require 'pp'
casts = []
-casts << {:long=>'key', :short=>'k', :type=>'string', :mandatory=>true, :default=>nil, :allowed=>nil, :disallowed=>nil}
-casts << {:long=>'dir', :short=>'d', :type=>'dir!', :mandatory=>true, :default=>nil, :allowed=>nil, :disallowed=>nil}
-casts << {:long=>'no_stream', :short=>'x', :type=>'flag', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
+casts << {long: 'key', short: 'k', type: 'string', mandatory: true, default: nil, allowed: nil, disallowed: nil}
+casts << {long: 'dir', short: 'd', type: 'dir!', mandatory: true, default: nil, allowed: nil, disallowed: nil}
+casts << {long: 'wrap', short: 'w', type: 'uint', mandatory: false, default: nil, allowed: nil, disallowed: "0"}
+casts << {long: 'compress', short: 'Z', type: 'string', mandatory: false, default: nil, allowed: "gzip,bzip,bzip2", disallowed: nil}
+casts << {long: 'no_stream', short: 'x', type: 'flag', mandatory: false, default: nil, allowed: nil, disallowed: nil}
options = Biopieces.options_parse(ARGV, casts)
-key = options[:key].to_sym
-
-fh_hash = {}
+key = options[:key].to_sym
+compress = options[:compress] ? options[:compress].to_sym : nil
+fh_hash = {}
Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
input.each_record do |record|
fasta_io = fh_hash[record[key].to_sym]
else
fasta_file = File.join(options[:dir], record[key] + ".fasta")
- fasta_io = Fasta.open(fasta_file, "w")
+ fasta_file << ".gz" if compress == :gzip
+ fasta_file << ".bz2" if compress == :bzip or compress == :bzip2
+ fasta_io = Fasta.open(fasta_file, "w", compress: compress)
fh_hash[record[key].to_sym] = fasta_io
end
- fasta_io.puts seq.to_fasta
+ fasta_io.puts seq.to_fasta(options[:wrap])
end
output.puts record unless options[:no_stream]
source "$BP_DIR/bp_test/lib/test.sh"
mkdir $tmp_dir
-
run "$bp -I $in -d $tmp_dir -k SEQ_NAME -x"
assert_no_diff_dir $tmp_dir $out.1
clean
+rm -rf $tmp_dir
+mkdir $tmp_dir
+run "$bp -I $in -d $tmp_dir -k SEQ_LEN -x"
+assert_no_diff_dir $tmp_dir $out.2
+clean
rm -rf $tmp_dir
+
mkdir $tmp_dir
+run "$bp -I $in -d $tmp_dir -k SEQ_LEN -Z gzip -x"
+gunzip $tmp_dir/*.gz
+assert_no_diff_dir $tmp_dir $out.2
+clean
+rm -rf $tmp_dir
-run "$bp -I $in -d $tmp_dir -k SEQ_LEN -x"
+mkdir $tmp_dir
+run "$bp -I $in -d $tmp_dir -k SEQ_LEN -Z bzip2 -x"
+bunzip2 $tmp_dir/*.bz2
assert_no_diff_dir $tmp_dir $out.2
clean
+rm -rf $tmp_dir
+mkdir $tmp_dir
+run "$bp -I $in -d $tmp_dir -k SEQ_LEN -w 4 -x"
+assert_no_diff_dir $tmp_dir $out.3
+clean
rm -rf $tmp_dir