fix up python server copyright notices. refs #1024

COPYING

@@ -1,6 +1,9 @@
 * Code is copyright 2009, 2010, 2011, 2012 Clinical Future, Inc.,
   distributed under AGPLv3. http://www.gnu.org/licenses/agpl-3.0.html
 
+* Python server based on Trait-o-matic by Xiaodi Wu
+  https://github.com/xwu/trait-o-matic/blob/master/LICENSE
+
 * Style sheet adapted from "Indigo" by Viktor Persson http://arcsin.se
   ("Feel free to use and modify but please provide credits.")
 

server/call_missing.py

@@ -1,5 +1,7 @@
 #!/usr/bin/python
-# Filename: call_missing.py
+# This code is part of GET-Evidence.
+# Copyright: see COPYING
+# Authors: see git-blame(1)
 
 """
 Find coding regions missing in a genome report.

server/codon.py

@@ -1,4 +1,6 @@
-# This code is part of the Trait-o-matic project and is governed by its license.
+# This code is part of GET-Evidence.
+# Copyright: see COPYING
+# Authors: see git-blame(1)
 
 one_letter_alphabet = {
     "Ala": "A",

server/compile_covered.py

@@ -1,4 +1,7 @@
 #!/usr/bin/python
+# This code is part of GET-Evidence.
+# Copyright: see COPYING
+# Authors: see git-blame(1)
 
 import re
 import os

server/config_names.py

@@ -1,5 +1,8 @@
 #!/usr/bin/python
-# Filename: config.py
+# This code is part of GET-Evidence.
+# Copyright: see COPYING
+# Authors: see git-blame(1)
+
 import os
 
 UPLOAD_DIR = os.getenv('UPLOAD')

server/count_variants.py

@@ -1,4 +1,7 @@
 #!/usr/bin/python
+# This code is part of GET-Evidence.
+# Copyright: see COPYING
+# Authors: see git-blame(1)
 
 import re
 import sys

server/fastq_to_fasta.py

@@ -1,5 +1,7 @@
 #!/usr/bin/python
-# Filename: fastq_to_fasta.py
+# This code is part of GET-Evidence.
+# Copyright: see COPYING
+# Authors: see git-blame(1)
 
 """
 usage: %prog fastq ...
@@ -39,4 +41,4 @@ def main():
             quality_length += len(line.rstrip())
 
 if __name__ == "__main__":
-    main()
+    main()

server/genome_analyzer.py

@@ -1,5 +1,7 @@
 #!/usr/bin/python
-# Filename: server.py
+# This code is part of GET-Evidence.
+# Copyright: see COPYING
+# Authors: see git-blame(1)
 
 """
 usage: %prog [options]

server/get_metadata.py

@@ -1,5 +1,7 @@
 #!/usr/bin/python
-# Filename: get_metadata.py
+# This code is part of GET-Evidence.
+# Copyright: see COPYING
+# Authors: see git-blame(1)
 
 """
 usage: %prog genome_gff_file

server/getev_pph2_extract.py

@@ -1,4 +1,7 @@
 #!/usr/bin/python
+# This code is part of GET-Evidence.
+# Copyright: see COPYING
+# Authors: see git-blame(1)
 
 """Extract scores from Polyphen 2 1.9GB data dump for GET-Evidence variants"""
 import re

server/gff2json.py

@@ -1,5 +1,7 @@
 #!/usr/bin/python
-# Filename: gff2json.py
+# This code is part of GET-Evidence.
+# Copyright: see COPYING
+# Authors: see git-blame(1)
 
 """
 usage: %prog gff_file

server/gff_dbsnp_query.py

@@ -1,5 +1,7 @@
 #!/usr/bin/python
-# Filename: gff_query_dbsnp.py
+# This code is part of GET-Evidence.
+# Copyright: see COPYING
+# Authors: see git-blame(1)
 
 """
 usage: %prog gff_file dbsnp_file [output_file]

server/gff_getevidence_map.py

@@ -1,5 +1,7 @@
 #!/usr/bin/python
-# Filename: gff_getevidence_map.py
+# This code is part of GET-Evidence.
+# Copyright: see COPYING
+# Authors: see git-blame(1)
 
 """
 usage: %prog nssnp.gff getev_flatfile.json[.gz] [output_file]

server/gff_nonsynonymous_filter.py

@@ -1,5 +1,7 @@
 #!/usr/bin/python
-# Filename: gff_nonsynonymous_filter.py
+# This code is part of GET-Evidence.
+# Copyright: see COPYING
+# Authors: see git-blame(1)
 
