Mercurial > repos > artbio > small_rna_maps
changeset 1:40972a8dfab9 draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit ad60e6655aabe30246043d95f14646b2527c9255
| author | artbio |
|---|---|
| date | Mon, 24 Jul 2017 12:31:04 -0400 |
| parents | 6d48150495e3 |
| children | 507383cce5a8 |
| files | small_rna_maps.py small_rna_maps.xml test-data/coverage.pdf test-data/doubled.tab test-data/doubled_mean.pdf test-data/mean.pdf test-data/median.pdf test-data/output.tab test-data/sizes.pdf |
| diffstat | 9 files changed, 2 insertions(+), 6174 deletions(-) [+] |
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--- a/small_rna_maps.py Mon Jul 24 06:28:45 2017 -0400 +++ b/small_rna_maps.py Mon Jul 24 12:31:04 2017 -0400 @@ -51,8 +51,6 @@ for pos in positions: if not map_dictionary[(chrom, pos+1, 'F')]: map_dictionary[(chrom, pos+1, 'F')] = [] - if not map_dictionary[(chrom, pos+1, 'R')]: - map_dictionary[(chrom, pos+1, 'R')] = [] if read.is_reverse: map_dictionary[(chrom, positions[-1]+1, 'R')].append(read.query_alignment_length) @@ -113,7 +111,6 @@ for chrom in self.chromosomes: coverage_dictionary[(chrom, 1, 'F')] = 0 coverage_dictionary[(chrom, self.chromosomes[chrom], 'F')] = 0 - for key in map_dictionary: coverage = self.bam_object.count_coverage( reference=key[0], @@ -132,7 +129,7 @@ {chrom: {polarity: {size: nbre of reads}}} ''' size_dictionary = defaultdict(lambda: defaultdict( - lambda: defaultdict( int ))) + lambda: defaultdict(int))) # to track empty chromosomes for chrom in self.chromosomes: if self.bam_object.count(chrom) == 0:
--- a/small_rna_maps.xml Mon Jul 24 06:28:45 2017 -0400 +++ b/small_rna_maps.xml Mon Jul 24 12:31:04 2017 -0400 @@ -1,4 +1,4 @@ -<tool id="small_rna_maps" name="small_rna_maps" version="0.9.0"> +<tool id="small_rna_maps" name="small_rna_maps" version="0.9.1"> <description></description> <requirements> <requirement type="package" version="1.11.2=py27_0">numpy</requirement>
--- a/test-data/doubled.tab Mon Jul 24 06:28:45 2017 -0400 +++ b/test-data/doubled.tab Mon Jul 24 12:31:04 2017 -0400 @@ -1,6339 +1,3205 @@ Dataset Chromosome Chrom_length Coordinate Nbr_reads Polarity Max Mean Median Coverage input1.bam_0 FBtr0070001 72 1 1 F 27 17.0 17.0 1 -input1.bam_0 FBtr0070001 72 1 0 R 27 0 0 1 input1.bam_0 FBtr0070001 72 2 0 F 27 0 0 1 -input1.bam_0 FBtr0070001 72 2 0 R 27 0 0 1 input1.bam_0 FBtr0070001 72 3 0 F 27 0 0 1 -input1.bam_0 FBtr0070001 72 3 0 R 27 0 0 1 input1.bam_0 FBtr0070001 72 4 0 F 27 0 0 1 -input1.bam_0 FBtr0070001 72 4 0 R 27 0 0 1 input1.bam_0 FBtr0070001 72 5 0 F 27 0 0 1 -input1.bam_0 FBtr0070001 72 5 0 R 27 0 0 1 input1.bam_0 FBtr0070001 