finishm 0.0.1
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- data/ext/src/third-party/zlib-1.2.3/minigzip +0 -0
- data/ext/src/third-party/zlib-1.2.3/minigzip.c +322 -0
- data/ext/src/third-party/zlib-1.2.3/msdos/Makefile.bor +109 -0
- data/ext/src/third-party/zlib-1.2.3/msdos/Makefile.dj2 +104 -0
- data/ext/src/third-party/zlib-1.2.3/msdos/Makefile.emx +69 -0
- data/ext/src/third-party/zlib-1.2.3/msdos/Makefile.msc +106 -0
- data/ext/src/third-party/zlib-1.2.3/msdos/Makefile.tc +94 -0
- data/ext/src/third-party/zlib-1.2.3/old/Makefile.riscos +151 -0
- data/ext/src/third-party/zlib-1.2.3/old/README +3 -0
- data/ext/src/third-party/zlib-1.2.3/old/descrip.mms +48 -0
- data/ext/src/third-party/zlib-1.2.3/old/os2/Makefile.os2 +136 -0
- data/ext/src/third-party/zlib-1.2.3/old/os2/zlib.def +51 -0
- data/ext/src/third-party/zlib-1.2.3/old/visual-basic.txt +160 -0
- data/ext/src/third-party/zlib-1.2.3/old/zlib.html +971 -0
- data/ext/src/third-party/zlib-1.2.3/projects/README.projects +41 -0
- data/ext/src/third-party/zlib-1.2.3/projects/visualc6/README.txt +73 -0
- data/ext/src/third-party/zlib-1.2.3/projects/visualc6/example.dsp +278 -0
- data/ext/src/third-party/zlib-1.2.3/projects/visualc6/minigzip.dsp +278 -0
- data/ext/src/third-party/zlib-1.2.3/projects/visualc6/zlib.dsp +609 -0
- data/ext/src/third-party/zlib-1.2.3/projects/visualc6/zlib.dsw +59 -0
- data/ext/src/third-party/zlib-1.2.3/qnx/package.qpg +141 -0
- data/ext/src/third-party/zlib-1.2.3/trees.c +1219 -0
- data/ext/src/third-party/zlib-1.2.3/trees.h +128 -0
- data/ext/src/third-party/zlib-1.2.3/trees.o +0 -0
- data/ext/src/third-party/zlib-1.2.3/uncompr.c +61 -0
- data/ext/src/third-party/zlib-1.2.3/uncompr.o +0 -0
- data/ext/src/third-party/zlib-1.2.3/win32/DLL_FAQ.txt +397 -0
- data/ext/src/third-party/zlib-1.2.3/win32/Makefile.bor +107 -0
- data/ext/src/third-party/zlib-1.2.3/win32/Makefile.emx +69 -0
- data/ext/src/third-party/zlib-1.2.3/win32/Makefile.gcc +141 -0
- data/ext/src/third-party/zlib-1.2.3/win32/Makefile.msc +126 -0
- data/ext/src/third-party/zlib-1.2.3/win32/VisualC.txt +3 -0
- data/ext/src/third-party/zlib-1.2.3/win32/zlib.def +60 -0
- data/ext/src/third-party/zlib-1.2.3/win32/zlib1.rc +39 -0
- data/ext/src/third-party/zlib-1.2.3/zconf.h +332 -0
- data/ext/src/third-party/zlib-1.2.3/zconf.in.h +332 -0
- data/ext/src/third-party/zlib-1.2.3/zlib.3 +159 -0
- data/ext/src/third-party/zlib-1.2.3/zlib.h +1357 -0
- data/ext/src/third-party/zlib-1.2.3/zutil.c +318 -0
- data/ext/src/third-party/zlib-1.2.3/zutil.h +269 -0
- data/ext/src/third-party/zlib-1.2.3/zutil.o +0 -0
- data/lib/assembly/a_b_visualiser.rb +169 -0
- data/lib/assembly/acyclic_connection_finder.rb +81 -0
- data/lib/assembly/all_orfs.rb +615 -0
- data/lib/assembly/bad_format_writer.rb +46 -0
- data/lib/assembly/bam_probe_read_selector.rb +48 -0
- data/lib/assembly/bubbly_assembler.rb +842 -0
- data/lib/assembly/c_probe_node_finder.rb +38 -0
- data/lib/assembly/connection_interpreter.rb +350 -0
- data/lib/assembly/contig_printer.rb +400 -0
- data/lib/assembly/coverage_based_graph_filter.rb +68 -0
- data/lib/assembly/depth_first_search.rb +63 -0
- data/lib/assembly/dijkstra.rb +216 -0
- data/lib/assembly/fluffer.rb +253 -0
- data/lib/assembly/graph_explorer.rb +85 -0
- data/lib/assembly/graph_generator.rb +315 -0
- data/lib/assembly/height_finder.rb +355 -0
- data/lib/assembly/hybrid_velvet_graph.rb +70 -0
- data/lib/assembly/input_genome.rb +182 -0
- data/lib/assembly/kmer_coverage_based_path_filter.rb +65 -0
- data/lib/assembly/node_finder.rb +171 -0
- data/lib/assembly/oriented_node_trail.rb +507 -0
- data/lib/assembly/paired_end_assembler.rb +53 -0
- data/lib/assembly/paired_end_neighbour_finder.rb +176 -0
- data/lib/assembly/probed_graph.rb +105 -0
- data/lib/assembly/read_input.rb +79 -0
- data/lib/assembly/read_to_node.rb +37 -0
- data/lib/assembly/scaffold_breaker.rb +126 -0
