+
Parameters:
+
+
+ -
+
+ the
+
+
+
+
+
+
+ —
+
+
InChIKey [String] of the entity
-
- format
+ The
- (String)
+
- (defaults to: "json")
-
—
-
the format of the query, 'text' (either JSON, CSV, or SDF)
+
format [String] the format of the query (Only JSON)
@@ -475,29 +587,29 @@ specified format.
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- # File 'lib/classyfire_api.rb', line 62
+ # File 'lib/classyfire_api.rb', line 105
def ClassyFireAPI.get_entity_classification(inchikey,format="json")
inchikey_id = inchikey.to_s.gsub('InChIKey=','')
@@ -608,7 +720,6 @@ specified format.
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- # File 'lib/classyfire_api.rb', line 37
+ # File 'lib/classyfire_api.rb', line 38
def ClassyFireAPI.get_query(query_id,format="json")
begin
@@ -669,6 +781,8 @@ specified format.
Retrieves the classification results for a given sequence.
+Use JSON.parse to get a the json object.
+
@@ -678,17 +792,16 @@ specified format.
- the
+ fingerprint
-
+ (String)
—
- fingerprint [String] the fingerprint (generated from the sequence using
-Digest::MD5).
+ the fingerprint (generated from the sequence using Digest::MD5).
- A text file displaying the classification results for the entity in the
+ A text displaying the classification results for the entity in the
specified format.
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|
- # File 'lib/classyfire_api.rb', line 88
+ # File 'lib/classyfire_api.rb', line 84
def ClassyFireAPI.get_sequence_classification(fingerprint,format="json")
begin
@@ -842,17 +955,17 @@ specified format.
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|
- # File 'lib/classyfire_api.rb', line 129
+ # File 'lib/classyfire_api.rb', line 130
def ClassyFireAPI.query_status(query_id)
begin
@@ -932,72 +1045,71 @@ retrieve the strutcure's classification from ClassyFire.
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|
- # File 'lib/classyfire_api.rb', line 311
+ # File 'lib/classyfire_api.rb', line 256
def ClassyFireAPI.retrieve_classification(input,output)
absolute_path = File.expand_path(input)
@@ -1058,7 +1170,6 @@ retrieve the strutcure's classification from ClassyFire.
e.message
end
end
-
res += "]}"
f_output.print res
end
@@ -1133,63 +1244,63 @@ format.
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|
- # File 'lib/classyfire_api.rb', line 380
+ # File 'lib/classyfire_api.rb', line 324
def ClassyFireAPI.retrieve_entities_json(input,output)
absolute_path = File.expand_path(input)
@@ -1216,7 +1327,7 @@ format.
puts i
begin
- inchikey = %x(/Applications/ChemAxon/JChem/bin/molconvert inchikey -s "#{h[key]}").strip
+ inchikey = %x(obabel -:"#{h[key]}" -oinchikey).strip.split("\t")[0]
qr = JSON.parse(ClassyFireAPI.get_entity_classification(inchikey,format="json"))
qr['identifier'] = key
@@ -1231,7 +1342,7 @@ format.
key = h.keys[-1]
begin
- inchikey = %x(/Applications/ChemAxon/JChem/bin/molconvert inchikey -s "#{h[key]}").strip
+ inchikey = %x(obabel -:"#{h[key]}" -oinchikey).strip.split("\t")[0]
qr = JSON.parse(ClassyFireAPI.get_entity_classification(inchikey,format="json"))
qr['identifier'] = key
@@ -1316,69 +1427,67 @@ format.
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|
- # File 'lib/classyfire_api.rb', line 442
+ # File 'lib/classyfire_api.rb', line 386
def ClassyFireAPI.retrieve_entities_sdf(input,output)
absolute_path = File.expand_path(input)
@@ -1400,7 +1509,7 @@ format.
puts i
begin
- inchikey = %x(/Applications/ChemAxon/JChem/bin/molconvert inchikey -s "#{h[key]}").strip
+ inchikey = %x(obabel -:"#{h[key]}" -oinchikey).strip.split("\t")[0]
qr = ClassyFireAPI.get_entity_classification(inchikey,format="sdf")
if qr.include?("The page you were looking for doesn't exist")
@@ -1419,9 +1528,8 @@ format.