72 6 0 F 27 0 0 1 -input1.bam_0 FBtr0070001 72 6 0 R 27 0 0 1 input1.bam_0 FBtr0070001 72 7 6 F 27 20.3 21.0 7 -input1.bam_0 FBtr0070001 72 7 0 R 27 0 0 7 input1.bam_0 FBtr0070001 72 8 3 F 27 21.3 21.0 10 -input1.bam_0 FBtr0070001 72 8 0 R 27 0 0 10 input1.bam_0 FBtr0070001 72 9 0 F 27 0 0 10 -input1.bam_0 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-input1.bam_1 FBtr0080663 71 41 0 R 56 0 0 3 input1.bam_1 FBtr0080663 71 42 0 F 56 0 0 3 -input1.bam_1 FBtr0080663 71 42 0 R 56 0 0 3 input1.bam_1 FBtr0080663 71 43 0 F 56 0 0 3 -input1.bam_1 FBtr0080663 71 43 0 R 56 0 0 3 input1.bam_1 FBtr0080663 71 44 0 F 56 0 0 2 -input1.bam_1 FBtr0080663 71 44 0 R 56 0 0 2 input1.bam_1 FBtr0080663 71 45 0 F 56 0 0 2 -input1.bam_1 FBtr0080663 71 45 0 R 56 0 0 2 input1.bam_1 FBtr0080663 71 46 0 F 56 0 0 2 -input1.bam_1 FBtr0080663 71 46 0 R 56 0 0 2 input1.bam_1 FBtr0080663 71 47 0 F 56 0 0 1 -input1.bam_1 FBtr0080663 71 47 0 R 56 0 0 1 input1.bam_1 FBtr0080663 71 50 1 F 56 17.0 17.0 1 -input1.bam_1 FBtr0080663 71 50 0 R 56 0 0 1 input1.bam_1 FBtr0080663 71 51 9 F 56 15.6 15.0 10 -input1.bam_1 FBtr0080663 71 51 0 R 56 0 0 10 input1.bam_1 FBtr0080663 71 52 0 F 56 0 0 10 -input1.bam_1 FBtr0080663 71 52 0 R 56 0 0 10 input1.bam_1 FBtr0080663 71 53 0 F 56 0 0 10 -input1.bam_1 FBtr0080663 71 53 0 R 56 0 0 10 input1.bam_1 FBtr0080663 71 54 0 F 56 0 0 10 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FBtr0080664 71 27 0 F 56 0 0 47 -input1.bam_1 FBtr0080664 71 27 0 R 56 0 0 47 input1.bam_1 FBtr0080664 71 28 2 F 56 16.0 16.0 33 -input1.bam_1 FBtr0080664 71 28 0 R 56 0 0 33 input1.bam_1 FBtr0080664 71 29 0 F 56 0 0 23 -input1.bam_1 FBtr0080664 71 29 0 R 56 0 0 23 input1.bam_1 FBtr0080664 71 30 0 F 56 0 0 23 -input1.bam_1 FBtr0080664 71 30 0 R 56 0 0 23 input1.bam_1 FBtr0080664 71 31 0 F 56 0 0 20 -input1.bam_1 FBtr0080664 71 31 0 R 56 0 0 20 input1.bam_1 FBtr0080664 71 32 1 F 56 15.0 15.0 13 -input1.bam_1 FBtr0080664 71 32 0 R 56 0 0 13 input1.bam_1 FBtr0080664 71 33 1 F 56 20.0 20.0 6 -input1.bam_1 FBtr0080664 71 33 0 R 56 0 0 6 input1.bam_1 FBtr0080664 71 34 1 F 56 16.0 16.0 7 -input1.bam_1 FBtr0080664 71 34 0 R 56 0 0 7 input1.bam_1 FBtr0080664 71 35 1 F 56 15.0 15.0 8 -input1.bam_1 FBtr0080664 71 35 0 R 56 0 0 8 input1.bam_1 FBtr0080664 71 36 1 F 56 21.0 21.0 7 -input1.bam_1 FBtr0080664 71 36 0 R 56 0 0 7 input1.bam_1 FBtr0080664 71 37 1 F 56 18.0 18.0 8 -input1.bam_1 FBtr0080664 71 37 0 R 56 0 0 8 input1.bam_1 FBtr0080664 71 38 1 F 56 15.0 15.0 9 -input1.bam_1 FBtr0080664 71 38 0 R 56 0 0 9 input1.bam_1 FBtr0080664 71 39 0 F 56 0 0 9 -input1.bam_1 FBtr0080664 71 39 0 R 56 0 0 9 input1.bam_1 FBtr0080664 