Mercurial > repos > miller-lab > genome_diversity
annotate aggregate_gd_indivs.xml @ 25:cba0d7a63b82
workaround for gd_genotype datatype
admix shift int -> float
| author | Richard Burhans <burhans@bx.psu.edu> |
|---|---|
| date | Wed, 29 May 2013 13:49:19 -0400 |
| parents | 95a05c1ef5d5 |
| children | 91e835060ad2 |
| rev | line source |
|---|---|
| 13 | 1 <tool id="gd_sum_gd_snp" name="Aggregate Individuals" version="1.0.0"> |
| 2 <description>: Append summary columns for a population</description> | |
| 3 | |
| 4 <command interpreter="python"> | |
|
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95a05c1ef5d5
update to devshed revision aaece207bd01
Richard Burhans <burhans@bx.psu.edu>
parents:
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diff
changeset
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5 aggregate_gd_indivs.py "$input" "$p1_input" "$output" |
| 13 | 6 #for $individual, $individual_col in zip($input.dataset.metadata.individual_names, $input.dataset.metadata.individual_columns) |
| 7 #set $arg = '%s:%s' % ($individual_col, $individual) | |
| 8 "$arg" | |
| 9 #end for | |
| 10 </command> | |
| 11 | |
| 12 <inputs> | |
| 13 <param name="input" type="data" format="gd_snp" label="SNP dataset" /> | |
| 14 <param name="p1_input" type="data" format="gd_indivs" label="Population individuals" /> | |
| 15 </inputs> | |
| 16 | |
| 17 <outputs> | |
| 18 <data name="output" format="gd_snp" metadata_source="input" /> | |
| 19 </outputs> | |
| 20 | |
| 21 <tests> | |
| 22 <test> | |
| 23 <param name="input" value="test_in/sample.gd_snp" ftype="gd_snp" /> | |
| 24 <param name="p1_input" value="test_in/a.gd_indivs" ftype="gd_indivs" /> | |
| 25 <output name="output" file="test_out/modify_snp_table/modify.gd_snp" /> | |
| 26 </test> | |
| 27 </tests> | |
| 28 | |
| 29 <help> | |
| 30 | |
| 31 **Dataset formats** | |
| 32 | |
| 33 The input datasets are in gd_snp_ and gd_indivs_ formats. | |
| 34 The output dataset is in gd_snp_ format. (`Dataset missing?`_) | |
| 35 | |
| 36 .. _gd_snp: ./static/formatHelp.html#gd_snp | |
| 37 .. _gd_indivs: ./static/formatHelp.html#gd_indivs | |
| 38 .. _Dataset missing?: ./static/formatHelp.html | |
| 39 | |
| 40 ----- | |
| 41 | |
| 42 **What it does** | |
| 43 | |
| 44 The user specifies that some of the individuals in a gd_snp dataset form a | |
| 45 "population", by supplying a list that has been previously created using the | |
| 46 Specify Individuals tool. The program appends a | |
| 47 new "entity" (set of four columns) to the gd_snp table, analogous to the columns | |
| 48 for an individual but containing summary data for the population as a group. | |
| 49 These four columns give the total counts for the two alleles, the "genotype" for | |
| 50 the population, and the maximum quality value, taken over all individuals in the | |
| 51 population. If all defined genotypes in the population are 2 (agree with the | |
| 52 reference), then the population's genotype is 2, and similarly for 0; otherwise | |
| 53 the genotype is 1 (unless all individuals have undefined genotype, in which case | |
| 54 it is -1). | |
| 55 | |
| 56 ----- | |
| 57 | |
| 58 **Example** | |
| 59 | |
| 60 - input gd_snp:: | |
| 61 | |
| 62 Contig161_chr1_4641264_4641879 115 C T 73.5 chr1 4641382 C 6 0 2 45 8 0 2 51 15 0 2 72 5 0 2 42 6 0 2 45 10 0 2 57 Y 54 0.323 0 | |
| 63 Contig48_chr1_10150253_10151311 11 A G 94.3 chr1 10150264 A 1 0 2 30 1 0 2 30 1 0 2 30 3 0 2 36 1 0 2 30 1 0 2 30 Y 22 +99. 0 | |
| 64 Contig20_chr1_21313469_21313570 66 C T 54.0 chr1 21313534 C 4 0 2 39 4 0 2 39 5 0 2 42 4 0 2 39 4 0 2 39 5 0 2 42 N 1 +99. 0 | |
| 65 etc. | |
| 66 | |
| 67 - input individuals:: | |
| 68 | |
| 69 9 PB1 | |
| 70 13 PB2 | |
| 71 17 PB3 | |
| 72 | |
| 73 - output:: | |
| 74 | |
| 75 Contig161_chr1_4641264_4641879 115 C T 73.5 chr1 4641382 C 6 0 2 45 8 0 2 51 15 0 2 72 5 0 2 42 6 0 2 45 10 0 2 57 Y 54 0.323 0 29 0 2 72 | |
| 76 Contig48_chr1_10150253_10151311 11 A G 94.3 chr1 10150264 A 1 0 2 30 1 0 2 30 1 0 2 30 3 0 2 36 1 0 2 30 1 0 2 30 Y 22 +99. 0 3 0 2 30 | |
| 77 Contig20_chr1_21313469_21313570 66 C T 54.0 chr1 21313534 C 4 0 2 39 4 0 2 39 5 0 2 42 4 0 2 39 4 0 2 39 5 0 2 42 N 1 +99. 0 13 0 2 42 | |
| 78 etc. | |
| 79 | |
| 80 </help> | |
| 81 </tool> |