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Auto get ref genes, variant handling #41

Merged
merged 166 commits into from
Feb 18, 2016
Merged

Auto get ref genes, variant handling #41

merged 166 commits into from
Feb 18, 2016

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martinghunt
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Many big changes:

  • download reference data from card, argannot or resfinder
  • handle variants properly
  • multithreading
  • a lot of refactoring

Martin Hunt added 30 commits December 8, 2015 12:57
Move genetic_code into refcheck.Checker class
cae568b
Add ref_genes_getter module
6555288
Remove bs4 dependency as pip cannot find it
20a0868
Add module amin_acid_variant
b166671
Require beautifulsoup4
ceb891e
Rename amino_acid_variant to sequence_variant
00ea328
Rename agrees_with_protein_seq to sanity_check_against_seq
d394cce
Add sequence_metadata
d9f72a6
Store variant types as strings; add trnaslate_seq option
8889943
Add __str__()
9cb44da
Add __eq__ and __le__
4e72a47
Add __eq__ and __le__
52ecebe
Add reference_data module
fe8a67b
Add gene checking functionality
e9173be
Use new reference_data instead of refcheck.Checker
2f2d242
Remove refcheck; make card download format match new sequence_metadat…
c818156 
…a format
Fix typo in filename
e925be6
warn with metadata problem instead of die
9641235
Add length info to bad genes error message
c2f15d4
Track which genes removed, so clearer output for user
6b2127c
Do not try to reverse complement genes
a16dc3e
Tidy up log lines of removed sequences
2ef8d2c
Add method make_catted_fasta
f049b53
Add test files for make_catted_fasta
12ff539
Change to use ReferenceData
1074d61
Add method sequence_type
b402ac8
Add methods sequence and sequence_length
708451d
Add method has_variant
6bc452a
Add method has_variant
eda4a9f
Split Cluster into several classes. This breaks everything. Now fix i…
7f6f1f9 
…t...
Martin Hunt added 28 commits February 17, 2016 11:42
Make line2dict a classmethod
3483d0e
fix _load_file for new report.tsv format
9ff620a
Store as dict of dicts
1d720fd
refactor _pc_id_of_longest
cef060d
refactor _to_summary_number -> _to_summary_number_for_seq
2a5b818
Add _to_summary_number_for_variant
703c79e
fix _gather_output_rows for new report.tsv format
f40c34e
Make filter_output_rows a classmethod
f33218c
make _write_tsv a classmethod
2a745f2
Convert dict to string for printing
ef6b72f
Should be a string
39cb54b
Make classmethod
3da951c
Make classmethod
ecce0cf
Make classmethod
6fcb36b
Use classmethods
0035f96
Update run() to work with previous commits
cad485a
Update with new column names
93fdaba
Reinstate unit test
0124d36
Add ";var" into column names that are variants
d3aab40
Rename JS candy to phandango
1af7813
tell phandango to colour columns consistently
4f6d802
Add N in required column
4af261c
use hit_both_strands flag
e0d462d
Use has_nonsynonymous_variants flag
32c4946
Bug fix when file not exists
b06a360
Filter small contigs
995edea
Bux fig getting has_nonynonymous_variants flag
cfbf573
Discard read pairs where both reads unmapped
0510055
martinghunt added a commit that referenced this pull request Feb 18, 2016
@martinghunt
Merge pull request #41 from martinghunt/auto_get_ref_genes
54bc465 
Auto get ref genes, variant handling
@martinghunt martinghunt merged commit 54bc465 into sanger-pathogens:master Feb 18, 2016
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