71 40 0 F 56 0 0 9 -input1.bam_1 FBtr0080664 71 40 0 R 56 0 0 9 input1.bam_1 FBtr0080664 71 41 0 F 56 0 0 9 -input1.bam_1 FBtr0080664 71 41 0 R 56 0 0 9 input1.bam_1 FBtr0080664 71 42 0 F 56 0 0 9 -input1.bam_1 FBtr0080664 71 42 0 R 56 0 0 9 input1.bam_1 FBtr0080664 71 43 0 F 56 0 0 9 -input1.bam_1 FBtr0080664 71 43 0 R 56 0 0 9 input1.bam_1 FBtr0080664 71 44 0 F 56 0 0 7 -input1.bam_1 FBtr0080664 71 44 0 R 56 0 0 7 input1.bam_1 FBtr0080664 71 45 0 F 56 0 0 7 -input1.bam_1 FBtr0080664 71 45 0 R 56 0 0 7 input1.bam_1 FBtr0080664 71 46 0 F 56 0 0 7 -input1.bam_1 FBtr0080664 71 46 0 R 56 0 0 7 input1.bam_1 FBtr0080664 71 47 0 F 56 0 0 6 -input1.bam_1 FBtr0080664 71 47 0 R 56 0 0 6 input1.bam_1 FBtr0080664 71 48 0 F 56 0 0 6 -input1.bam_1 FBtr0080664 71 48 0 R 56 0 0 6 input1.bam_1 FBtr0080664 71 49 0 F 56 0 0 6 -input1.bam_1 FBtr0080664 71 49 0 R 56 0 0 6 input1.bam_1 FBtr0080664 71 50 2 F 56 16.0 16.0 6 -input1.bam_1 FBtr0080664 71 50 0 R 56 0 0 6 input1.bam_1 FBtr0080664 71 51 7 F 56 15.0 15.0 13 -input1.bam_1 FBtr0080664 71 51 0 R 56 0 0 13 input1.bam_1 FBtr0080664 71 52 1 F 56 15.0 15.0 14 -input1.bam_1 FBtr0080664 71 52 0 R 56 0 0 14 input1.bam_1 FBtr0080664 71 53 0 F 56 0 0 12 -input1.bam_1 FBtr0080664 71 53 0 R 56 0 0 12 input1.bam_1 FBtr0080664 71 54 0 F 56 0 0 12 -input1.bam_1 FBtr0080664 71 54 0 R 56 0 0 12 input1.bam_1 FBtr0080664 71 55 0 F 56 0 0 11 -input1.bam_1 FBtr0080664 71 55 0 R 56 0 0 11 input1.bam_1 FBtr0080664 71 56 1 F 56 16.0 16.0 12 -input1.bam_1 FBtr0080664 71 56 0 R 56 0 0 12 input1.bam_1 FBtr0080664 71 57 0 F 56 0 0 11 -input1.bam_1 FBtr0080664 71 57 0 R 56 0 0 11 input1.bam_1 FBtr0080664 71 58 0 F 56 0 0 11 -input1.bam_1 FBtr0080664 71 58 0 R 56 0 0 11 input1.bam_1 FBtr0080664 71 59 0 F 56 0 0 11 -input1.bam_1 FBtr0080664 71 59 0 R 56 0 0 11 input1.bam_1 FBtr0080664 71 60 0 F 56 0 0 11 -input1.bam_1 FBtr0080664 71 60 0 R 56 0 0 11 input1.bam_1 FBtr0080664 71 61 0 F 56 0 0 11 -input1.bam_1 FBtr0080664 71 61 0 R 56 0 0 11 input1.bam_1 FBtr0080664 71 62 0 F 56 0 0 11 -input1.bam_1 FBtr0080664 71 62 0 R 56 0 0 11 input1.bam_1 FBtr0080664 71 63 0 F 56 0 0 11 -input1.bam_1 FBtr0080664 71 63 0 R 56 0 0 11 input1.bam_1 FBtr0080664 71 64 0 F 56 0 0 11 -input1.bam_1 FBtr0080664 71 64 0 R 56 0 0 11 input1.bam_1 FBtr0080664 71 65 0 F 56 0 0 11 -input1.bam_1 FBtr0080664 71 65 0 R 56 0 0 11 input1.bam_1 FBtr0080664 71 66 0 F 56 0 0 2 -input1.bam_1 FBtr0080664 71 66 0 R 56 0 0 2 input1.bam_1 FBtr0080664 71 67 0 F 56 0 0 1 -input1.bam_1 FBtr0080664 71 67 0 R 56 0 0 1 input1.bam_1 FBtr0080664 71 68 0 F 56 0 0 1 -input1.bam_1 FBtr0080664 71 68 0 R 56 0 0 1 input1.bam_1 FBtr0080664 71 69 0 F 56 0 0 1 -input1.bam_1 FBtr0080664 71 69 0 R 56 0 0 1 input1.bam_1 FBtr0080664 71 70 0 F 56 0 0 1 -input1.bam_1 FBtr0080664 71 70 0 R 56 0 0 1 input1.bam_1 FBtr0080664 71 71 0 F 56 0 0 1 -input1.bam_1 FBtr0080664 71 71 0 R 56 0 0 1
