Move biom lib to featureiolib.

workflows/gene_diversity/components/biomsampling.py

@@ -37,7 +37,7 @@ def merge_samples( input_biom, merge_dump, output_biom, min_evidence_nb=None ):
                                 observation (@see Biom.reset_count_by_replicates_evidence).
     """
     import pickle
-    from workflows.gene_diversity.lib.Biom import BiomIO
+    from jflow.featureio import BiomIO
     
     # Retrieve merge rules
     merge = open(merge_dump, "rb")
@@ -59,7 +59,7 @@ def filter_and_bootstrap( input_biom, output_biom, observation_threshold, nb_del
     """
      @summary :
     """
-    from workflows.gene_diversity.lib.Biom import BiomIO
+    from jflow.featureio import BiomIO
     
     biom = BiomIO.from_json( input_biom )
     # Filter
@@ -79,7 +79,7 @@ def filter_seq( input_fasta, input_biom, output_fasta ):
       @param input_biom : [str] path to the file with the IDs of kept sequences (biom file).
       @param output_fasta : [str] path to the filtered fasta.
     """
-    from workflows.gene_diversity.lib.Biom import BiomIO
+    from jflow.featureio import BiomIO
     import jflow.seqio as seqio
     
     biom = BiomIO.from_json( input_biom )

workflows/gene_diversity/components/cdhit.py

@@ -44,7 +44,7 @@ def to_biom( output_biom, clusters_file, precluster_sample_sep, precluster_size_
                                  precluster_size_sep.
                                  Example : precluster_size_sep=';' where sequence ID = 'seq10001;83'.
     """
-    from workflows.gene_diversity.lib.Biom import Biom, BiomIO
+    from jflow.featureio import Biom, BiomIO
     
     samples_seen = dict()
     biom = Biom( generated_by='cdhit', matrix_type="sparse" )
@@ -116,7 +116,7 @@ def rename_seq( input_fasta, clusters_file, renamed_fasta ):
     clusters_fh.close()
     
     # Rename sequences
-    reader = seqio.SequenceReader( input_fasta )
+    reader = seqio.FastaReader( input_fasta )
     out_fh = open( renamed_fasta, "w" )
     for id, desc, seq, qual in reader :
         seqio.writefasta( out_fh, [[cluster_representative[id], desc, seq, qual]] )

workflows/gene_diversity/components/geneotuclassify.py

@@ -31,7 +31,7 @@ def biom_to_count( biom_file, count_file ):
       @param biom_file : [str] path to the biom to process.
       @param count_file : [str] path to the output file.
     """
-    from workflows.gene_diversity.lib.Biom import Biom, BiomIO
+    from jflow.featureio import BiomIO
     
     biom = BiomIO.from_json( biom_file )
     out_fh = open( count_file, "w" )
@@ -62,7 +62,7 @@ def biom_to_krona( exec_path, stem_path_krona, biom_file, log_file ):
       @param biom_file : [str] path to the biom to process.
       @param log_file : [str] path to the log file.
     """
-    from workflows.gene_diversity.lib.Biom import Biom, BiomIO
+    from jflow.featureio import BiomIO
     from subprocess import Popen, PIPE
     import sys
     
@@ -90,7 +90,7 @@ def add_tax_metadata( biom_file, blast_file, taxonomy_file, output_file ):
       @param output_file : [string] the path to the output file.
     """
     import os
-    from workflows.gene_diversity.lib.Biom import Biom, BiomIO
+    from jflow.featureio import BiomIO
     
     def init_cluster_count(sample_names):
         samples_count = {}

workflows/gene_diversity/lib/biomstat.py

@@ -27,7 +27,7 @@ def observations_depth( input_biom, output_depth ):
                 3<TAB>0<TAB>0.000
                 4<TAB>5<TAB>5.000
     """
-    from workflows.gene_diversity.lib.Biom import BiomIO
+    from jflow.featureio import BiomIO
     
     obs_depth = list()
     nb_observ = 0
@@ -56,7 +56,7 @@ def samples_hclassification( input_biom, output_dendrogram, distance_method, lin
     from scipy.spatial.distance import pdist, squareform
     from scipy.cluster.hierarchy import linkage, dendrogram
     import scipy.cluster.hierarchy
-    from workflows.gene_diversity.lib.Biom import BiomIO
+    from jflow.featureio import BiomIO
         
     def add_node( node, parent ):
         """

workflows/gene_diversity/workflow.properties

@@ -43,12 +43,14 @@ merge.group = SAMPLES section
 read_1.name = Reads 1
 read_1.flag = --read-1
 read_1.help = The path to the Read 1.
+read_1.type = localfile
 read_1.action = append
 read_1.required = True
 #    Parameter read-2
 read_2.name = Reads 2
 read_2.flag = --read-2
 read_2.help = The path to the Read 2.
+read_2.type = localfile
 read_2.action = append
 read_2.required = True
 #    Parameter samples_names