Adding the header

pjotrp · Nov 7, 2014 · f767adb · f767adb
1 parent 23fa81a
commit f767adb
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Showing 3 changed files with 53 additions and 23 deletions.
diff --git a/README.md b/README.md
@@ -236,10 +236,12 @@ can be
 
 ```Javascript
 =HEADER
+<% require 'json' %>
 [
-  { "Meta": {
-      "query" : <%= hit.query %>
-    }
+  { "HEADER": {
+    "options":  <%= options.to_h.to_json %>,
+    "files":    <%= ARGV %>,
+    "version":  "<%= BLASTXML_VERSION %>"
   },
 =BODY
   { "<%= hit.parent.query_def %>": {
@@ -252,12 +254,28 @@ can be
 ]
 ```
 
-Note that the template is smart enough to remove the final comma ','
-from the last BODY element, though you can also inject in the template something like
+may generate something like
 
-
-```ruby
-  <%= ( body.last? ? "", "," ) %>.
+```Javascript
+[
+  { "HEADER": {
+    "options":  {"template":"template/blast2json2.erb","filter":"hsp.evalue>0.01"},
+    "files":    ["test/data/nt_example_blastn.m7"],
+    "version":  "2.0.2-pre1"
+  },
+  { "I_1 [477 - 884] ": {
+    "num":       41,
+    "id":        "lcl|X_42251",
+    "len":       153,
+    "E-value":   0.0247015,
+  },
+  { "I_1 [477 - 884] ": {
+    "num":       43,
+    "id":        "lcl|V_105720",
+    "len":       180,
+    "E-value":   0.0247015,
+  }
+]
 ```
 
 ## Additional options

diff --git a/bin/blastxmlparser b/bin/blastxmlparser
@@ -129,6 +129,7 @@ begin
 
   raise "No input file(s) defined" if ARGV.size == 0
 
+
   ARGV.each do | fn |
     logger.info("XML parsing #{fn}")
     parser_type = options.parser
@@ -149,6 +150,7 @@ begin
     chunks = []
     chunks_count = 0
     NUM_CHUNKS=10_000
+    print template.header(binding) if template
 
     process = lambda { |iter2,i|  # Process one BLAST iter block
       if parser_type == :nosplit
@@ -225,6 +227,7 @@ begin
             process.call(iter,i)
           }
     end
+    print template.footer(binding) if template
   end
 rescue OptionParser::InvalidOption => e
   $stderr.print e.message

diff --git a/template/blast2json2.erb b/template/blast2json2.erb
@@ -1,19 +1,28 @@
 =HEADER
-/* TEST HEADER */
+<% require 'json' %>
+[
+  { "HEADER": {
+    "options":  <%= options.to_h.to_json %>,
+    "files":    <%= ARGV %>,
+    "version":  "<%= BLASTXML_VERSION %>"
+  },
+
 =BODY
+  { "<%= hit.parent.query_def %>": {
+    "query_id":  "<%= hit.parent.query_id %>",
+    "num":       <%= hit.hit_num %>,
+    "accession": "<%= hit.accession %>",
+    "id":        "<%= hit.hit_id %>",
+    "len":       <%= hit.len %>,
+    "E-value":   <%= hsp.evalue %>,
+    "identity":  <%= hsp.identity %>,
+    "align_len": <%= hsp.align_len %>,
+    "bitscore":  <%= hsp.bit_score %>,
+    "qseq":      "<%= hsp.qseq %>",
+    "midline":   "<%= hsp.midline %>", 
+    "hseq":      "<%= hsp.hseq %>",
+  },
 
-{ "<%= hit.parent.query_def %>": {
-  "query_id":  "<%= hit.parent.query_id %>",
-  "num":       <%= hit.hit_num %>,
-  "accession": "<%= hit.accession %>",
-  "id":        "<%= hit.hit_id %>",
-  "len":       <%= hit.len %>,
-  "E-value":   <%= hsp.evalue %>,
-  "identity":  <%= hsp.identity %>,
-  "align_len": <%= hsp.align_len %>,
-  "bitscore":  <%= hsp.bit_score %>,
-  "qseq":      "<%= hsp.qseq %>",
-  "midline":   "<%= hsp.midline %>", 
-  "hseq":      "<%= hsp.hseq %>",
-};
+=FOOTER
+]