diff --git a/COPYING b/COPYING index 43b5aa8..235509d 100644 --- a/COPYING +++ b/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.") diff --git a/server/call_missing.py b/server/call_missing.py index 37bf319..a685b36 100644 --- a/server/call_missing.py +++ b/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. diff --git a/server/codon.py b/server/codon.py index a70588f..d541b71 100644 --- a/server/codon.py +++ b/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", diff --git a/server/compile_covered.py b/server/compile_covered.py index 48f4ab6..391def7 100644 --- a/server/compile_covered.py +++ b/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 diff --git a/server/config_names.py b/server/config_names.py index e5317d4..d95c0d6 100644 --- a/server/config_names.py +++ b/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') diff --git a/server/count_variants.py b/server/count_variants.py index f04bb22..9b762e5 100644 --- a/server/count_variants.py +++ b/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 diff --git a/server/fastq_to_fasta.py b/server/fastq_to_fasta.py index 6a7d721..08201af 100644 --- a/server/fastq_to_fasta.py +++ b/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() \ No newline at end of file + main() diff --git a/server/genome_analyzer.py b/server/genome_analyzer.py index 1e9081d..6e574c4 100755 --- a/server/genome_analyzer.py +++ b/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] diff --git a/server/get_metadata.py b/server/get_metadata.py index a49cc86..91adbfe 100755 --- a/server/get_metadata.py +++ b/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 diff --git a/server/getev_pph2_extract.py b/server/getev_pph2_extract.py index 8ae3907..f069f3a 100644 --- a/server/getev_pph2_extract.py +++ b/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 diff --git a/server/gff2json.py b/server/gff2json.py index f60d303..b7a3eaa 100644 --- a/server/gff2json.py +++ b/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 diff --git a/server/gff_dbsnp_query.py b/server/gff_dbsnp_query.py index 06a218d..feeb2e9 100644 --- a/server/gff_dbsnp_query.py +++ b/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] diff --git a/server/gff_getevidence_map.py b/server/gff_getevidence_map.py index 96042c0..241eaf0 100644 --- a/server/gff_getevidence_map.py +++ b/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] diff --git a/server/gff_nonsynonymous_filter.py b/server/gff_nonsynonymous_filter.py index c8afc99..2528326 100644 --- a/server/gff_nonsynonymous_filter.py +++ b/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] diff --git a/server/gff_trio_phase.py b/server/gff_trio_phase.py index 8459aee..eaa9b86 100755 --- a/server/gff_trio_phase.py +++ b/server/gff_trio_phase.py @@ -1,7 +1,7 @@ #!/usr/bin/python -# Filename: gff_trio_phase.py -# Author: Evan Maxwell (evanmaxwell@gmail.com) -# Date: April 2011 +# This code is part of GET-Evidence. +# Copyright: see COPYING +# Authors: see git-blame(1) import re import optparse diff --git a/server/gff_twobit_query.py b/server/gff_twobit_query.py index 8c7dd94..ae722b9 100755 --- a/server/gff_twobit_query.py +++ b/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] diff --git a/server/parse_variant_counts.py b/server/parse_variant_counts.py index a1bcd16..2a3990e 100644 --- a/server/parse_variant_counts.py +++ b/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""" diff --git a/server/progresstracker.py b/server/progresstracker.py index 15fe33e..503fa6d 100644 --- a/server/progresstracker.py +++ b/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 diff --git a/server/setup.py b/server/setup.py index 92900fb..baa1690 100644 --- a/server/setup.py +++ b/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 # --- diff --git a/server/utils/bed.py b/server/utils/bed.py index 6351258..7d25504 100644 --- a/server/utils/bed.py +++ b/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 diff --git a/server/utils/codon_intersect.py b/server/utils/codon_intersect.py index c9c3490..b1c3479 100644 --- a/server/utils/codon_intersect.py +++ b/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 \ No newline at end of file + return start_exon, end_exon, coding_intervals diff --git a/server/utils/fasta.py b/server/utils/fasta.py index 2403f51..ef07983 100644 --- a/server/utils/fasta.py +++ b/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 -# --- -# This code is part of the Trait-o-matic project and is governed by its license. import textwrap diff --git a/server/utils/gff.py b/server/utils/gff.py index 511c35f..a9e1590 100644 --- a/server/utils/gff.py +++ b/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 diff --git a/server/utils/intervals.py b/server/utils/intervals.py index defa307..fd38ec6 100644 --- a/server/utils/intervals.py +++ b/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 * diff --git a/server/utils/omim.py b/server/utils/omim.py index 7549312..cb4568f 100644 --- a/server/utils/omim.py +++ b/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): diff --git a/server/utils/substitution_matrix.py b/server/utils/substitution_matrix.py index a151ced..3aaf373 100644 --- a/server/utils/substitution_matrix.py +++ b/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''' diff --git a/server/utils/transcript.py b/server/utils/transcript.py index 6cb864d..a587542 100644 --- a/server/utils/transcript.py +++ b/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 = {}):