fixed symlink trouble

git-svn-id: http://biopieces.googlecode.com/svn/trunk@376 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/bp_bin/00README b/bp_bin/00README
new file mode 100644 (file)
index 0000000..70c8816
--- /dev/null
+++ b/bp_bin/00README
@@ -0,0 +1,5 @@
+This directory should only contain Biopiece executables.
+
+
+
+Martin A. Hansen, June 2008

diff --git a/bp_bin/add_ident b/bp_bin/add_ident
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/bp_bin/add_ident
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/bp_bin/align_seq b/bp_bin/align_seq
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/bp_bin/align_seq
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/bp_bin/analyze_bed b/bp_bin/analyze_bed
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/bp_bin/analyze_bed
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/bp_bin/analyze_seq b/bp_bin/analyze_seq
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/bp_bin/analyze_seq
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/bp_bin/analyze_tags b/bp_bin/analyze_tags
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/bp_bin/analyze_tags
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/bp_bin/analyze_vals b/bp_bin/analyze_vals
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/bp_bin/analyze_vals
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/bp_bin/assemble_tag_contigs b/bp_bin/assemble_tag_contigs
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/bp_bin/assemble_tag_contigs
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/bp_bin/blast_seq b/bp_bin/blast_seq
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/bp_bin/blast_seq
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/bp_bin/blat_seq b/bp_bin/blat_seq
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/bp_bin/blat_seq
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/bp_bin/calc_bit_scores b/bp_bin/calc_bit_scores
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/bp_bin/calc_bit_scores
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/bp_bin/calc_fixedstep b/bp_bin/calc_fixedstep
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/bp_bin/calc_fixedstep
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/bp_bin/complement_seq b/bp_bin/complement_seq
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/bp_bin/complement_seq
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/bp_bin/complexity_seq b/bp_bin/complexity_seq
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/bp_bin/complexity_seq
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/bp_bin/compute b/bp_bin/compute
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/bp_bin/compute
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/bp_bin/count_records b/bp_bin/count_records
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/bp_bin/count_records
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/bp_bin/count_vals b/bp_bin/count_vals
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/bp_bin/count_vals
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/bp_bin/create_blast_db b/bp_bin/create_blast_db
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/bp_bin/create_blast_db
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/bp_bin/create_vmatch_index b/bp_bin/create_vmatch_index
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/bp_bin/create_vmatch_index
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/bp_bin/create_weight_matrix b/bp_bin/create_weight_matrix
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/bp_bin/create_weight_matrix
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/bp_bin/extract_seq b/bp_bin/extract_seq
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/bp_bin/extract_seq
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/bp_bin/flip_tab b/bp_bin/flip_tab
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/bp_bin/flip_tab
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/bp_bin/fold_seq b/bp_bin/fold_seq
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/bp_bin/fold_seq
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/bp_bin/format_genome b/bp_bin/format_genome
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/bp_bin/format_genome
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/bp_bin/get_genome_align b/bp_bin/get_genome_align
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/bp_bin/get_genome_align
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/bp_bin/get_genome_phastcons b/bp_bin/get_genome_phastcons
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/bp_bin/get_genome_phastcons
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/bp_bin/get_genome_seq b/bp_bin/get_genome_seq
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/bp_bin/get_genome_seq
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/bp_bin/grab b/bp_bin/grab
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/bp_bin/grab
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/bp_bin/head_records b/bp_bin/head_records
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/bp_bin/head_records
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/bp_bin/invert_align b/bp_bin/invert_align
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/bp_bin/invert_align
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/bp_bin/length_seq b/bp_bin/length_seq
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/bp_bin/length_seq
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/bp_bin/length_vals b/bp_bin/length_vals
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/bp_bin/length_vals
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/bp_bin/list_biopieces b/bp_bin/list_biopieces
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/bp_bin/list_biopieces