 """
 usage: %prog gff_file twobit_file transcript_file [output_file]

server/gff_trio_phase.py

@@ -1,7 +1,7 @@
 #!/usr/bin/python
-# Filename: gff_trio_phase.py
-# Author: Evan Maxwell ([email protected])
-# Date: April 2011
+# This code is part of GET-Evidence.
+# Copyright: see COPYING
+# Authors: see git-blame(1)
 
 import re
 import optparse

server/gff_twobit_query.py

@@ -1,5 +1,7 @@
 #!/usr/bin/python
-# Filename: gff_query_twobit.py
+# This code is part of GET-Evidence.
+# Copyright: see COPYING
+# Authors: see git-blame(1)
 
 """
 usage: %prog gff_file twobit_file [output_file]

server/parse_variant_counts.py

@@ -1,4 +1,7 @@
 #!/usr/bin/python
+# This code is part of GET-Evidence.
+# Copyright: see COPYING
+# Authors: see git-blame(1)
 
 """Parse output from count_variants.py"""
 

server/progresstracker.py

@@ -1,3 +1,7 @@
+# This code is part of GET-Evidence.
+# Copyright: see COPYING
+# Authors: see git-blame(1)
+
 """Tracking and logging progress and reporting metadata during processing"""
 
 import simplejson as json

server/setup.py

@@ -1,5 +1,7 @@
 #!/usr/bin/python
-# Filename: setup.py
+# This code is part of GET-Evidence.
+# Copyright: see COPYING
+# Authors: see git-blame(1)
 
 # A setup script to install the _twobit module
 # ---

server/utils/bed.py

@@ -1,9 +1,9 @@
 #!/usr/bin/python
-# Filename: bed.py
+# This code is part of GET-Evidence.
+# Copyright: see COPYING
+# Authors: see git-blame(1)
 
 # A BED file parser
-# ---
-# This code is part of the Trait-o-matic project and is governed by its license.
 
 from warnings import warn
 from intervals import Interval, IntervalFile

server/utils/codon_intersect.py

@@ -1,9 +1,9 @@
 #!/usr/bin/python
-# Filename: codon_intersect.py
+# This code is part of GET-Evidence.
+# Copyright: see COPYING
+# Authors: see git-blame(1)
 
 # A useful utility function for retrieving coding sequence fragments
-# ---
-# This code is part of the Trait-o-matic project and is governed by its license.
 
 def codon_intersect(start, end, exons, codon_position):
     """Returns a tuple to express the intervals in genomic sequence
@@ -169,4 +169,4 @@ def codon_intersect(start, end, exons, codon_position):
         coding_intervals.reverse()
 
     # finally, return the stuff we want
-    return start_exon, end_exon, coding_intervals
+    return start_exon, end_exon, coding_intervals

server/utils/fasta.py

@@ -1,10 +1,10 @@
 #!/usr/bin/python
-# Filename: fasta.py
+# This code is part of GET-Evidence.
+# Copyright: see COPYING
+# Authors: see git-blame(1)
 
 # A quick-and-dirty FASTA file parser
 # based in part on the example at <http://www.dalkescientific.com/writings/NBN/parsing.html>
-# ---
-# This code is part of the Trait-o-matic project and is governed by its license.
 
 import textwrap
 

server/utils/gff.py

@@ -1,9 +1,9 @@
 #!/usr/bin/python
-# Filename: gff.py
+# This code is part of GET-Evidence.
+# Copyright: see COPYING
+# Authors: see git-blame(1)
 
 # A GFF file parser
-# ---
-# This code is part of the Trait-o-matic project and is governed by its license.
 
 from warnings import warn
 from intervals import Interval, IntervalFile

server/utils/intervals.py

@@ -1,9 +1,9 @@
 #!/usr/bin/python
-# Filename: intervals.py
+# This code is part of GET-Evidence.
+# Copyright: see COPYING
+# Authors: see git-blame(1)
 
 # A basic set of functionality for files that specify intervals
-# ---
-# This code is part of the Trait-o-matic project and is governed by its license.
 
 from warnings import warn
 from bitset import *

server/utils/omim.py

@@ -1,9 +1,9 @@
 #!/usr/bin/python
-# Filename: omim.py
+# This code is part of GET-Evidence.
+# Copyright: see COPYING
+# Authors: see git-blame(1)
 
 # A prototype OMIM parser
-# ---
-# This code is part of the Trait-o-matic project and is governed by its license.
 
 class OMIMRecord(object):
     def __init__(self, d):

server/utils/substitution_matrix.py

@@ -1,5 +1,8 @@
 #!/usr/bin/python
-# Filename: substitution_matrix.py
+# This code is part of GET-Evidence.
+# Copyright: see COPYING
+# Authors: see git-blame(1)
+
 '''Takes two amino acids with single letter code,
 returns the BLOSUM100 value for the pair.
 Uses get-evidence/public_html/lib/blosum100.txt'''

server/utils/transcript.py

@@ -1,5 +1,7 @@
 #!/usr/bin/python
-# Filename: transcript.py
+# This code is part of GET-Evidence.
+# Copyright: see COPYING
+# Authors: see git-blame(1)
 
 class Transcript:
     def __init__(self, transcript_data, column_specs = {}):