nofilter option added to micca.api.msa.nast() and to msa command; ver…

…sion updated to 1.4.0; documentation improved

CHANGES.rst

@@ -1,6 +1,12 @@
 CHANGES
 =======
 
+Version 1.4.0
+-------------
+* nofilter option added to micca.api.msa.nast() (do not remove positions which
+  are gaps in every sequenceces) and to the msa command (--nast-nofilter option);
+* Documentation improved.
+
 Version 1.3.0
 -------------
 * Swarm clustering algorithm added to micca otu;

doc/source/index.rst

@@ -6,19 +6,18 @@
 .. include:: ../../README.rst
 
 
-
 .. toctree::
    :maxdepth: 1
    :caption: Getting Started
-   
+
    install
    run
    databases
-   
+
 .. toctree::
    :maxdepth: 1
    :caption: Tutorials
-   
+
    singleend
    pairedend
    phyloseq
@@ -43,8 +42,7 @@
 
 .. Indices and tables
 .. ==================
-.. 
+..
 .. * :ref:`genindex`
 .. * :ref:`modindex`
 .. * :ref:`search`
-

doc/source/otu.rst

@@ -27,7 +27,7 @@ The :doc:`commands/otu` command returns in a single directory 5 files:
    otus.fasta
       FASTA containing the representative sequences (OTUs)::
 
-         >DENOVO1
+       >DENOVO1
      	 GACGAACGCTGGCGGCGTGCCTAACACATGCAAGTCGAACGGGG...
      	 >DENOVO2
      	 GATGAACGCTAGCTACAGGCTTAACACATGCAAGTCGAGGGGCA...
@@ -40,8 +40,8 @@ The :doc:`commands/otu` command returns in a single directory 5 files:
       ids::
 
          DENOVO1 IS0AYJS04JQKIS;sample=Mw_01
-	 DENOVO2 IS0AYJS04JL6RS;sample=Mw_01
-	 DENOVO3 IS0AYJS04H4XNN;sample=Mw_01
+	       DENOVO2 IS0AYJS04JL6RS;sample=Mw_01
+	       DENOVO3 IS0AYJS04H4XNN;sample=Mw_01
 	 ...
 
    hits.txt
@@ -50,12 +50,12 @@ The :doc:`commands/otu` command returns in a single directory 5 files:
       identity (if available), see :ref:`otu-definition_identity`::
 
          IS0AYJS04JE658;sample=Mw_01; IS0AYJS04I4XYN;sample=Mw_01 99.4
-	 IS0AYJS04JPH34;sample=Mw_01; IS0AYJS04JVUBC;sample=Mw_01 98.0
-	 IS0AYJS04I67XN;sample=Mw_01; IS0AYJS04JVUBC;sample=Mw_01 99.7
+	       IS0AYJS04JPH34;sample=Mw_01; IS0AYJS04JVUBC;sample=Mw_01 98.0
+	       IS0AYJS04I67XN;sample=Mw_01; IS0AYJS04JVUBC;sample=Mw_01 99.7
 	 ...
 
    otuschim.fasta
-      (only for 'denovo_greedy' and 'open_ref' mathods, when
+      (only for 'denovo_greedy', 'denovo_swarm' and 'open_ref' mathods, when
       ``-c/--rmchim`` is specified) FASTA file containing the chimeric
       otus.
 

docker/README.md

@@ -11,6 +11,7 @@ The RDP Classifier is included.
 ## Available Tags/Versions
 
 - latest: GitHub snapshot (master)
+- 1.4.0: micca 1.4.0 (RDP Classifier release 2.11 included)
 - 1.3.0: micca 1.3.0 (RDP Classifier release 2.11 included)
 - 1.2.2: micca 1.2.2 (RDP Classifier release 2.11 included)
 

micca/__init__.py

@@ -1,5 +1,5 @@
 import os
 
-__version__ = "1.3.0"
+__version__ = "1.4.0"
 
 THIRDPARTY_BIN_PATH = os.path.join(os.path.dirname(__file__), "thirdparty_bin")

micca/api/msa.py

@@ -166,7 +166,7 @@ def _aln_to_seqs(aln, query, target):
 
 
 def nast(input_fn, template_fn, output_fn, notaligned_fn=None, hits_fn=None,
-         ident=0.75, threads=1, mincov=0.75, strand="both"):
+         ident=0.75, threads=1, mincov=0.75, strand="both", nofilter=False):
 
     output_dir = os.path.dirname(output_fn)
 
@@ -269,24 +269,30 @@ def nast(input_fn, template_fn, output_fn, notaligned_fn=None, hits_fn=None,
     hits_temp_handle.close()
     output_temp_handle.close()
     hits_out_handle.close()
+    os.remove(hits_temp_fn)
+    os.remove(template_wg_temp_fn)
 
     # remove columns which are gaps in every sequence
-    output_temp_handle = open(output_temp_fn, "rb")
-    output_handle = open(output_fn, "wb")
-    for title, seq in SimpleFastaParser(output_temp_handle):
-        seqout = "".join(np.array(list(seq))[msa_cov > 0])
-        output_handle.write(">{}\n{}\n".format(title, seqout))
-    output_temp_handle.close()
-    output_handle.close()
+    if nofilter:
+        os.rename(output_temp_fn, output_fn)
+    else:
+        output_temp_handle = open(output_temp_fn, "rb")
+        output_handle = open(output_fn, "wb")
+        for title, seq in SimpleFastaParser(output_temp_handle):
+            seqout = "".join(np.array(list(seq))[msa_cov > 0])
+            output_handle.write(">{}\n{}\n".format(title, seqout))
+        output_temp_handle.close()
+        output_handle.close()
+        os.remove(output_temp_fn)
 
     if hits_fn is None:
         os.remove(hits_out_fn)
     else:
         os.rename(hits_out_fn, hits_fn)
 
-    os.remove(template_wg_temp_fn)
-    os.remove(hits_temp_fn)
-    os.remove(output_temp_fn)
+
+
+
 
 
 def muscle(input_fn, output_fn, maxiters=16):

micca/cmds/msa.py

@@ -111,6 +111,10 @@ def main(argv):
                             help="write hits on a TAB delimited file with the "
                             "query sequence id, the template sequence id and "
                             "the identity.")
+    group_nast.add_argument('--nast-nofilter', default=False, action="store_true",
+                            help="do not remove positions which are gaps in "
+                            "every sequenceces (useful if you want to apply "
+                            "a Lane mask filter before the tree inference).")
     args = parser.parse_args(argv)
 
 
@@ -129,7 +133,8 @@ def main(argv):
                 ident=args.nast_id,
                 threads=args.nast_threads,
                 mincov=args.nast_mincov,
-                strand=args.nast_strand)
+                strand=args.nast_strand,
+                nofilter=args.nast_nofilter)
         else:
             micca.api.msa.muscle(
                 input_fn=args.input,

micca/cmds/otu.py

@@ -133,7 +133,8 @@ def main(argv):
                        "open_ref"],
                        help="clustering method (default %(default)s)")
     group.add_argument('-d', '--id', default=0.97, type=float,
-                       help="sequence identity threshold (0.0 to 1.0, "
+                       help="sequence identity threshold (for 'denovo_greedy', "
+                       "'closed_ref' and 'open_ref', 0.0 to 1.0, "
                        "default %(default)s).")
     group.add_argument('-n', '--mincov', default=0.75, type=float,
                        help="reject sequence if the fraction of alignment "