- data/lib/assembly/sequence_hasher.rb +71 -0
- data/lib/assembly/single_coherent_paths_between_nodes.rb +533 -0
- data/lib/assembly/single_coherent_wanderer.rb +261 -0
- data/lib/assembly/single_ended_assembler.rb +441 -0
- data/lib/assembly/velvet_c_binding.rb +54 -0
- data/lib/assembly/velvet_graph_sequence_extractor.rb +123 -0
- data/lib/external/VERSION +1 -0
- data/lib/finishm/assemble.rb +224 -0
- data/lib/finishm/explore.rb +217 -0
- data/lib/finishm/finisher.rb +303 -0
- data/lib/finishm/fluff.rb +122 -0
- data/lib/finishm/gapfiller.rb +325 -0
- data/lib/finishm/orfs_finder.rb +88 -0
- data/lib/finishm/path_counter.rb +90 -0
- data/lib/finishm/primers.rb +425 -0
- data/lib/finishm/primers_check.rb +176 -0
- data/lib/finishm/roundup.rb +344 -0
- data/lib/finishm/sequence.rb +142 -0
- data/lib/finishm/visualise.rb +430 -0
- data/lib/finishm/wander.rb +270 -0
- data/lib/kmer_abundance_pattern.rb +79 -0
- data/lib/kmer_multi_abundance_file.rb +48 -0
- data/lib/oligo_designer.rb +88 -0
- data/lib/priner.rb +66 -0
- data/spec/acyclic_connection_finder_spec.rb +551 -0
- data/spec/all_orfs_spec.rb +443 -0
- data/spec/assemble_spec.rb +186 -0
- data/spec/bubbly_assembler_spec.rb +707 -0
- data/spec/c_node_finder_spec.rb +58 -0
- data/spec/connection_interpreter_spec.rb +284 -0
- data/spec/contig_printer_spec.rb +291 -0
- data/spec/coverage_based_graph_filter_spec.rb +102 -0
- data/spec/data/6_3e4e5e6e.1vANME.bam +0 -0
- data/spec/data/6_3e4e5e6e.1vANME.bam.bai +0 -0
- data/spec/data/acyclic_connection_finder/1/probes.fa +5 -0
- data/spec/data/acyclic_connection_finder/1/random1.fa +2 -0
- data/spec/data/acyclic_connection_finder/1/random1.sammy.fa.gz +0 -0
- data/spec/data/acyclic_connection_finder/1/random2.fa +2 -0
- data/spec/data/acyclic_connection_finder/1/random2.sammy.fa.gz +0 -0
- data/spec/data/assembly/1_simple_bubble_uneven_coverage/random3000.fa +39 -0
- data/spec/data/assembly/1_simple_bubble_uneven_coverage/random3000.slightly_changed.fa +39 -0
- data/spec/data/assembly/1_simple_bubble_uneven_coverage/reads_combined.fa.gz +0 -0
- data/spec/data/assembly_visualiser/Contig_6_1_to_250.fa.kmers31 +220 -0
- data/spec/data/assembly_visualiser/Contig_7_1_to_250.fa.kmers31 +220 -0
- data/spec/data/assembly_visualiser/Graph +46 -0
- data/spec/data/assembly_visualiser/start_kmers1 +2 -0
- data/spec/data/bands.csv +1 -0
- data/spec/data/c_probe_node_finder/1/CnyUnifiedSeq +0 -0
- data/spec/data/c_probe_node_finder/1/CnyUnifiedSeq.names +544 -0
- data/spec/data/c_probe_node_finder/1/Graph2 +668 -0
- data/spec/data/c_probe_node_finder/1/LastGraph +668 -0
- data/spec/data/c_probe_node_finder/1/Log +756 -0
- data/spec/data/c_probe_node_finder/1/PreGraph +11 -0
- data/spec/data/c_probe_node_finder/1/Roadmaps +2009 -0
- data/spec/data/c_probe_node_finder/1/contigs.fa +29 -0
- data/spec/data/c_probe_node_finder/1/stats.txt +6 -0
- data/spec/data/contig_printer/1/HOWTO_RECREATE +17 -0
- data/spec/data/contig_printer/1/contigs.fa +4 -0
- data/spec/data/contig_printer/1/seq.fa +2408 -0
- data/spec/data/contig_printer/1/seq.fa.svg +153 -0
- data/spec/data/contig_printer/1/seq.fa.velvet/Graph2 +2953 -0
- data/spec/data/contig_printer/1/seq.fa.velvet/LastGraph +2953 -0
- data/spec/data/contig_printer/1/seq.fa.velvet/Log +21 -0
- data/spec/data/contig_printer/1/seq.fa.velvet/PreGraph +27 -0
- data/spec/data/contig_printer/1/seq.fa.velvet/Roadmaps +5182 -0
- data/spec/data/contig_printer/1/seq.fa.velvet/Sequences +3612 -0
- data/spec/data/contig_printer/1/seq.fa.velvet/contigs.fa +36 -0
- data/spec/data/contig_printer/1/seq.fa.velvet/stats.txt +14 -0
- data/spec/data/contig_printer/1/seq.faVseq2_1to550.fa.bam +0 -0
- data/spec/data/contig_printer/1/seq.faVseq2_1to550.fa.bam.bai +0 -0
- data/spec/data/contig_printer/1/seq.node12.fa +4 -0
- data/spec/data/contig_printer/1/seq1_1to550.fa +2 -0
- data/spec/data/contig_printer/1/seq2_1to550.fa +2 -0
