panacheextract 0.0.1 → 0.0.2
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- checksums.yaml +4 -4
- data/lib/panacheextract.rb +26 -0
- metadata +1 -1
checksums.yaml
CHANGED
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@@ -1,7 +1,7 @@
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1
1
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---
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2
2
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SHA256:
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3
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-
metadata.gz:
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4
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-
data.tar.gz:
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3
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metadata.gz: 13c2aba9cc2b3cf40fd1f6985665dc69b32575cb21089b4efb2ea498a86ed89d
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4
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data.tar.gz: bd6372a9715899cce3173320de7f6fbd6f2ed7292cc583eae0a1fdcae43bf5a0
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5
5
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SHA512:
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6
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-
metadata.gz:
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7
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-
data.tar.gz:
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6
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metadata.gz: 8f290b6ec359eaaf6450a127113fc2a6b7cc099d03e26fe27a485277faa96349d600a2f714f7657c9a7f87cf20d2a2b3277c9ebcc5f81527dc7e38d36ad29dcf
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7
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data.tar.gz: 07af17b4f13ea4d620e7b22dc50c9811dc9d4411463156c60c91ea20172153a364b29e512053851ff768342316d0d082e5183b06863f012cb751808d68aa6d76
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data/lib/panacheextract.rb
CHANGED
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@@ -90,3 +90,29 @@ def getspecific(ids, inputalignment, outalignmentfile, del = "None")
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90
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return(delselect)
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end
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end
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def delcoordinates(ids, inputalignment, outalignment)
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95
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id = ids.to_s
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readiter = File.open(inputalignment, "r").readlines
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97
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writefile = File.new(outalignment, "w")
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98
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for i in 0..readiter.length
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writefile.write(readiter[i]) if readiter[i].to_s.strip.split[0] == "s"
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end
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writefile.close
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readopen = File.open(outalignment, "r").readlines
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ids = []
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sequences = []
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ids_start = []
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ids_end = []
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for i in 0..readopen.length
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readopen.each { | iter | ids.push(iter.to_s.strip.split[1]) if iter.to_s.strip.split[1] == id }
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readopen.each { | iter | sequences.push(iter.to_s.strip.split[6]) if iter.to_s.strip.split[1] == id }
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readopen.each { | iter | ids_start.push(iter.to_s.strip.split[2]) if iter.to_s.strip.split[1] == id }
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111
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readopen.each { | iter | ids_end.push(iter.to_s.strip.split[5]) if iter.to_s.strip.split[1] == id }
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end
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delselected = []
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for i in 0..sequences.length
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delselected.push([ids_start[i], ids_end[i]]) if sequences[i].to_s.count("-") >=1
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end
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return(delselected)
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end
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