ecopcr: fixed and improved the options to keep nuclotides around the

amplicon

python/obitools3/commands/ecopcr.pyx

@@ -107,14 +107,20 @@ def addOptions(parser):
                        help="Defines the method used for estimating the Tm (melting temperature) between the primers and their corresponding "
                             "target sequences. SANTALUCIA: 1, or OWCZARZY: 2. Default: 1.")
 
+    group.add_argument('--keep-primers', '-p',
+                       action="store_true", 
+                       dest="ecopcr:keep-primers",
+                       default=False,
+                       help="Whether to keep the primers attached to the output sequences (default: the primers are cut out).")
+
     group.add_argument('--keep-nucs', '-D',
                        action="store", 
                        dest="ecopcr:keep-nucs",
-                       metavar="<INTEGER>",
+                       metavar="<N>",
                        type=int,
                        default=0,
-                       help="Keeps the specified number of nucleotides on each side of the in silico amplified sequences, "
-                            "(already including the amplified DNA fragment plus the two target sequences of the primers).")
+                       help="Keeps N nucleotides on each side of the in silico amplified sequences, "
+                            "not including the primers (implying that primers are automatically kept if N > 0).")
 
     group.add_argument('--kingdom-mode', '-k',
                        action="store_true", 
@@ -185,7 +191,7 @@ def run(config):
                   config['ecopcr']['min-length'], config['ecopcr']['max-length'], \
                   restrict_to_taxids_p, ignore_taxids_p, \
                   config['ecopcr']['circular'], config['ecopcr']['salt-concentration'], config['ecopcr']['salt-correction-method'], \
-                  config['ecopcr']['keep-nucs'], config['ecopcr']['kingdom-mode']) < 0:
+                  config['ecopcr']['keep-nucs'], config['ecopcr']['keep-primers'], config['ecopcr']['kingdom-mode']) < 0:
         raise Exception("Error running ecopcr")
 
     # Save command config in DMS comments

python/obitools3/dms/capi/obiecopcr.pxd

@@ -23,6 +23,7 @@ cdef extern from "obi_ecopcr.h" nogil:
                    double salt_concentration,
                    int salt_correction_method,
                    int keep_nucleotides,
+                   bint keep_primers,
                    bint kingdom_mode)
 
     

python/obitools3/version.py

@@ -1,5 +1,5 @@
 major = 3
 minor = 0
-serial= '0-beta3'
+serial= '0-beta4'
 
 version ="%d.%02d.%s" % (major,minor,serial)