- data/spec/data/contig_printer/1/seq2_1to550.fa.fai +1 -0
- data/spec/data/explore/1/2seqs.sammy.fa +12004 -0
- data/spec/data/explore/1/HOWTO_RECREATE.txt +6 -0
- data/spec/data/explore/1/a.fa +2 -0
- data/spec/data/explore/1/seq1_and_a.fa +3 -0
- data/spec/data/explore/1/seq2.fa +2 -0
- data/spec/data/fluff/1/2seqs.sammy.fa +12004 -0
- data/spec/data/fluff/1/HOWTO_RECREATE.txt +5 -0
- data/spec/data/fluff/1/seq1.fa +2 -0
- data/spec/data/fluff/1/seq2.fa +2 -0
- data/spec/data/gapfilling/1/reads.fa +171 -0
- data/spec/data/gapfilling/1/trail_with_Ns.fa +5 -0
- data/spec/data/gapfilling/1/velvetAssembly/Graph2 +130 -0
- data/spec/data/gapfilling/1/velvetAssembly/LastGraph +130 -0
- data/spec/data/gapfilling/1/velvetAssembly/Log +199 -0
- data/spec/data/gapfilling/1/velvetAssembly/PreGraph +7 -0
- data/spec/data/gapfilling/1/velvetAssembly/Roadmaps +239 -0
- data/spec/data/gapfilling/1/velvetAssembly/Sequences +281 -0
- data/spec/data/gapfilling/1/velvetAssembly/contigs.fa +12 -0
- data/spec/data/gapfilling/1/velvetAssembly/stats.txt +4 -0
- data/spec/data/gapfilling/2/HOWTO_recreate +17 -0
- data/spec/data/gapfilling/2/reference.fa +2 -0
- data/spec/data/gapfilling/2/reference_part1.fa +4 -0
- data/spec/data/gapfilling/2/reference_part2.fa +4 -0
- data/spec/data/gapfilling/2/sammy_reads.fa.gz +0 -0
- data/spec/data/gapfilling/2/with_gaps.fa +4 -0
- data/spec/data/gapfilling/3/HOWTO_recreate +4 -0
- data/spec/data/gapfilling/3/reads.fa.gz +0 -0
- data/spec/data/gapfilling/3/reference_part1.fa +4 -0
- data/spec/data/gapfilling/3/reference_part2.fa +4 -0
- data/spec/data/gapfilling/3/with_gaps.fa +4 -0
- data/spec/data/gapfilling/4/HOWTO_recreate +1 -0
- data/spec/data/gapfilling/4/reads.fa.gz +0 -0
- data/spec/data/gapfilling/5/HOWTO_RECREATE +7 -0
- data/spec/data/gapfilling/5/answer.fna +2 -0
- data/spec/data/gapfilling/5/gappy.fna +2 -0
- data/spec/data/gapfilling/5/reads.fa +17961 -0
- data/spec/data/gapfilling/5/velvet51_3.5/LastGraph +8337 -0
- data/spec/data/gapfilling/5/velvet51_3.5/Sequences +20921 -0
- data/spec/data/gapfilling/6/random1.fa +28 -0
- data/spec/data/gapfilling/6/random2.fa +28 -0
- data/spec/data/gapfilling/6/random_sequence_length_2000 +0 -0
- data/spec/data/gapfilling/6/reads.random1.fa.gz +0 -0
- data/spec/data/gapfilling/6/reads.random2.fa.gz +0 -0
- data/spec/data/gapfilling/6/to_gapfill.fa +22 -0
- data/spec/data/kmer_profile_to_assembly/multiple_abundance_file1.csv +2 -0
- data/spec/data/kmers_count1.csv +2 -0
- data/spec/data/kmers_count2.csv +3 -0
- data/spec/data/out +3 -0
- data/spec/data/positive_latching_pair.fa +2 -0
- data/spec/data/primers.csv +4 -0
- data/spec/data/read_selection_by_kmer/blacklist1.txt +1 -0
- data/spec/data/read_selection_by_kmer/input.fasta +6 -0
- data/spec/data/read_selection_by_kmer/whitelist1.txt +1 -0
- data/spec/data/read_selection_by_kmer/whitelist2.txt +2 -0
- data/spec/data/read_to_node/1_a_graph/HOWTO_RECREATE.txt +2 -0
- data/spec/data/read_to_node/1_a_graph/LastGraph +6695 -0
- data/spec/data/read_to_node/1_a_graph/ReadToNode.bin +0 -0
- data/spec/data/read_to_node/2_no_read256_or_259/HOWTO_RECREATE.txt +3 -0
- data/spec/data/read_to_node/2_no_read256_or_259/LastGraph +6693 -0
- data/spec/data/read_to_node/2_no_read256_or_259/ReadToNode.bin +0 -0
- data/spec/data/read_to_node/3_no_last_read/LastGraph +6694 -0
- data/spec/data/read_to_node/3_no_last_read/ReadToNode.bin +0 -0
- data/spec/data/t/details.txt +5 -0
- data/spec/data/t/details.txt.srt +5 -0
- data/spec/data/t/location.txt +3 -0
- data/spec/data/t/location.txt.srt +3 -0
- data/spec/data/tweak/1_gap_then_unscaffolded/answer.fa +2 -0
- data/spec/data/tweak/1_gap_then_unscaffolded/reads.fa.gz +0 -0
- data/spec/data/tweak/1_gap_then_unscaffolded/scaffolds.fa +6 -0
- data/spec/data/tweak/2_second_genome/answer2.fa +2 -0
- data/spec/data/tweak/2_second_genome/reads.fa.gz +0 -0
- data/spec/data/tweak/3_variant/answer.fa +2 -0
