panacheextract 0.0.1 → 0.0.2

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
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-  data.tar.gz: 8a36048fe0516f70386ff1f8031c8edf516fa3f178d2269c2595ea34a56da044
+  metadata.gz: 13c2aba9cc2b3cf40fd1f6985665dc69b32575cb21089b4efb2ea498a86ed89d
+  data.tar.gz: bd6372a9715899cce3173320de7f6fbd6f2ed7292cc583eae0a1fdcae43bf5a0
 SHA512:
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+  metadata.gz: 8f290b6ec359eaaf6450a127113fc2a6b7cc099d03e26fe27a485277faa96349d600a2f714f7657c9a7f87cf20d2a2b3277c9ebcc5f81527dc7e38d36ad29dcf
+  data.tar.gz: 07af17b4f13ea4d620e7b22dc50c9811dc9d4411463156c60c91ea20172153a364b29e512053851ff768342316d0d082e5183b06863f012cb751808d68aa6d76

data/lib/panacheextract.rb

@@ -90,3 +90,29 @@ def getspecific(ids, inputalignment, outalignmentfile, del = "None")
         return(delselect)
     end
 end
+
+def delcoordinates(ids, inputalignment, outalignment)
+        id = ids.to_s
+        readiter = File.open(inputalignment, "r").readlines
+        writefile = File.new(outalignment, "w")
+        for i in 0..readiter.length
+            writefile.write(readiter[i]) if readiter[i].to_s.strip.split[0] == "s"
+        end
+        writefile.close
+        readopen = File.open(outalignment, "r").readlines
+        ids = []
+        sequences = []
+        ids_start = []
+        ids_end = []
+        for i in 0..readopen.length 
+            readopen.each { | iter | ids.push(iter.to_s.strip.split[1]) if iter.to_s.strip.split[1] == id }
+            readopen.each { | iter | sequences.push(iter.to_s.strip.split[6]) if iter.to_s.strip.split[1] == id }
+            readopen.each { | iter | ids_start.push(iter.to_s.strip.split[2]) if iter.to_s.strip.split[1] == id }
+            readopen.each { | iter | ids_end.push(iter.to_s.strip.split[5]) if iter.to_s.strip.split[1] == id }
+        end
+        delselected = []
+        for i in 0..sequences.length 
+            delselected.push([ids_start[i], ids_end[i]]) if sequences[i].to_s.count("-") >=1
+        end
+        return(delselected)
+end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: panacheextract
 version: !ruby/object:Gem::Version
-  version: 0.0.1
+  version: 0.0.2
 platform: ruby
 authors:
 - Gaurav Sablok