upgraded dependencies

[biopieces.git] / bp_bin / uclust_seq

diff --git a/bp_bin/uclust_seq b/bp_bin/uclust_seq
index 1f5202a42f75201866f6affee4e219de06295651..5b162c414c2cdb249b4c2a518d1ca61062205e41 100755 (executable)
--- a/bp_bin/uclust_seq
+++ b/bp_bin/uclust_seq
@@ -36,6 +36,7 @@ casts = []
 casts << {long: 'no_sort',  short: 'n', type: 'flag',  mandatory: false, default: nil, allowed: nil, disallowed: nil}
 casts << {long: 'comp',     short: 'c', type: 'flag',  mandatory: false, default: nil, allowed: nil, disallowed: nil}
 casts << {long: 'identity', short: 'i', type: 'float', mandatory: true,  default: 0.9, allowed: nil, disallowed: nil}
+casts << {long: 'cpus',     short: 'C', type: 'uint',  mandatory: false, default: 1,   allowed: nil, disallowed: "0"}
 
 options = Biopieces.options_parse(ARGV, casts)
 
@@ -70,8 +71,8 @@ end
 Biopieces.open(file_records, options[:stream_out]) do |input, output|
   input.each_record do |record|
     if record[:SEQ_NAME] and record[:SEQ]
-      if hash[record[:SEQ_NAME].to_sym]
-        us = hash[record[:SEQ_NAME].to_sym]
+      seq_name = record[:SEQ_NAME].split(/\s+/).first.to_sym
+      if us = hash[seq_name]
         record[:CLUSTER] = us[:CLUSTER].to_i
         record[:IDENT]   = us[:IDENT].to_i
         record[:IDENT] = '*' if us[:TYPE] == 'S'