- data/spec/data/tweak/3_variant/lesser_answer.fa +2 -0
- data/spec/data/tweak/3_variant/reads.fa.gz +0 -0
- data/spec/data/tweak/3_variant/with_gaps.fa +2 -0
- data/spec/data/velvet_test_trails/Assem/Graph +17 -0
- data/spec/data/velvet_test_trails/Assem/Graph2 +40 -0
- data/spec/data/velvet_test_trails/Assem/LastGraph +40 -0
- data/spec/data/velvet_test_trails/Assem/Log +35 -0
- data/spec/data/velvet_test_trails/Assem/PreGraph +9 -0
- data/spec/data/velvet_test_trails/Assem/Roadmaps +89 -0
- data/spec/data/velvet_test_trails/Assem/Sequences +50 -0
- data/spec/data/velvet_test_trails/Assem/a.svg +53 -0
- data/spec/data/velvet_test_trails/Assem/contigs.fa +15 -0
- data/spec/data/velvet_test_trails/Assem/stats.txt +5 -0
- data/spec/data/velvet_test_trails/node_fwds.fa +8 -0
- data/spec/data/velvet_test_trails/node_seqs.fa +9 -0
- data/spec/data/velvet_test_trails/nodes_fwd_rev.fa +16 -0
- data/spec/data/velvet_test_trails/read1.fa +2 -0
- data/spec/data/velvet_test_trails/reads.fa +50 -0
- data/spec/data/velvet_test_trails_reverse/Assem/LastGraph +17 -0
- data/spec/data/velvet_test_trails_reverse/Assem/a.svg +53 -0
- data/spec/data/velvet_test_trails_reverse/reads_reversed.fa +10 -0
- data/spec/data/visualise/1/LastGraph +6695 -0
- data/spec/data/visualise/2_paired_end/HOWTO_RECREATE.txt +10 -0
- data/spec/data/visualise/2_paired_end/rand1.fa +2 -0
- data/spec/data/visualise/2_paired_end/rand2.fa +2 -0
- data/spec/data/visualise/2_paired_end/with_gaps.fa +8 -0
- data/spec/data/visualise/2_paired_end/with_gaps.read_pairs.fa.gz +0 -0
- data/spec/data/wander/1/random1.fa +2 -0
- data/spec/data/wander/1/random1.sammy.fa +804 -0
- data/spec/depth_first_search_spec.rb +190 -0
- data/spec/dijkstra_spec.rb +143 -0
- data/spec/explore_spec.rb +29 -0
- data/spec/fluffer_spec.rb +155 -0
- data/spec/gapfiller_spec.rb +107 -0
- data/spec/graph_explorer_spec.rb +475 -0
- data/spec/graph_generator_spec.rb +99 -0
- data/spec/height_finder_spec.rb +306 -0
- data/spec/kmer_abundance_pattern_spec.rb +56 -0
- data/spec/kmer_coverage_based_path_filter_spec.rb +73 -0
- data/spec/kmer_profile_finder_spec.rb +38 -0
- data/spec/kmers_count_tabulate_spec.rb +120 -0
- data/spec/oriented_node_trail_spec.rb +221 -0
- data/spec/paired_end_neighbours_spec.rb +126 -0
- data/spec/paths_between_nodes_spec.rb +349 -0
- data/spec/priner_spec.rb +7 -0
- data/spec/read_input_spec.rb +23 -0
- data/spec/read_selection_by_kmer_spec.rb +166 -0
- data/spec/read_to_node_spec.rb +35 -0
- data/spec/roundup_spec.rb +366 -0
- data/spec/scaffold_breaker_spec.rb +144 -0
- data/spec/sequence_spec.rb +43 -0
- data/spec/single_coherent_paths_between_nodes_spec.rb +492 -0
- data/spec/single_coherent_wanderer_spec.rb +120 -0
- data/spec/single_ended_assembler_spec.rb +398 -0
- data/spec/spec_helper.rb +310 -0
- data/spec/velvet_graph_sequence_extractor_spec.rb +80 -0
- data/spec/visualise_spec.rb +105 -0
- data/spec/wander_spec.rb +119 -0
- data/spec/watch_for_changes.sh +16 -0
- data/validation/fasta_compare.rb +72 -0
- data/validation/gapfill_simulate_perfect.rb +108 -0
- metadata +899 -0
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import std.getopt;
|
8
|
+
|
9
|
+
void main(string[] args){
|
10
|
+
bool usePercentages = false;
|
11
|
+
int minCount = 1;
|
12
|
+
string trace = "info";
|
13
|
+
getopt(args,
|
14
|
+
"percentage", &usePercentages,
|
15
|
+
"min-count", &minCount,
|
16
|
+
"trace", &trace
|
17
|
+
);
|
18
|
+
|
19
|
+
//Create an array of open file handles, one for each argument given
|
20
|
+
auto filenames = args[1 .. $];
|
21
|
+
int[] totalCounts = new int[filenames.length];
|
22
|
+
int kmerLength = 0;
|
23
|
+
|
24
|
+
foreach(i, file; filenames){
|
25
|
+
int count = 0;
|
26
|
+
auto f = File(file);
|
27
|
+
char[] line;
|
28
|
+
while (f.readln(line)){
|
29
|
+
//foreach(line; f.byLine()){
|
30
|
+
if (kmerLength==0){
|
31
|
+