--- a/test-data/output.tab Mon Jul 24 06:28:45 2017 -0400 +++ b/test-data/output.tab Mon Jul 24 12:31:04 2017 -0400 @@ -1,6144 +1,3109 @@ Dataset Chromosome Chrom_length Coordinate Nbr_reads Polarity Max Mean Median Coverage input1.bam FBtr0070001 72 1 1 F 27 17.0 17.0 1 -input1.bam FBtr0070001 72 1 0 R 27 0 0 1 input1.bam FBtr0070001 72 2 0 F 27 0 0 1 -input1.bam FBtr0070001 72 2 0 R 27 0 0 1 input1.bam FBtr0070001 72 3 0 F 27 0 0 1 -input1.bam FBtr0070001 72 3 0 R 27 0 0 1 input1.bam FBtr0070001 72 4 0 F 27 0 0 1 -input1.bam FBtr0070001 72 4 0 R 27 0 0 1 input1.bam FBtr0070001 72 5 0 F 27 0 0 1 -input1.bam FBtr0070001 72 5 0 R 27 0 0 1 input1.bam FBtr0070001 72 6 0 F 27 0 0 1 -input1.bam FBtr0070001 72 6 0 R 27 0 0 1 input1.bam FBtr0070001 72 7 6 F 27 20.3 21.0 7 -input1.bam FBtr0070001 72 7 0 R 27 0 0 7 input1.bam FBtr0070001 72 8 3 F 27 21.3 21.0 10 -input1.bam FBtr0070001 72 8 0 R 27 0 0 10 input1.bam FBtr0070001 72 9 0 F 27 0 0 10 -input1.bam FBtr0070001 72 9 0 R 27 0 0 10 input1.bam FBtr0070001 72 10 0 F 27 0 0 10 -input1.bam FBtr0070001 72 10 0 R 27 0 0 10 input1.bam FBtr0070001 72 11 2 F 27 20.5 20.5 12 -input1.bam FBtr0070001 72 11 0 R 27 0 0 12 input1.bam FBtr0070001 72 12 0 F 27 0 0 12 -input1.bam FBtr0070001 72 12 0 R 27 0 0 12 input1.bam FBtr0070001 72 13 0 F 27 0 0 12 -input1.bam FBtr0070001 72 13 0 R 27 0 0 12 input1.bam FBtr0070001 72 14 0 F 27 0 0 12 -input1.bam FBtr0070001 72 14 0 R 27 0 0 12 input1.bam FBtr0070001 72 15 0 F 27 0 0 12 -input1.bam FBtr0070001 72 15 0 R 27 0 0 12 input1.bam FBtr0070001 72 16 1 F 27 19.0 19.0 13 -input1.bam FBtr0070001 72 16 0 R 27 0 0 13 input1.bam FBtr0070001 72 17 1 F 27 23.0 23.0 14 -input1.bam FBtr0070001 72 17 0 R 27 0 0 14 input1.bam FBtr0070001 72 18 1 F 27 16.0 16.0 14 -input1.bam FBtr0070001 72 18 0 R 27 0 0 14 input1.bam FBtr0070001 72 19 0 F 27 0 0 14 -input1.bam FBtr0070001 72 19 0 R 27 0 0 14 input1.bam FBtr0070001 72 20 0 F 27 0 0 14 -input1.bam FBtr0070001 72 20 0 R 27 0 0 14 input1.bam FBtr0070001 72 21 0 F 27 0 0 14 -input1.bam FBtr0070001 72 21 0 R 27 0 0 14 input1.bam FBtr0070001 72 22 0 F 27 0 0 14 -input1.bam FBtr0070001 72 22 0 R 27 0 0 14 input1.bam FBtr0070001 72 23 0 F 27 0 0 13 -input1.bam FBtr0070001 72 23 0 R 27 0 0 13 input1.bam FBtr0070001 72 24 0 F 27 0 0 13 -input1.bam FBtr0070001 72 24 0 R 27 0 0 13 input1.bam FBtr0070001 72 25 0 F 27 0 0 13 -input1.bam FBtr0070001 