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/bp_bin/list_genomes b/bp_bin/list_genomes
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/bp_bin/list_genomes
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/bp_bin/lowercase_seq b/bp_bin/lowercase_seq
new file mode 100755 (executable)
index 0000000..b51df83
--- /dev/null
+++ b/bp_bin/lowercase_seq
@@ -0,0 +1,178 @@
+#!/usr/bin/python
+
+import os, string, sys, getopt, Args, optparse
+
+record_delimiter = "\n---\n"
+
+class Lowercase_seq:
+       in_stream = None
+       out_stream = None
+       eo_buffer = False
+       buffer = ''
+       rec_dic = {}
+       rec_num = 0
+
+       ###########################################
+       def __init__(self):
+               pass
+       ###########################################
+
+       ###########################################
+       def open_streams(self, input_file, output_file):
+               #print input_file, output_file
+               if input_file == '':
+                       self.in_stream = sys.stdin
+                       #print "in_stream = <STDIN>"
+               else:
+                       try:
+                               self.in_stream = open(input_file, 'r')
+                               #print "in_stream = %s" % (input_file)
+                       except:
+                               raise IOError
+
+               if output_file == '':
+                       self.out_stream = sys.stdout
+                       #print "out_stream = <STDOUT>"
+               else:
+                       try:
+                               self.out_stream = open(output_file, 'w')
+                               #print "out_stream = %s" % (output_file)
+                       except:
+                               raise IOError
+       ###########################################
+
+       ###########################################
+       def close_streams(self):
+               if self.in_stream:
+                       self.in_stream.close()
+               if self.out_stream:
+                       self.out_stream.close()
+       ###########################################
+
+       ###########################################
+       def get_record(self):
+               rec = ''
+               eof_flag = False
+               while not self.eo_buffer:
+                       #print "STDIN.ISATTY :", self.in_stream.isatty()
+
+                       if self.in_stream.isatty():
+                               eof_flag = True
+
+                       if eof_flag:
+                               if self.buffer == '':
+                                       self.eo_buffer = True
+                                       break
+                       else:
+                               tmp = self.in_stream.read(1000)
+                       if not tmp:
+                               eof_flag = True
+
+                       self.buffer = self.buffer + tmp
+                       delim_index = self.buffer.find(record_delimiter)
+                       if delim_index >= 0:
+                               rec = self.buffer[:delim_index]
+                               self.buffer = self.buffer[delim_index + len(record_delimiter):]
+                               break
+               return rec
+       ###########################################
+
+       ###########################################
+       def process_record(self, rec):
+               #print "PARSE_RECORD"
+               #print rec
+               #print "==="
+               lines = rec.split("\n")
+               self.rec_num += 1
+               self.rec_dic[self.rec_num] = {}
+               for l in lines:
+                       toks = l.split(": ")
+                       if toks[0]=="SEQ":
+                               self.rec_dic[self.rec_num][toks[0]] = toks[1].lower()
+                       else:
+                               self.rec_dic[self.rec_num][toks[0]] = toks[1]
+                       #self.rec_dic[self.rec_num][toks[0]] = toks[1]
+               #print self.rec_dic[self.rec_num]
+               return self.rec_num
+       ###########################################
+
+       ###########################################
+       def put_record(self, r_num):
+               rec = self.rec_dic[r_num]
+               for k in rec.keys():
+                       #print "%s: %s" % (k, rec[k])
+                       self.out_stream.write("%s: %s\n" % (k, rec[k]))
+               #print "---"
+               self.out_stream.write("---\n")
+       ###########################################
+
+       ###########################################
+       def print_usage(self, opt):
+               #print opt
+               bp_dir = os.environ['BP_DIR']
+               usage_path = bp_dir + os.path.sep + "bp_usage" + os.path.sep + "lowercase_seq.wiki"
+               os.system("print_usage -i %s %s" % (usage_path, opt))
+       ###########################################
+
+
+# main
+
+lc_seq = Lowercase_seq()
+
+try:
+       opts, args = getopt.getopt(sys.argv[1:], "I:O:?vx", ["stream_in=", "stream_out=", "help", "verbose", "no_stream"])
+except getopt.GetoptError, err:
+       # print help information and exit:
+       print str(err) # will print something like "option -a not recognized"
+       lc_seq.print_usage("")
+       sys.exit(2)
+
+
+if len(opts)==0:
+       lc_seq.print_usage("")
+       sys.exit(1)
+
+stream_in = ""
+stream_out = ""
+verbose = False
+for o, a in opts:
+       if o in ("-I", "--stream_in"):
+               stream_in = a
+       elif o in ("-O", "--stream_out"):
+               stream_out = a
+       elif o == "-?":
+               lc_seq.print_usage("")
+               sys.exit(1)
+       elif o == "--help":
+               lc_seq.print_usage("-?")