kmerLength = 101;//to!int(indexOf(line, " "));
|
32
|
+
stderr.writeln("Detected kmer length of ",kmerLength);
|
33
|
+
}
|
34
|
+
int thisCount = to!int(line[kmerLength+1 .. $-1]);
|
35
|
+
//int thisCount = to!int(line[kmerLength+1 .. $]);
|
36
|
+
count += thisCount;
|
37
|
+
//if (count > 4000002){break;}
|
38
|
+
}
|
39
|
+
totalCounts[i] = count;
|
40
|
+
}
|
41
|
+
stderr.writeln("Finished ccounting total kmers, totals were: ",totalCounts);
|
42
|
+
|
43
|
+
if(false){
|
44
|
+
bool allFinished = false;
|
45
|
+
bool[] finished = new bool[filenames.length];
|
46
|
+
foreach (f; finished){f=false;}
|
47
|
+
|
48
|
+
File[] files = new File[filenames.length];
|
49
|
+
foreach(i; 0 .. files.length){
|
50
|
+
files[i] = File(filenames[i]);
|
51
|
+
}
|
52
|
+
|
53
|
+
struct KmerCount {
|
54
|
+
char[101] kmer;
|
55
|
+
int count;
|
56
|
+
}
|
57
|
+
KmerCount[] currentRows = new KmerCount[files.length];
|
58
|
+
char[] lineBuffer;
|
59
|
+
foreach (i; 0..currentRows.length){
|
60
|
+
//read in the line to teh buffer, so memory is not reallocated
|
61
|
+
files[i].readln(lineBuffer);
|
62
|
+
currentRows[i].kmer = chomp(files[i].readln(currentRows[i].kmer))[0..kmerLength];
|
63
|
+
currentRows[i].count = to!int(line[kmerLength+1..$]);
|
64
|
+
}
|
65
|
+
|
66
|
+
//write headers
|
67
|
+
enum ctr = ctRegex!(".*/(.+)");
|
68
|
+
foreach(f; filenames){
|
69
|
+
write("\t",match(f, ctr).captures[1]);
|
70
|
+
}
|
71
|
+
writeln();
|
72
|
+
|
73
|
+
string[] toPrint = new string[filenames.length+1];
|
74
|
+
int kmersCounted = 0;
|
75
|
+
while (!allFinished){
|
76
|
+
kmersCounted += 1;
|
77
|
+
if (kmersCounted % (1024*1024) == 0){stderr.writeln("Processed ",kmersCounted," kmers.");}
|
78
|
+
//Find the lowest kmer
|
79
|
+
string lowestKmer = null;
|
80
|
+
foreach (kc; currentRows){
|
81
|
+
if (lowestKmer == null || kc.kmer < lowestKmer){
|
82
|
+
lowestKmer = kc.kmer;
|
83
|
+
}
|
84
|
+
}
|
85
|
+
|
86
|
+
//Go through each file, printing the number of this kmer found
|
87
|
+
int totalObservations = 0;
|
88
|
+
toPrint[0] = lowestKmer;
|
89
|
+
foreach (i, kc; currentRows){
|
90
|
+
if (kc.kmer == lowestKmer){
|
91
|
+
totalObservations += kc.count;
|
92
|
+
if (usePercentages){
|
93
|
+
toPrint[i+1] = to!string(to!float(kc.count)/totalCounts[i]);
|
94
|
+
} else {
|
95
|
+
toPrint[i+1] = to!string(kc.count);
|
96
|
+
}
|
97
|
+
|
98
|
+
// Read a new line in, check if this file is finished
|
99
|
+
auto line = files[i].readln;
|
100
|
+
if (line == null){
|
101
|
+
finished[i] = true;
|
102
|
+
allFinished = true; //guilty until proven innocent
|
103
|
+
foreach(f; finished){
|
104
|
+
if (!f){
|
105
|
+
allFinished = false;
|
106
|
+
}
|
107
|
+
}
|
108
|
+
currentRows[i].kmer = null;
|
109
|
+
currentRows[i].count = -1;
|
110
|
+
} else {
|
111
|
+
//Regular line to be read in
|
112
|
+
currentRows[i].kmer = line[0..kmerLength];
|
113
|
+
currentRows[i].count = to!int(line[kmerLength+1..$-1]);
|
114
|
+
}
|
115
|
+
} else {
|
116
|
+
toPrint[i+1] = "0";
|
117
|
+
}
|
118
|
+
}
|
119
|
+
if (totalObservations >= minCount){
|
120
|
+
writeln(join(toPrint, "\t"));
|
121
|
+
}
|
122
|
+
}
|
123
|
+
}}
|
@@ -0,0 +1,84 @@
|
|
1
|
+
#!/usr/bin/env ruby
|
2
|
+
|
3
|
+
require 'optparse'
|
4
|
+
require 'bio-logger'
|
5
|
+
require 'csv'
|
6
|
+
require 'progressbar'
|
7
|
+
require 'tempfile'
|
8
|
+
require 'systemu'
|
9
|
+
|
10
|
+
SCRIPT_NAME = File.basename(__FILE__); LOG_NAME = SCRIPT_NAME.gsub('.rb','')
|
11
|
+
|
12
|
+
# Parse command line options into the options hash
|
13
|
+
options = {
|
14
|
+
:logger => 'stderr',
|
15
|
+
:log_level => 'info',
|
16
|
+
:min_count => 1,
|
17
|
+
}
|
18
|
+
o = OptionParser.new do |opts|
|
19
|
+
opts.banner = "
|
20
|
+
Usage: #{SCRIPT_NAME} <kmers_count_output1> [<kmers_count_output2> ..]
|
21
|
+
|
22
|
+
Take a list of files output from libngs' kmers_count tool, after being run through gnu sort.
