends updates

[mikerobeson]

Moved function write_synced_barcodes_fastq and its test code to format.py and test_format.py respectively as per #1243.

Also:

• Updated to skbio.io code.
• removed test_join_paired_ends.py as all relevant test code is now in test_format.py

[ghost]

Build results will soon be (or already are) available at: http://ci.qiime.org/job/qiime-github-pr/1256/

[ghost]

Build results will soon be (or already are) available at: http://ci.qiime.org/job/qiime-github-pr/1258/

[gregcaporaso]

Could you replace that link with this one:
http://scikit-bio.org/docs/latest/generated/skbio.io.fastq.html#format-specification

[gregcaporaso]

retest this please

[mikerobeson]

Done. I went through and updated broken code to relevant skbio code in:

• test_format.py
• format.py

The updated code in these two files pass all unit tests on my local machine.

I've also updated the link to the skbio fastq format information as requested in 'join_paired_ends.py'

[ghost]

Build results will soon be (or already are) available at: http://ci.qiime.org/job/qiime-github-pr/1278/

[ebolyen]

remove this comment

[ghost]

Build results will soon be (or already are) available at: http://ci.qiime.org/job/qiime-github-pr/1437/

[jairideout]

retest this please

[ghost]

Build results will soon be (or already are) available at: http://ci.qiime.org/job/qiime-github-pr/1439/

[gregcaporaso]

@mikerobeson, thanks for these edits. @jairideout and I are working on prepping 1.9.0 now, and decided that we're going to not merge this for now, and re-assign for the 2.0.0. Our motivation for this is that this would be the only code in QIIME 1.9.0 that uses the new skbio fastq parsers, and it's not a good idea for the code base to be using different parsers for the same file format due to possible inconsistencies. We'll integrate these changes when we port all of the fastq parsing in QIIME to use the new parsers.

Sorry we didn't notice the issue with porting to the new skbio parsers sooner. As always, we really appreciate your contributions to QIIME so thanks again!

[mikerobeson]

Was I not supposed to use skbio? I used skbio because the test code warned me of deprecated code and specified that I use skbio. :-(