i += 1
end
key = h.keys[-1]
- begin
- inchikey = %x(/Applications/ChemAxon/JChem/bin/molconvert inchikey -s "#{h[key]}").strip
+ begin
+ inchikey = %x(obabel -:"#{h[key]}" -oinchikey).strip.split("\t")[0]
qr = ClassyFireAPI.get_entity_classification(inchikey,format="sdf")
if qr.include?("The page you were looking for doesn't exist")
@@ -1438,8 +1546,7 @@ format.
e.message
end
end
- end
+end
|
@@ -1509,19 +1616,19 @@ slice_length [Integer] The maximum number of entries for each query input
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- # File 'lib/classyfire_api.rb', line 229
+ # File 'lib/classyfire_api.rb', line 239
def ClassyFireAPI.submit_queries_from_directory(folder,slice_length,type="STRUCTURE")
if File.directory?(folder)
@@ -1552,7 +1659,7 @@ slice_length [Integer] The maximum number of entries for each query input
Submits a ClassyFire query in a JSON format.
-if there is an error.
+if there is an error. Use JSON.parse to get a the json object.
@@ -1638,7 +1745,6 @@ slice_length [Integer] The maximum number of entries for each query input
-14
15
16
17
@@ -1653,10 +1759,11 @@ slice_length [Integer] The maximum number of entries for each query input
26
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+29
+30
|
- # File 'lib/classyfire_api.rb', line 14
+ # File 'lib/classyfire_api.rb', line 15
def ClassyFireAPI.submit_query(label,input, type='STRUCTURE')
begin
@@ -1682,7 +1789,7 @@ slice_length [Integer] The maximum number of entries for each query input
|
- # File 'lib/classyfire_api.rb', line 151
+ # File 'lib/classyfire_api.rb', line 152
-def ClassyFireAPI.submit_query_input_in_chunks(input_file,slice_length, start, type='STRUCTURE')
+def ClassyFireAPI.submit_query_input_in_chunks(input_file,slice_length=1000, start=1, type='STRUCTURE')
@start_time = Time.now
absolute_path = File.expand_path(input_file)
f = File.open(absolute_path, 'r')
input = []
lines = File.readlines(absolute_path)
-
+ i = 0
lines.uniq.each do |line|
+ i += 1
sline = line.strip.split("\t")
if sline.length == 1
input <<"#{sline[0]}"
- elsif sline.length >= 2
- input <<"#{sline[0]}\t#{sline[1]}"
+ elsif sline.length == 2
+ input <<"#{sline[0]}\t#{sline[1]}"
end
+ input <<"#{sline[0]}"
end
query_ids = []
subdivised_groups = input.uniq.each_slice(slice_length).to_a
puts "nr of subdivised_groups: #{subdivised_groups.length}"
- puts subdivised_groups[0]
- sleeping_time = 120
- initial_nr_of_jobs = 60
+ sleeping_time = 240
+ initial_nr_of_jobs = 30
i = start
while i < initial_nr_of_jobs
- title = File.basename(absolute_path).split(".")[0] + "_yannick" + "_part_#{i}"
+
+ title = File.basename(absolute_path).split(".")[0] + "_yannick" + "_part_#{i}"
if i <= subdivised_groups.length
- begin
- puts "submitting #{title}"
+ puts "\n\n\n\n---------------------- -----------"
+ puts "submitting #{title}"
+ puts subdivised_groups[i-1].join("\n")
q = submit_query(title,subdivised_groups[i-1].join("\n"),type)
- query_ids << JSON.parse(q)['id']
- rescue Exception => e
- puts e.message
- puts e.backtrace.inspect
- end
- i = i + 1
+ query_ids << JSON.parse(q)['id']
+ i = i + 1
+ else
+ break
end
end
@@ -1853,9 +1978,9 @@ framgments from the index 'start'.
sleep(sleeping_time)
puts "Waking up at #{Time.now - @start_time}"
- while i < subdivised_groups.length
+ while i >= initial_nr_of_jobs && i < subdivised_groups.length
k = 0
- for k in (i..(i+80))
+ for k in (i..(i + initial_nr_of_jobs))
title = File.basename(absolute_path).split(".")[0] + "_yannick" + "_part_#{k}"
i = i + 1
begin
@@ -1875,210 +2000,6 @@ framgments from the index 'start'.
|
-