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compmetagen · Oct 8, 2014 · edc99ad · edc99ad
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diff --git a/R/micca2ps.R b/R/micca2ps.R
@@ -2,8 +2,7 @@ library(phyloseq)
 
 import_micca = function(otufilename=NULL, taxonomyfilename=NULL,
                         samplefilename=NULL, treefilename=NULL) {
-    rank = c("Kingdom", "Phylum", "Class", "Order", "Family", "Genus",
-        "Species")
+    rank = c("Kingdom", "Phylum", "Class", "Order", "Family", "Genus", "Species")
     argumentlist = list()
     if (!is.null(otufilename)) {
         otu_frame = read.csv(otufilename, sep="\t", header=T, row.names=1,

diff --git a/docs/source/command_ref/micca_merge.rst b/docs/source/command_ref/micca_merge.rst
@@ -0,0 +1,4 @@
+``micca-merge``
+===============
+
+.. command-output:: micca-merge --help
diff --git a/docs/source/command_ref/micca_rarefy.rst b/docs/source/command_ref/micca_rarefy.rst
@@ -1,7 +1,7 @@
 ``micca-rarefy``
 ================
 
-Rarefies an OTU table with a depth of ``perc``% of the least abundant
+Rarefies an OTU table with a depth of ``perc`` % of the least abundant
 sample.
 
 .. command-output:: micca-rarefy --help
diff --git a/docs/source/command_ref/micca_test.rst b/docs/source/command_ref/micca_test.rst
@@ -0,0 +1,4 @@
+``micca-test``
+==============
+
+.. command-output:: micca-test --help
diff --git a/docs/source/install.rst b/docs/source/install.rst
@@ -98,4 +98,3 @@ Install micca
       NumPy... OK
       pandas... OK
       RDP Classifier... OK
-
diff --git a/docs/source/tutorials/16S.rst b/docs/source/tutorials/16S.rst
@@ -59,7 +59,7 @@ The length threshold 200 and quality threshold 16 values (black point)
 are selected as a compromise between quality filtering and minimum
 reads length.
 
-Using the choosed parameters, run the following command on all the
+Using the chosen parameters, run the following command on all the
 samples:
 
 .. code-block:: sh
@@ -122,19 +122,19 @@ following:
 **representatives.fasta**
     a FASTA file containing the representative sequence for each OTU::
     
-        >sample1||F4HTPAO07H4B1Q
-	GTCCACGCCGTAAACGGTGGATGCTGGATGTGGGGCCCGTTCCACGGGTTCCGTGTCGGA
-	GCTAACGCGTTAAGCATCCCGCCTGGGGAGTACGGCCGCAAGGCTAAAACTCAAAGAAAT
-	TGACGGGGCCCGCACAAGCGGCGGAGCATGCGGATTAATTCGATGCAACGCGAAGAACCT
-	TACCTGGGCTTGACATGTTCCCGACGGTCGTAGAGATACGGCTTCCCTTCGGGGCGGGTT
-	CACAGGTGGTGCATGGTC
-	>sample3||F4HTPAO05FO0LC
-	GTCCACGCCGTAAACGATGAATACTAGGTGTTGGGAAGCATTGCTTCTCGGTGCCGTCGC
-	AAACGCAGTAAGTATTCCACCTGGGGAGTACGTTCGCAAGAATGAAACTCAAAGGAATTG
-	ACGGGGACCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGAAGCAACGCGAAGAACCTT
-	ACCAAGTCTTGACATCCTTCTGACCGGTACTTAACCGTACCTTCTCTTCGGAGCAGGAGT
-	GACAGGTGGTGCATGGTT
-	...
+    >sample1||F4HTPAO07H4B1Q
+    GTCCACGCCGTAAACGGTGGATGCTGGATGTGGGGCCCGTTCCACGGGTTCCGTGTCGGA
+    GCTAACGCGTTAAGCATCCCGCCTGGGGAGTACGGCCGCAAGGCTAAAACTCAAAGAAAT
+    TGACGGGGCCCGCACAAGCGGCGGAGCATGCGGATTAATTCGATGCAACGCGAAGAACCT
+    TACCTGGGCTTGACATGTTCCCGACGGTCGTAGAGATACGGCTTCCCTTCGGGGCGGGTT
+    CACAGGTGGTGCATGGTC
+    >sample3||F4HTPAO05FO0LC
+    GTCCACGCCGTAAACGATGAATACTAGGTGTTGGGAAGCATTGCTTCTCGGTGCCGTCGC
+    AAACGCAGTAAGTATTCCACCTGGGGAGTACGTTCGCAAGAATGAAACTCAAAGGAATTG
+    ACGGGGACCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGAAGCAACGCGAAGAACCTT
+    ACCAAGTCTTGACATCCTTCTGACCGGTACTTAACCGTACCTTCTCTTCGGAGCAGGAGT
+    GACAGGTGGTGCATGGTT
+    ...
 
 **taxonomy.txt**
     a two-columns, tab-delimited file containing the taxonomy assigned
@@ -174,7 +174,7 @@ The command will be:
 
     micca-otu-denovo preprocessed/*.fastq -c -t blast -o otu_rdp \
         --blast-ref greengenes_2013_05/rep_set/97_otus.fasta \
-	--blast-ref-taxonomy greengenes_2013_05/taxonomy/97_otu_taxonomy.txt
+	    --blast-ref-taxonomy greengenes_2013_05/taxonomy/97_otu_taxonomy.txt
 
 
 Building the phylogenetic tree
@@ -216,4 +216,4 @@ You can perform a midpoint rooting of the tree by
 
 .. [DeFilippo2010] De Filippo et al. Impact of diet in shaping gut microbiota revealed by
                    a comparative study in children from Europe and rural Africa. Proceedings of the
-		   National Academy of Sciences, 2010.
+                   National Academy of Sciences, 2010.
diff --git a/docs/source/tutorials/phyloseq.rst b/docs/source/tutorials/phyloseq.rst
@@ -27,4 +27,4 @@ Now, you can import ``micca`` outputs defined in :doc:`16S`:
     source("micca2ps.R")
     ps = import_micca(otufilename="otu_rdp/otu_table.txt",
                       taxonomyfilename="otu_rdp/taxonomy.txt", 
-    		      treefilename="phylo_pynast/tree_rooted.tre")
+    		          treefilename="phylo_pynast/tree_rooted.tre")
Original file line number	Diff line number	Diff line change
Expand Up		@@ -98,4 +98,3 @@ Install micca
		NumPy... OK
		pandas... OK
		RDP Classifier... OK