|
23
|
+
|
24
|
+
Create a table, where the columns are each file, the rows are each kmer, and
|
25
|
+
the cells are the percent of that file's kmer actually is that kmer.\n\n"
|
26
|
+
|
27
|
+
|
28
|
+
opts.on("--output-file FILENAME", "Output file path [required]") do |arg|
|
29
|
+
options[:output_file] = arg
|
30
|
+
end
|
31
|
+
|
32
|
+
opts.on("--percentage", "description [default: #{options[:eg]}]") do
|
33
|
+
raise "not yet implemented"
|
34
|
+
options[:percentage_outputs] = true
|
35
|
+
end
|
36
|
+
opts.on("--min-count COUNT", "require at least this many kmers to be output into the output file [default: #{options[:min_count]}]") do |arg|
|
37
|
+
raise "not yet implemented"
|
38
|
+
options[:min_count] = arg.to_i
|
39
|
+
end
|
40
|
+
|
41
|
+
# logger options
|
42
|
+
opts.separator "\nVerbosity:\n\n"
|
43
|
+
opts.on("-q", "--quiet", "Run quietly, set logging to ERROR level [default INFO]") {options[:log_level] = 'error'}
|
44
|
+
opts.on("--logger filename",String,"Log to file [default #{options[:logger]}]") { |name| options[:logger] = name}
|
45
|
+
opts.on("--trace options",String,"Set log level [default INFO]. e.g. '--trace debug' to set logging level to DEBUG"){|s| options[:log_level] = s}
|
46
|
+
end; o.parse!
|
47
|
+
if ARGV.length == 0 or options[:output_file].nil?
|
48
|
+
$stderr.puts o
|
49
|
+
exit 1
|
50
|
+
end
|
51
|
+
# Setup logging
|
52
|
+
Bio::Log::CLI.logger(options[:logger]); Bio::Log::CLI.trace(options[:log_level]); log = Bio::Log::LoggerPlus.new(LOG_NAME); Bio::Log::CLI.configure(LOG_NAME)
|
53
|
+
|
54
|
+
filenames = ARGV
|
55
|
+
raise "I need more than 1 file" unless filenames.length > 1
|
56
|
+
log.info "Joining these files: #{filenames.inspect}"
|
57
|
+
|
58
|
+
# run gnu join on each file
|
59
|
+
current_build_file = filenames[0] #Build off the current build file first, then a tempfile subsequently
|
60
|
+
|
61
|
+
Tempfile.open('kmers_join1') do |tempfile1|
|
62
|
+
Tempfile.open('kmers_join2') do |tempfile2|
|
63
|
+
filenames.each_with_index do |file, i|
|
64
|
+
next if i==0
|
65
|
+
|
66
|
+
first_file_output_fields = (2..(i+1)).to_a.collect{|n| "1.#{n.to_s}"}.join(',')
|
67
|
+
cmd = "join -a1 -a2 -e 0 -o0,#{first_file_output_fields},2.2 #{current_build_file.inspect} #{file} >#{tempfile2.path}"
|
68
|
+
log.info "At #{Time.now}, running #{cmd}.."
|
69
|
+
status, stdout, stderr = systemu cmd
|
70
|
+
raise stderr unless stderr == ''
|
71
|
+
raise 'exitstatus bad1!' unless status.exitstatus == 0
|
72
|
+
status, stdout, stderr = systemu "mv #{tempfile2.path} #{tempfile1.path}"
|
73
|
+
raise stderr unless stderr == ''
|
74
|
+
raise 'exitstatus bad2!' unless status.exitstatus == 0
|
75
|
+
current_build_file = tempfile1.path
|
76
|
+
end
|
77
|
+
status, stdout, stderr = systemu "mv #{current_build_file} #{options[:output_file]}"
|
78
|
+
raise stderr unless stderr == ''
|
79
|
+
raise 'exitstatus bad3!' unless status.exitstatus == 0
|
80
|
+
end
|
81
|
+
end
|
82
|
+
|
83
|
+
|
84
|
+
|
@@ -0,0 +1,108 @@
|
|
1
|
+
#!/usr/bin/env ruby
|
2
|
+
|
3
|
+
require 'optparse'
|
4
|
+
require 'bio-logger'
|
5
|
+
require 'csv'
|
6
|
+
|
7
|
+
SCRIPT_NAME = File.basename(__FILE__); LOG_NAME = SCRIPT_NAME.gsub('.rb','')
|
8
|
+
|
9
|
+
# Parse command line options into the options hash
|
10
|
+
options = {
|
11
|
+
:logger => 'stderr',
|
12
|
+
:log_level => 'info',
|
13
|
+
}
|
14
|
+
o = OptionParser.new do |opts|
|
15
|
+
opts.banner = "
|
16
|
+
Usage: #{SCRIPT_NAME} <arguments>
|
17
|
+
|
18
|
+
Takes a list of PCR primers that were put in several lanes (not all primers in all lanes), and a list of bands that were found, and decipher which bands are the result of which primer pairs, as best as possible\n\n"
|
19
|
+
|
20
|
+
opts.on("--bands-file FILE", "tsv file, with the band names as the first column, and the lane numbers that they appear in as the second column (comma separated) [required]") do |arg|
|
21
|
+
options[:bands_file] = arg
|
22
|
+
end
|
23
|
+
opts.on("--primers-file FILE", "tsv file, with the lane names as the first column, and the set of primers numbers that are in each lane as the second column (comma separated) [required]") do |arg|
|
24
|
+
options[:primers_file] = arg
|
25
|
+
end
|
26
|
+
|
27
|
+
# logger options
|
28
|
+
opts.separator "\nVerbosity:\n\n"
|
29
|
+
opts.on("-q", "--quiet", "Run quietly, set logging to ERROR level [default INFO]") {options[:log_level] = 'error'}
|
30
|
+
opts.on("--logger filename",String,"Log to file [default #{options[:logger]}]") { |name| options[:logger] = name}
|
31
|
+
opts.on("--trace options",String,"Set log level [default INFO]. e.g. '--trace debug' to set logging level to DEBUG"){|s| options[:log_level] = s}
|
32
|
+
end; o.parse!
|
33
|
+
if ARGV.length != 0 or options[:bands_file].nil? or options[:primers_file].nil?