72 25 0 R 27 0 0 13 input1.bam FBtr0070001 72 26 0 F 27 0 0 13 -input1.bam FBtr0070001 72 26 0 R 27 0 0 13 input1.bam FBtr0070001 72 27 2 F 27 23.5 23.5 14 -input1.bam FBtr0070001 72 27 0 R 27 0 0 14 input1.bam FBtr0070001 72 28 0 F 27 0 0 11 -input1.bam FBtr0070001 72 28 0 R 27 0 0 11 input1.bam FBtr0070001 72 29 0 F 27 0 0 8 -input1.bam FBtr0070001 72 29 0 R 27 0 0 8 input1.bam FBtr0070001 72 30 1 F 27 23.0 23.0 9 -input1.bam FBtr0070001 72 30 0 R 27 0 0 9 input1.bam FBtr0070001 72 31 11 F 27 23.0 23.0 18 -input1.bam FBtr0070001 72 31 0 R 27 0 0 18 input1.bam FBtr0070001 72 32 27 F 27 22.0 22.0 44 -input1.bam FBtr0070001 72 32 0 R 27 0 0 44 input1.bam FBtr0070001 72 33 0 F 27 0 0 44 -input1.bam FBtr0070001 72 33 0 R 27 0 0 44 input1.bam FBtr0070001 72 34 1 F 27 20.0 20.0 44 -input1.bam FBtr0070001 72 34 0 R 27 0 0 44 input1.bam FBtr0070001 72 35 0 F 27 0 0 43 -input1.bam FBtr0070001 72 35 0 R 27 0 0 43 input1.bam FBtr0070001 72 36 0 F 27 0 0 43 -input1.bam FBtr0070001 72 36 0 R 27 0 0 43 input1.bam FBtr0070001 72 37 0 F 27 0 0 43 -input1.bam FBtr0070001 72 37 0 R 27 0 0 43 input1.bam FBtr0070001 72 38 0 F 27 0 0 43 -input1.bam FBtr0070001 72 38 0 R 27 0 0 43 input1.bam FBtr0070001 72 39 0 F 27 0 0 43 -input1.bam FBtr0070001 72 39 0 R 27 0 0 43 input1.bam FBtr0070001 72 40 0 F 27 0 0 42 -input1.bam FBtr0070001 72 40 0 R 27 0 0 42 input1.bam FBtr0070001 72 41 0 F 27 0 0 42 -input1.bam FBtr0070001 72 41 0 R 27 0 0 42 input1.bam FBtr0070001 72 42 0 F 27 0 0 42 -input1.bam FBtr0070001 72 42 0 R 27 0 0 42 input1.bam FBtr0070001 72 43 0 F 27 0 0 42 -input1.bam FBtr0070001 72 43 0 R 27 0 0 42 input1.bam FBtr0070001 72 44 0 F 27 0 0 42 -input1.bam FBtr0070001 72 44 0 R 27 0 0 42 input1.bam FBtr0070001 72 45 0 F 27 0 0 42 -input1.bam FBtr0070001 72 45 0 R 27 0 0 42 input1.bam FBtr0070001 72 46 0 F 27 0 0 42 -input1.bam FBtr0070001 72 46 0 R 27 0 0 42 input1.bam FBtr0070001 72 47 0 F 27 0 0 42 -input1.bam FBtr0070001 72 47 0 R 27 0 0 42 input1.bam FBtr0070001 72 48 0 F 27 0 0 42 -input1.bam FBtr0070001 72 48 0 R 27 0 0 42 input1.bam FBtr0070001 72 49 0 F 27 0 0 42 -input1.bam FBtr0070001 72 49 0 R 27 0 0 42 input1.bam FBtr0070001 72 50 0 F 27 0 0 41 -input1.bam FBtr0070001 72 50 0 R 27 0 0 41 input1.bam FBtr0070001 72 51 0 F 27 0 0 40 -input1.bam FBtr0070001 72 51 0 R 27 0 0 40 input1.bam FBtr0070001 72 52 0 F 27 0 0 40 -input1.bam FBtr0070001 72 52 0 R 27 0 0 40 input1.bam FBtr0070001 72 53 0 F 27 0 0 39 -input1.bam FBtr0070001 72 53 0 R 27 0 0 39 input1.bam FBtr0070001 72 72 0 F 27 0 0 0 input1.bam FBtr0070533 72 1 1 F 5 15.0 15.0 1 -input1.bam 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