+               sys.exit(1)
+       elif o in ("-v", "--verbose"):
+               verbose = True
+       #else:
+       #       assert False
+       #       print_usage()
+
+try:
+       lc_seq.open_streams(stream_in, stream_out)
+except:
+       sys.stderr.write("%s\n" % ("IOError"))
+       sys.exit(1)
+
+
+while True:
+       rec = lc_seq.get_record()
+       if rec=='':
+               break
+       rec_num = lc_seq.process_record(rec)
+       lc_seq.put_record(rec_num)
+
+lc_seq.close_streams()
+
+#source = "Dmel_tRNAs_key_record_tuples.txt"
+#lc_seq.open_stream(source)
+
+#lc_seq.get_record()
+#lc_seq.put_record()
+
+
+

diff --git a/bp_bin/match_seq b/bp_bin/match_seq
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/bp_bin/match_seq
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/bp_bin/max_vals b/bp_bin/max_vals
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/bp_bin/max_vals
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/bp_bin/mean_vals b/bp_bin/mean_vals
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/bp_bin/mean_vals
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/bp_bin/median_vals b/bp_bin/median_vals
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/bp_bin/median_vals
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/bp_bin/merge_records b/bp_bin/merge_records
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/bp_bin/merge_records
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/bp_bin/merge_vals b/bp_bin/merge_vals
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/bp_bin/merge_vals
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/bp_bin/min_vals b/bp_bin/min_vals
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/bp_bin/min_vals
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/bp_bin/oligo_freq b/bp_bin/oligo_freq
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/bp_bin/oligo_freq
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/bp_bin/patscan_seq b/bp_bin/patscan_seq
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/bp_bin/patscan_seq
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/bp_bin/plot_chrdist b/bp_bin/plot_chrdist
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/bp_bin/plot_chrdist
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/bp_bin/plot_histogram b/bp_bin/plot_histogram
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/bp_bin/plot_histogram
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/bp_bin/plot_karyogram b/bp_bin/plot_karyogram
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/bp_bin/plot_karyogram
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/bp_bin/plot_lendist b/bp_bin/plot_lendist
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/bp_bin/plot_lendist
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/bp_bin/plot_matches b/bp_bin/plot_matches
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/bp_bin/plot_matches
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/bp_bin/plot_phastcons_profiles b/bp_bin/plot_phastcons_profiles
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/bp_bin/plot_phastcons_profiles
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/bp_bin/plot_seqlogo b/bp_bin/plot_seqlogo
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/bp_bin/plot_seqlogo
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/bp_bin/print_usage b/bp_bin/print_usage
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/bp_bin/print_usage
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/bp_bin/random_records b/bp_bin/random_records
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/bp_bin/random_records
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/bp_bin/read_2bit b/bp_bin/read_2bit
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/bp_bin/read_2bit
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/bp_bin/read_bed b/bp_bin/read_bed
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/bp_bin/read_bed
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/bp_bin/read_blast_tab b/bp_bin/read_blast_tab
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/bp_bin/read_blast_tab
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/bp_bin/read_embl b/bp_bin/read_embl
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/bp_bin/read_embl
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/bp_bin/read_fasta b/bp_bin/read_fasta
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/bp_bin/read_fasta
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/bp_bin/read_fixedstep b/bp_bin/read_fixedstep
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/bp_bin/read_fixedstep
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/bp_bin/read_gff b/bp_bin/read_gff
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/bp_bin/read_gff
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/bp_bin/read_mysql b/bp_bin/read_mysql
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/bp_bin/read_mysql
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/bp_bin/read_phastcons b/bp_bin/read_phastcons
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/bp_bin/read_phastcons
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/bp_bin/read_psl b/bp_bin/read_psl
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/bp_bin/read_psl
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/bp_bin/read_soft b/bp_bin/read_soft
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/bp_bin/read_soft
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/bp_bin/read_solexa b/bp_bin/read_solexa
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/bp_bin/read_solexa
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/bp_bin/read_solid b/bp_bin/read_solid
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/bp_bin/read_solid
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/bp_bin/read_stockholm b/bp_bin/read_stockholm
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/bp_bin/read_stockholm
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/bp_bin/read_tab b/bp_bin/read_tab
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/bp_bin/read_tab
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/bp_bin/read_ucsc_config b/bp_bin/read_ucsc_config
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/bp_bin/read_ucsc_config
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/bp_bin/remove_adaptor b/bp_bin/remove_adaptor
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/bp_bin/remove_adaptor
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/bp_bin/remove_indels b/bp_bin/remove_indels
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/bp_bin/remove_indels
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/bp_bin/remove_keys b/bp_bin/remove_keys
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/bp_bin/remove_keys
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/bp_bin/remove_mysql_tables b/bp_bin/remove_mysql_tables
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/bp_bin/remove_mysql_tables
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/bp_bin/remove_ucsc_tracks b/bp_bin/remove_ucsc_tracks
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/bp_bin/remove_ucsc_tracks
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/bp_bin/rename_keys b/bp_bin/rename_keys
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/bp_bin/rename_keys
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/bp_bin/reverse_seq b/bp_bin/reverse_seq
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/bp_bin/reverse_seq
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/bp_bin/shuffle_seq b/bp_bin/shuffle_seq
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/bp_bin/shuffle_seq
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/bp_bin/soap_seq b/bp_bin/soap_seq
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/bp_bin/soap_seq
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/bp_bin/sort_records b/bp_bin/sort_records
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/bp_bin/sort_records
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/bp_bin/split_bed b/bp_bin/split_bed
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/bp_bin/split_bed
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/bp_bin/split_seq b/bp_bin/split_seq
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/bp_bin/split_seq
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/bp_bin/split_vals b/bp_bin/split_vals
new file mode 100755 (executable)
index 0000000..a510c58
--- /dev/null
+++ b/bp_bin/split_vals
@@ -0,0 +1,66 @@
+#!/usr/bin/env perl -w
+
+use strict;
+use Data::Dumper;
+use Time::HiRes qw( gettimeofday );
+use Getopt::Long qw( :config bundling );
+use Maasha::Biopieces;
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+my ( $script, $t0, $t1, %options, $in, $out, $record, @vals, $i );
+
+$t0 = Time::HiRes::gettimeofday();
+
+$script = ( split "/", $0 )[ -1 ];
+
+Maasha::Biopieces::log_biopiece();
+
+GetOptions(
+    \%options,
+    'key|k=s',
+    'keys|K=s',
+    'delimit|d=s',
+    'stream_in|I=s',
+    'stream_out|O=s',
+    'verbose|v',
+    'help|?'
