Commit 02d39bb8 authored by Penom Nom's avatar Penom Nom
Browse files

No commit message

No commit message
parent 12ebd2f5
......@@ -34,11 +34,11 @@ def to_biom( output_biom, clusters_file, precluster_sample_sep, precluster_size_
@summary : Write a biom file from cdhit results.
@param output_biom : [str] path to the output file.
@param clusters_file : [str] path to the '.clstr' file.
@param precluster_size_sep : [char] used if sequences provided to Cdhit are pre-clusters (ex : dereplication step before cd-hit). The number of sequences
@param precluster_size_sep : [str] used if sequences provided to Cdhit are pre-clusters (ex : dereplication step before cd-hit). The number of sequences
represented by each pre-cluster can be added to the end of its ID. In this place the number is separated by the character
precluster_size_sep.
Example : precluster_size_sep=';' where sequence ID = 'seq10001;83'.
@param precluster_size_sep : [char] used if sequences provided to Cdhit come from differents samples ("none" otherwise). The sample name is stored in each
@param precluster_size_sep : [str] used if sequences provided to Cdhit come from differents samples ("none" otherwise). The sample name is stored in each
sequence id. It is separated by the character precluster_sample_sep and it is placed before the pre-cluster size information.
Example : sequence ID = 'seq10001|lake_spot_1;83'.
OR
......@@ -142,11 +142,11 @@ class Cdhit (Analysis):
@param word_length : [int] word length.
@param distance_method : [str] distance method for the hierarchical clustering. Accepted values @see biomstat.samples_hclassification.
@param linkage_method : [str] linkage method for the hierarchical clustering. Accepted values @see biomstat.samples_hclassification.
@param precluster_size_sep : [char] used if sequences provided to Cdhit are pre-clusters (ex : dereplication step before cd-hit).
@param precluster_size_sep : [str] used if sequences provided to Cdhit are pre-clusters (ex : dereplication step before cd-hit).
The number of sequences represented by each pre-cluster can be added to the end of its ID.
In this place the number is separated by the character precluster_size_sep.
Example : precluster_size_sep=';' where sequence ID = 'seq10001;83'.
@param precluster_sample_sep : [char] used if sequences provided to Cdhit come from differents samples. The sample name is stored in
@param precluster_sample_sep : [str] used if sequences provided to Cdhit come from differents samples. The sample name is stored in
each sequence id. It is separated by the character precluster_sample_sep and it is placed before the
pre-cluster size information.
Example : sequence ID = 'seq10001|lake_spot_1;83'.
......
Supports Markdown
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment