Add utilities for whole-genome coordinate. #103
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@@ Coverage Diff @@
## master #103 +/- ##
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+ Coverage 84.94% 85.22% +0.27%
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Files 60 61 +1
Lines 3966 4019 +53
Branches 400 403 +3
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+ Hits 3369 3425 +56
Misses 197 197
+ Partials 400 397 -3
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test/cljam/util/t_whole_genome.clj
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| (testing "whole-genome -> chr" | ||
| (are [?wg-pos ?chr-and-pos] | ||
| (= (wg/to-chr-and-pos idx ?wg-pos) ?chr-and-pos) | ||
| 0 nil |
src/cljam/util/whole_genome.clj
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| [e-offset {e-name :name e-len :len}] (first (rsubseq offset->ref <= (dec end')))] | ||
| (if (= s-offset e-offset) | ||
| [{:chr s-name, :start (- start' s-offset), :end (min (- end' s-offset) s-len)}] | ||
| (concat |
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to-regions returns a vector when the region is in a ref, returning a lazy sequence when not. I think it should return a vector in both cases.
src/cljam/util/whole_genome.clj
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| (map (fn [r offset] [(:name r) {:offset offset, :len (:len r)}]) refs) | ||
| (into {}))) | ||
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| (defn to-whole-genome-coord |
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-> is used for conversion functions in cljam. I prefer ->whole-genome-coord.
src/cljam/util/whole_genome.clj
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| (reductions + 0)) | ||
| refs))) | ||
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| (defn to-chr-and-pos |
src/cljam/util/whole_genome.clj
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| (when (<= 1 (- wg-pos offset) len) | ||
| [name (- wg-pos offset)]))) | ||
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| (defn to-regions |
src/cljam/util/whole_genome.clj
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| @@ -0,0 +1,53 @@ | |||
| (ns cljam.util.whole-genome | |||
| "Utilities for conversions between chromosomal positions and whole-genome positions.") | |||
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Please wrap a line at 80 characters if possible. cf. clojure-style-guide#80-character-limits
src/cljam/util/whole_genome.clj
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| (ns cljam.util.whole-genome | ||
| "Utilities for conversions between chromosomal positions and whole-genome positions.") | ||
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| (defn create-chr-to-whole-genome-index |
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In cljam, create-* is used for file-generating functions such as bam-indexer/create-index and dict/create-dict. I think make-* is better for this function, or simply chr-to-whole-genome-index is also good.
src/cljam/util/whole_genome.clj
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| (when (<= 1 pos len) | ||
| (inc (+ offset (dec pos)))))) | ||
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| (defn create-whole-genome-to-chr-index |
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Same as the comment on create-chr-to-whole-genome-index
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Thank you so much for the advice! 馃槀 I also modified |
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Perfect, thanks! |
Summary
This PR adds some utilities for conversion between chromosomal positions and positions in whole-genome coordinate like this one and this one.
Tests
lein test :all馃啑