protk 1.4.4.beta1 → 1.4.4.beta2
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- checksums.yaml +4 -4
- data/bin/mzid_to_protxml.rb +2 -1
- data/lib/protk/mzidentml_doc.rb +2 -1
- data/lib/protk/protein_group.rb +2 -1
- 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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SHA1:
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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: f278e7fe8e3a0955907a13952ced4fa0d772c204
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4
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+
data.tar.gz: 513fb214683486b9d3596a9b9f0956107d611170
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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: e59fcb0724cbf42b8f63e65ca6d88fd91c7d45d3981964358c82e040f9235e2ce6768251d088966044827cadf5c9ce46f189345d3c27293d0b10b44daf018c10
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7
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+
data.tar.gz: 36329dca4cf416fc2b9bd6f0d395895ee2fd32fdba2f6ebd75c5d26ed21b497dc890cfc6bcf36b1f08bc7f3954bae76adea64450a431d6ac365a2930191997cc
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data/bin/mzid_to_protxml.rb
CHANGED
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@@ -71,7 +71,8 @@ protein_groups.each do |group_node|
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71
71
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if group_prob >= tool.minprob.to_f
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72
72
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$stdout.write "\n" if tool.debug
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73
73
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$protk.log "Writing group with probability #{group_prob}" , :info
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74
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-
group = ProteinGroup.from_mzid(group_node,mzid_doc,tool.minprob.to_f)
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74
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+
group = ProteinGroup.from_mzid(group_node,mzid_doc,tool.minprob.to_f)
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75
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+
# require 'byebug';byebug
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75
76
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prot_xml_writer.append_protein_group(group.as_protxml)
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76
77
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n_written+=1
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77
78
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end
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data/lib/protk/mzidentml_doc.rb
CHANGED
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@@ -127,8 +127,9 @@ class MzIdentMLDoc < Object
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127
127
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128
128
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# Memoized because it gets called for every protein in a group
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|
129
129
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def get_proteins_for_group(group_node)
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130
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+
# puts group_node.attributes['group_number']
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130
131
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@proteins_for_group_cache ||= Hash.new do |h,key|
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131
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-
h[key] = self.find(
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|
132
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+
h[key] = self.find(key,"ProteinDetectionHypothesis")
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|
132
133
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end
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133
134
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@proteins_for_group_cache[group_node]
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134
135
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end
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data/lib/protk/protein_group.rb
CHANGED
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@@ -68,7 +68,8 @@ class ProteinGroup
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|
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68
68
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def as_protxml()
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69
69
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node = XML::Node.new('protein_group')
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70
70
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node["group_number"] = self.group_number.to_s
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71
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-
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|
71
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+
# require 'byebug';byebug
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|
72
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+
node["group_probability"] = (self.group_probability * 0.01).to_s
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|
72
73
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self.proteins.each { |prot| node << prot.as_protxml }
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73
74
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node
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|
74
75
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end
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