|
34
|
+
$stderr.puts o
|
35
|
+
exit 1
|
36
|
+
end
|
37
|
+
# Setup logging
|
38
|
+
Bio::Log::CLI.logger(options[:logger]); Bio::Log::CLI.trace(options[:log_level]); log = Bio::Log::LoggerPlus.new(LOG_NAME); Bio::Log::CLI.configure(LOG_NAME)
|
39
|
+
|
40
|
+
|
41
|
+
# Read in the bands
|
42
|
+
bands_to_lanes = {}
|
43
|
+
CSV.foreach(options[:bands_file], :col_sep => "\t") do |row|
|
44
|
+
raise "Malformed bands file in this line: #{row.inspect}" unless row.length == 2
|
45
|
+
|
46
|
+
band_name = row[0]
|
47
|
+
raise "Two bands were labeled the same way, as #{band_name.inspect}" if bands_to_lanes.key?(band_name)
|
48
|
+
|
49
|
+
lanes_of_this_band = row[1].split(/[,\s]/).collect{|c| c.strip}
|
50
|
+
bands_to_lanes[band_name] = lanes_of_this_band
|
51
|
+
end
|
52
|
+
log.info "Parsed in #{bands_to_lanes.length} bands, found #{bands_to_lanes.collect{|k,v| v.length}.join(',')} lanes each, respectively"
|
53
|
+
|
54
|
+
# Read in the primer sets
|
55
|
+
lanes_to_primers = {}
|
56
|
+
CSV.foreach(options[:primers_file], :col_sep => "\t") do |row|
|
57
|
+
raise "Malformed primers file in this line: #{row.inspect}" unless row.length == 2
|
58
|
+
|
59
|
+
lane_name = row[0]
|
60
|
+
raise "Two lanes were labeled the same way, as #{lane_name.inspect}" if lanes_to_primers.key?(lane_name)
|
61
|
+
|
62
|
+
primers_of_this_band = row[1].split(/[,\s]/).collect{|c| c.strip}
|
63
|
+
lanes_to_primers[lane_name] = primers_of_this_band
|
64
|
+
end
|
65
|
+
log.info "Parsed in #{lanes_to_primers.length} lanes, with #{lanes_to_primers.collect{|k,v| v.length}.join(',')} primers each, respectively"
|
66
|
+
|
67
|
+
|
68
|
+
# Go through each pairing of primers. Which primer sets explain each band?
|
69
|
+
all_primers = lanes_to_primers.values.flatten.sort.uniq
|
70
|
+
lanes = lanes_to_primers.keys
|
71
|
+
bands = bands_to_lanes.keys
|
72
|
+
|
73
|
+
bands_to_explaining_primer_pairs = {}
|
74
|
+
|
75
|
+
bands.each do |band|
|
76
|
+
log.debug "Going after band #{band}"
|
77
|
+
all_primers.combination(2) do |array|
|
78
|
+
|
79
|
+
primer1 = array.sort[0]
|
80
|
+
primer2 = array.sort[1]
|
81
|
+
log.debug "Testing primers #{primer1}/#{primer2} agreement with band #{band}"
|
82
|
+
|
83
|
+
band_agrees_with_this_primer_pair = true
|
84
|
+
lanes.each do |lane|
|
85
|
+
band_is_in_this_lane = bands_to_lanes[band].include?(lane)
|
86
|
+
primers_here = lanes_to_primers[lane]
|
87
|
+
if band_is_in_this_lane and (!primers_here.include?(primer1) or !primers_here.include?(primer2))
|
88
|
+
log.debug "primer pair #{primer1}/#{primer2} fails for band #{band} because band was present but at least one primer wasn't, in lane #{lane}"
|
89
|
+
band_agrees_with_this_primer_pair = false
|
90
|
+
end
|
91
|
+
if !band_is_in_this_lane and (primers_here.include?(primer1) and primers_here.include?(primer2))
|
92
|
+
log.debug "primer pair #{primer1}/#{primer2} fails for band #{band} because band was not present but both primers were, in lane #{lane}"
|
93
|
+
band_agrees_with_this_primer_pair = false
|
94
|
+
end
|
95
|
+
end
|
96
|
+
|
97
|
+
if band_agrees_with_this_primer_pair
|
98
|
+
log.debug "Found a suitable pair of primers for band #{band}: #{primer1}/#{primer2}"
|
99
|
+
bands_to_explaining_primer_pairs[band] ||= []
|
100
|
+
bands_to_explaining_primer_pairs[band].push array
|
101
|
+
end
|
102
|
+
end
|
103
|
+
|
104
|
+
puts [
|
105
|
+
band,
|
106
|
+
bands_to_explaining_primer_pairs[band].nil? ? 'none' : bands_to_explaining_primer_pairs[band].collect{|a| "(#{a.join(',')})"}.join(', ')
|
107
|
+
].join("\t")
|
108
|
+
end
|
@@ -0,0 +1,119 @@
|
|
1
|
+
#!/usr/bin/env ruby
|
2
|
+
|
3
|
+
require 'optparse'
|
4
|
+
require 'bio-logger'
|
5
|
+
require 'bio'
|
6
|
+
require 'progressbar'
|
7
|
+
|
8
|
+
$:.unshift File.join(File.dirname(__FILE__),'..','lib')
|
9
|
+
require 'priner'
|
10
|
+
|
11
|
+
if __FILE__ == $0 #needs to be removed if this script is distributed as part of a rubygem
|
12
|
+
SCRIPT_NAME = File.basename(__FILE__); LOG_NAME = SCRIPT_NAME.gsub('.rb','')
|
13
|
+
|
14
|
+
# Parse command line options into the options hash
|
15
|
+
options = {
|
16
|
+
:logger => 'stderr',
|
17
|
+
:reverse_complement => false,
|
18
|
+
