Code

Group snps#90

Code

Merged

martinghunt merged 64 commits intosanger-pathogens:mastersanger-pathogens/ariba:masterfrom martinghunt:group_snpsmartinghunt/ariba:group_snpsCopy head branch name to clipboardMay 26, 2016

+1,414-446

Commits

Commits on May 23, 2016

• Add identifier attribute

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• New identifier column in input tsv file

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• Add new idetifier column in metadata tsv file

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• New identifier column in input tsv file

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• New identifier column in input tsv file

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• Template for new class AlnToMetadata

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Commits on May 24, 2016

• Code to load input files

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  ba7a3b8

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• new method _check_seq_lengths_same

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• New method _make_unpadded_seqs

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  4897d02

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• New method _insertion_coords

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  6c2cab9

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• New method _check_coding_seq

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• New method _check_insertion_coords

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  56dd574

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• new method _check_sequences

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• New method _check_variants_match_sequences

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• New method _variant_ids_are_unique

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  2163d57

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• New method _make_unpadded_insertion_coords

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  db16b70

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• New method _unpadded_to_padded_nt_position

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• new method _padded_to_unpadded_nt_position

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• New method _variants_to_tsv_lines

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  76eb76b

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• Add test for noncoding sequences

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Commits on May 25, 2016

• Remove amino acids parameter

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• Add run method

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• write cluster file

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  5e6b1c6

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• Add task aln2meta

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  a76f56e

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• Bug fix getting insertion positions

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  120c596

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• do not permanently change genetic code

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• more careful to not change genetic code. Tests all pass

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  e3dee9a

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• Add variant identifier column

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• Require metadata lines to have 5 columns. 5th col no longer optionnal

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• Use new 5 column metadata lines

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  c357aa9

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• Use new 5 column metadata lines

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  7304a3e

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• Add Error class

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  41b9418

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• Bug fix ignoring separator. Tests added

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  6f83ca0

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• Report columns with their numbers

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  6e7be2f

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• 5 cols in metadata files

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• Sort for reprducibility and unit testing

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  978c1b8

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• Metadata has 5 columns

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• Use new 5 column format

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• Separate variant fields with a colon

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• Get variant group

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• variant descriptions are now colon-delimited

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• New :-delimited var fields

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• New :-delimited var fields

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• New :-delimited var fields

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  18f8984

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• New method has_var_groups

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• new method _var_groups

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• Get var_groups

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• New method _get_all_var_groups

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• Add test files for method _get_all_var_groups

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  6f7335b

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• Output var groups if wanted

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• Add option --var_groups

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• Add 'vgroup:' to start of variant group columns

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• Remove debugging print

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• Change vgroup: to vgroup.

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  9d4d0e1

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• Bug fix catching nonunique names

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Commits on May 26, 2016

• Get ref name and grouping info of variants

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• refactor _variant_column_names_tuples, returns tuples

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• New option var_cols

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• Return variant group name

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• Tuples include variant group name

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• Check if known_var is 1

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  ffceb14

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• Fix test, it is supposed to have known variant

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  2cd9f42

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• Add groups variant column

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• Update to use new variant_cols option

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