nugen_barcode_splitter 0.0.10 → 0.0.11
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data/bin/nugen_barcode_splitter
CHANGED
@@ -5,7 +5,7 @@ require "nugen_barcode_splitter"
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5
5
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require "fileutils"
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6
6
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7
7
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usage =<<EOF
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8
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-
V E R S I O N - 0 . 0 .
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8
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+
V E R S I O N - 0 . 0 . 11
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9
9
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#{$0} [options] -p project_dir -o out_dir -c sample_sheet_nugen
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10
10
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_____________________________________________________________________________
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11
11
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@@ -79,13 +79,14 @@ class Merger
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79
79
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rev_out_files[i].write(rev_line)
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80
80
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for k in 1..3
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81
81
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fwd_file.readline()
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82
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-
rev_splitted_files[i].readline if marker2
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83
82
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compare_line_fwd = fwd_splitted_files[i].readline()
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84
83
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fwd_out_files[i].write("NNNN"+compare_line_fwd) if k == 1
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85
84
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fwd_out_files[i].write(compare_line_fwd) if k == 2
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86
85
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fwd_out_files[i].write("@@@@"+compare_line_fwd) if k == 3
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87
86
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rev_out_files[i].write(rev_file.readline())
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88
87
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end
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88
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+
fwd_file.lineno = fwd_file.lineno - 1
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89
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+
rev_file.lineno = rev_file.lineno - 1
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89
90
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end
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90
91
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end
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91
92
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if !marker && !rev_splitted_files[i].eof?
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@@ -111,6 +112,8 @@ class Merger
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111
112
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rev_out_files[i].write("@@@@"+compare_line_rev) if k == 3
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112
113
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fwd_out_files[i].write(fwd_file.readline())
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113
114
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end
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115
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+
fwd_file.lineno = fwd_file.lineno - 1
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116
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+
rev_file.lineno = rev_file.lineno - 1
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114
117
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end
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115
118
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end
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116
119
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break if !marker
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@@ -4,18 +4,26 @@ class NugenTemplate
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4
4
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5
5
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def initialize(fastq_multx, options)
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6
6
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@template =<<EOF
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7
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-
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8
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-
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9
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-
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10
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-
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7
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+
gunzip -c <%= @read %> | #{fastq_multx} \\
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8
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+
--bcfile <%= @barcodes %> #{options} <%= @options %> \\
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9
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+
--prefix <%= @lane_dir %>/<%= @direction %> \\
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10
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+
--suffix ".fq"
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11
11
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EOF
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12
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+
# @template =<<EOF
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13
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+
##{fastq_multx} #{options} <%= @barcodes %> \\
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14
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+
# <(gunzip -c <%= @read %>) \\
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15
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+
# -o <%= @lane_dir %>/<%= @direction %>.%.fq \\
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16
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+
# >> <%= @lane_dir %>/nugen_demultiplexing.log
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17
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+
#EOF
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12
18
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end
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13
19
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14
20
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def fill(lane, number, lane_dir, barcodes, read, is_fwd)
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15
21
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if is_fwd
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16
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-
direction = "R1_#{number}"
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22
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+
direction = "R1_#{number}_"
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23
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+
options = "--bol"
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17
24
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else
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18
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-
direction = "R2_#{number}"
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25
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+
direction = "R2_#{number}_"
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26
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+
options = "--eol"
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19
27
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end
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20
28
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context = {
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21
29
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:lane => lane,
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@@ -23,7 +31,8 @@ EOF
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23
31
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:lane_dir => lane_dir,
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24
32
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:barcodes => barcodes,
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25
33
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:read => read,
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26
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-
:direction => direction
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34
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+
:direction => direction,
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35
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+
:options => options
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27
36
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}
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28
37
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29
38
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eruby = Erubis::Eruby.new(@template)
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