From 011aa63246bfb2928cc666440db67b61e0e33f64 Mon Sep 17 00:00:00 2001 From: dereneaton Date: Thu, 31 Mar 2016 16:48:31 -0700 Subject: [PATCH] readme update and optim for multi_muscle_align increased --- README.rst | 4 ++-- docs/tutorial_intro_cli.rst | 2 +- ipyrad/assemble/cluster_within.py | 6 +++--- 3 files changed, 6 insertions(+), 6 deletions(-) diff --git a/README.rst b/README.rst index 6ce4cfdf..4b55eb87 100644 --- a/README.rst +++ b/README.rst @@ -12,9 +12,9 @@ Tutorials Documentation is in the works_, for now there are working example tutorials_. -.. _tutorials: http://nbviewer.ipython.org/github/dereneaton/ipyrad/tree/master/tests/ +.. _tutorials: http://ipyrad.readthedocs.org/en/latest/userguide.html -.. _works: http://ipyrad.readthedocs.org/en/latest/ +.. _works: http://ipyrad.readthedocs.org/en/latest/ Installation ------------ diff --git a/docs/tutorial_intro_cli.rst b/docs/tutorial_intro_cli.rst index d42a0e96..2b7dfaa5 100644 --- a/docs/tutorial_intro_cli.rst +++ b/docs/tutorial_intro_cli.rst @@ -214,7 +214,7 @@ separate line with a tab between them. .. code-block:: bash - cat ./data/sim_rad_test_barcodes.txt + cat ./ipsimdata/sim_rad_test_barcodes.txt .. parsed-literal:: 1A_0 CATCAT diff --git a/ipyrad/assemble/cluster_within.py b/ipyrad/assemble/cluster_within.py index d7d4c3da..84466864 100644 --- a/ipyrad/assemble/cluster_within.py +++ b/ipyrad/assemble/cluster_within.py @@ -779,9 +779,9 @@ def multi_muscle_align(data, sample, ipyclient): ## get the number of clusters clustfile = os.path.join(data.dirs.clusts, sample.name+".clust.gz") clustio = gzip.open(clustfile, 'rb') - optim = 100 - if sample.stats.clusters_total > 500: - optim = int(sample.stats.clusters_total/len(ipyclient))//2 + optim = 1000 + #if sample.stats.clusters_total > 500: + # optim = int(sample.stats.clusters_total/len(ipyclient))//2 LOGGER.debug("optim for align chunks: %s", optim) ## write optim clusters to each tmp file