+);
+
+$options{ "keys" }    = [ split ",", $options{ "keys" } ] if defined $options{ "keys" };
+$options{ "delimit" } = '_' if not defined $options{ "delimit" };
+
+$in  = Maasha::Biopieces::read_stream( $options{ "stream_in" } );
+$out = Maasha::Biopieces::write_stream( $options{ "stream_out" } );
+
+while ( $record = Maasha::Biopieces::get_record( $in ) )
+{
+    if ( exists $options{ 'key' } and exists $record->{ $options{ 'key' } } )
+    {
+        @vals = split /$options{ 'delimit' }/, $record->{ $options{ 'key' } };
+    
+        for ( $i = 0; $i < @vals; $i++ )
+        {
+            if ( defined $options{ "keys" } and defined $options{ "keys" }->[ $i ] ) {
+                $record->{ $options{ "keys" }->[ $i ] } = $vals[ $i ];
+            } else {
+                $record->{ $options{ 'key' } . "_$i" } = $vals[ $i ];
+            }
+        }
+    }
+
+    Maasha::Biopieces::put_record( $record, $out );
+}
+
+$t1 = Time::HiRes::gettimeofday();
+
+print STDERR "Program: $script" . ( " " x ( 25 - length( $script ) ) ) . sprintf( "Run time: %.4f\n", ( $t1 - $t0 ) ) if $options{ 'verbose' };
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+__END__
+

diff --git a/bp_bin/sum_vals b/bp_bin/sum_vals
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/bp_bin/sum_vals
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/bp_bin/tile_seq b/bp_bin/tile_seq
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/bp_bin/tile_seq
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/bp_bin/translate_seq b/bp_bin/translate_seq
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/bp_bin/translate_seq
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/bp_bin/transliterate_seq b/bp_bin/transliterate_seq
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/bp_bin/transliterate_seq
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/bp_bin/transliterate_vals b/bp_bin/transliterate_vals
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/bp_bin/transliterate_vals
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/bp_bin/uniq_vals b/bp_bin/uniq_vals
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/bp_bin/uniq_vals
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/bp_bin/upload_to_ucsc b/bp_bin/upload_to_ucsc
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/bp_bin/upload_to_ucsc
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/bp_bin/uppercase_seq b/bp_bin/uppercase_seq
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/bp_bin/uppercase_seq
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/bp_bin/vmatch_seq b/bp_bin/vmatch_seq
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/bp_bin/vmatch_seq
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/bp_bin/write_2bit b/bp_bin/write_2bit
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/bp_bin/write_2bit
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/bp_bin/write_align b/bp_bin/write_align
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/bp_bin/write_align
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/bp_bin/write_bed b/bp_bin/write_bed
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/bp_bin/write_bed
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/bp_bin/write_blast b/bp_bin/write_blast
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/bp_bin/write_blast
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/bp_bin/write_fasta b/bp_bin/write_fasta
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/bp_bin/write_fasta
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/bp_bin/write_fixedstep b/bp_bin/write_fixedstep
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/bp_bin/write_fixedstep
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/bp_bin/write_psl b/bp_bin/write_psl
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/bp_bin/write_psl
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/bp_bin/write_solid b/bp_bin/write_solid
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/bp_bin/write_solid
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/bp_bin/write_tab b/bp_bin/write_tab
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/bp_bin/write_tab
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;

diff --git a/bp_bin/write_ucsc_config b/bp_bin/write_ucsc_config
new file mode 100755 (executable)
index 0000000..fdf5bd2
--- /dev/null
+++ b/bp_bin/write_ucsc_config
@@ -0,0 +1,6 @@
+#!/usr/bin/env perl
+
+use warnings;
+use strict;
+
+use Maasha::BioRun;