:gc_clamp_length => 2,
|
19
|
+
:min_melting_temperature => 56,
|
20
|
+
:max_melting_temperature => 62,
|
21
|
+
:min_primer_length => 15,
|
22
|
+
}
|
23
|
+
o = OptionParser.new do |opts|
|
24
|
+
opts.banner = "
|
25
|
+
Usage: #{SCRIPT_NAME} <arguments> <sequence>
|
26
|
+
|
27
|
+
Take a sequence, and find an oligos that fit certain parameters. Sort of like primer3_core but only look for single oligos, not pairs.\n\n"
|
28
|
+
|
29
|
+
opts.on("-s", "--sequence-file FILE", "Fasta file of sequences [required]") do |arg|
|
30
|
+
options[:input_file] = arg
|
31
|
+
end
|
32
|
+
|
33
|
+
opts.separator "\nOptional arguments:\n\n"
|
34
|
+
opts.on("-r", "--reverse-complement", "Design primers pointing backwards off the start of the sequence in reverse, not off the end forwards [default: #{options[:reverse_complement]}]") do
|
35
|
+
options[:reverse_complement] = true
|
36
|
+
end
|
37
|
+
|
38
|
+
# logger options
|
39
|
+
opts.separator "\nVerbosity:\n\n"
|
40
|
+
opts.on("-q", "--quiet", "Run quietly, set logging to ERROR level [default INFO]") {Bio::Log::CLI.trace('error')}
|
41
|
+
opts.on("--logger filename",String,"Log to file [default #{options[:logger]}]") { |name| options[:logger] = name}
|
42
|
+
opts.on("--trace options",String,"Set log level [default INFO]. e.g. '--trace debug' to set logging level to DEBUG"){|s| Bio::Log::CLI.trace(s)}
|
43
|
+
end; o.parse!
|
44
|
+
if ARGV.length != 0
|
45
|
+
$stderr.puts o
|
46
|
+
exit 1
|
47
|
+
end
|
48
|
+
# Setup logging. bio-logger defaults to STDERR not STDOUT, I disagree
|
49
|
+
Bio::Log::CLI.logger(options[:logger]); log = Bio::Log::LoggerPlus.new(LOG_NAME); Bio::Log::CLI.configure(LOG_NAME)
|
50
|
+
|
51
|
+
# Read the contigs in
|
52
|
+
contigs = []
|
53
|
+
Bio::FlatFile.foreach(options[:input_file]) do |entry|
|
54
|
+
contigs.push entry.seq.to_s
|
55
|
+
end
|
56
|
+
log.info "Read in #{contigs.length} contigs from #{options[:contigs_file]}"
|
57
|
+
raise unless contigs.length == 1
|
58
|
+
|
59
|
+
seq = contigs[0]
|
60
|
+
|
61
|
+
# Reverse complement if required
|
62
|
+
if options[:reverse_complement]
|
63
|
+
seq = Bio::Sequence::NA.new(seq).reverse_complement.to_s
|
64
|
+
end
|
65
|
+
seq.upcase!
|
66
|
+
|
67
|
+
raise "Whackiness in the supplied sequence! #{seq}" unless seq.match(/^[ATGC]+$/)
|
68
|
+
raise unless options[:min_primer_length] > options[:gc_clamp_length]
|
69
|
+
|
70
|
+
# Find out all those positions that have a GC clamp of enough
|
71
|
+
gc_clamped_positions = []
|
72
|
+
(0...seq.length).each do |pos|
|
73
|
+
next unless pos-options[:min_primer_length] >= -1
|
74
|
+
|
75
|
+
if seq[pos-options[:gc_clamp_length]+1..pos].match(/^[GC]+$/)
|
76
|
+
gc_clamped_positions << pos
|
77
|
+
end
|
78
|
+
end
|
79
|
+
log.info "Found #{gc_clamped_positions.length} positions with a suitable GC-clamp"
|
80
|
+
|
81
|
+
# Find those with suitable melting temperatures
|
82
|
+
designer = OligoDesigner.new
|
83
|
+
progress = ProgressBar.new('primer_finding', gc_clamped_positions.length)
|
84
|
+
gc_clamped_positions.each do |pos|
|
85
|
+
# Iteratively make primers longer. Start with min primer length, end when the Tm exceeds the maximum allowable
|
86
|
+
current_length = options[:min_primer_length]
|
87
|
+
|
88
|
+
over_tm_max = false
|
89
|
+
while !over_tm_max and pos-current_length >= 0
|
90
|
+
oligo = seq[pos-current_length+1..pos]
|
91
|
+
tm = designer.melting_temperature oligo
|
92
|
+
puts oligo
|
93
|
+
puts tm
|
94
|
+
exit
|
95
|
+
|
96
|
+
if tm > options[:min_melting_temperature]
|
97
|
+
if tm < options[:max_melting_temperature]
|
98
|
+
# This is a hit
|
99
|
+
cur_seq = oligo
|
100
|
+
if options[:reverse_complement]
|
101
|
+
cur_seq = Bio::Sequence::NA.new(cur_seq).reverse_complement.to_s
|
102
|
+
end
|
103
|
+
|
104
|
+
puts [
|
105
|
+
cur_seq, tm
|
106
|
+
].join("\t")
|
107
|
+
else
|
108
|
+
over_tm_max = true
|
109
|
+
break #making the primer longer can only result in higher melting temperatures, and we are already over the max
|
110
|
+
end
|
111
|
+
end
|
112
|
+
current_length += 1
|
113
|
+
end
|
114
|
+
progress.inc
|
115
|
+
end
|
116
|
+
progress.finish
|
117
|
+
|
118
|
+
|
119
|
+
end #end if running as a script
|