bugfix

- limit cov float to three decimals
- fix taxify
- changed tax file to hits file in help

Author: DRL

bloblib/BtCore.py

@@ -437,7 +437,7 @@ def calculateGC(self, seq):
                      if self.agct_count > 0 else 0.0)
 
     def addCov(self, lib_name, cov):
-        self.covs[lib_name] = cov
+        self.covs[lib_name] = float("{0:.3f}".format(cov)) # changed to three decimal digits
 
     def addReadCov(self, lib_name, read_cov):
         self.read_cov[lib_name] = read_cov

bloblib/create.py

@@ -4,17 +4,16 @@
 """usage: blobtools create     -i FASTA [-y FASTATYPE] [-o PREFIX] [--title TITLE]
                               [-b BAM...] [-s SAM...] [-a CAS...] [-c COV...]
                               [--nodes <NODES>] [--names <NAMES>] [--db <NODESDB>]
-                              [-t TAX...] [-x TAXRULE...] [-m INT] [--tax_collision_random]
+                              [-t HITS...] [-x TAXRULE...] [-m INT] [--tax_collision_random]
                               [-h|--help]
 
     Options:
         -h --help                       show this
         -i, --infile FASTA              FASTA file of assembly. Headers are split at whitespaces.
         -y, --type FASTATYPE            Assembly program used to create FASTA. If specified,
                                         coverage will be parsed from FASTA header.
-                                        (Parsing supported for 'spades', 'soap',
-                                            'velvet', 'abyss', 'platanus')
-        -t, --taxfile TAX...            Taxonomy file in format (qseqid\\ttaxid\\tbitscore)
+                                        (Parsing supported for 'spades', 'velvet', 'platanus')
+        -t, --hitsfile HITS...          Hits file in format (qseqid\\ttaxid\\tbitscore)
                                         (e.g. BLAST output "--outfmt '6 qseqid staxids bitscore'")
         -x, --taxrule <TAXRULE>...      Taxrule determines how taxonomy of blobs
                                         is computed [default: bestsum]
@@ -61,7 +60,7 @@ def main():
     bam_fs = args['--bam']
     cov_fs = args['--cov']
     cas_fs = args['--cas']
-    hit_fs = args['--taxfile']
+    hit_fs = args['--hitsfile']
     prefix = args['--out']
     nodesDB_f = args['--db']
     names_f = args['--names']

bloblib/taxify.py

@@ -62,10 +62,11 @@ def main():
             if diamond_f:
                 output.append("%s\t%s\t%s\t%s" % (line[0], taxid_d[line[1]], line[11], "\t".join(line[1:])))
             else:
-                if line[1] == 'N/A' or force:
+                if line[1] == 'N/A' or force: # so that it does not overwrite existing taxIDs
                     output.append("%s\t%s\t%s" % (line[0], taxid_d[line[3]], "\t".join(line[2:5])))
                 else:
                     print BtLog.warn_d['10'] % (idx+1, line[0], line[1])
+                    output.append("%s\t%s\t%s" % (line[0], line[1], "\t".join(line[2:5])))
 
     if output:
         with open(out_f, "w") as fh: