addition of LEA-Seq method #1514
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Implements Low-Error Amplicon Sequencing (LEA-Seq) method, described in: Faith, Jeremiah J., et al. "The long-term stability of the human gut microbiota." Science 341.6141 (2013).
Implements Low-Error Amplicon Sequencing (LEA-Seq) method, described in: Faith, Jeremiah J., et al. "The long-term stability of the human gut microbiota." Science 341.6141 (2013).
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Build results will soon be (or already are) available at: http://ci.qiime.org/job/qiime-github-pr/824/ |
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@ElBrogrammer just so you are aware this is in, take a quick look at it if you have some time this week |
| #!/usr/bin/env python | ||
| from __future__ import division | ||
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| __author__ = "Jai Ram Rideout" |
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You can change the author to yourself since you wrote most of this.
| log_out: string | ||
| to be printed in log file | ||
| """ | ||
| log_out = "Quality filter results\nTotal number of input sequences: {}\nBarcode not in mapping file: {}\nSequence shorter than threshold: {}\nBarcode errors exceeds limit: {}\nPrimer mismatch count: {}\n\nTotal number seqs written: {}".format(input_seqs_count, barcode_not_in_map_count, seq_too_short_count, barcode_errors_exceed_max_count, primer_mismatch_count, total_seqs_kept) |
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Few more comments. @charudatta-navare I recomend to run |
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Thanks @josenavas! @charudatta-navare if you can take care of the issues pointed by Jose, we should be close to wrapping this up. |
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@josenavas @cleme @jairideout |
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Build results will soon be (or already are) available at: http://ci.qiime.org/job/qiime-github-pr/1212/ |
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Looks like the checks are failing due to a different issue (pip can't proceed with requirement 'pynast==1.2.2 (from qiime==1.8.0-dev)' due to a pre-existing build directory.) The tests are passing on my machine, so I think when the problem with pynast installation is solved, the tests should pass. |
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I am not exactly sure why you are getting that error, I think I read somewhere running pip with --force-reinstall on the install requirements fixes this, but not sure. @jairideout @gregcaporaso @josenavas any suggestions on this? |
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The error comes in automated testing of the build on Jenkins. The tests fail after running for just over a minute. |
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Retest this please |
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Sometimes re-testing works |
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Build results will soon be (or already are) available at: http://ci.qiime.org/job/qiime-github-pr/1214/ |
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retest this please |
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Build results will soon be (or already are) available at: http://ci.qiime.org/job/qiime-github-pr/1216/ |
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@charudatta-navare I don't see any issues with this. However, before merging, can you pull form upstream and push again? Now that #1700 has been merged, I'm not completely sure if all your |
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Build results will soon be (or already are) available at: http://ci.qiime.org/job/qiime-github-pr/1241/ |
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Build results will soon be (or already are) available at: http://ci.qiime.org/job/qiime-github-pr/1242/ |
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Thanks for pointing that out, @josenavas! It needed a few changes in skbio imports, but that tests are passing now. |
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Great! Thanks for the hard work @charudatta-navare |
Implements Low-Error Amplicon Sequencing (LEA-Seq) method, described in: Faith, Jeremiah J., et al. "The long-term stability of the human gut microbiota." Science 341.6141 (2013).
I need to add a couple of functions in split_libraries_lea_seq.py, and I need to add unit tests. I will add those soon.