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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

Commits on Dec 8, 2015

  1. Move genetic_code into refcheck.Checker class

    Martin Hunt committed Dec 8, 2015
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Commits on Dec 14, 2015

  1. Add ref_genes_getter module

    Martin Hunt committed Dec 14, 2015
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  2. Remove bs4 dependency as pip cannot find it

    Martin Hunt committed Dec 14, 2015
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  3. Add module amin_acid_variant

    Martin Hunt committed Dec 14, 2015
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Commits on Dec 16, 2015

  1. Require beautifulsoup4

    Martin Hunt committed Dec 16, 2015
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Commits on Dec 17, 2015

  1. Rename amino_acid_variant to sequence_variant

    Martin Hunt committed Dec 17, 2015
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  2. Rename agrees_with_protein_seq to sanity_check_against_seq

    Martin Hunt committed Dec 17, 2015
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  3. Add sequence_metadata

    Martin Hunt committed Dec 17, 2015
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  4. Store variant types as strings; add trnaslate_seq option

    Martin Hunt committed Dec 17, 2015
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  5. Add __str__()

    Martin Hunt committed Dec 17, 2015
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Commits on Dec 21, 2015

  1. Add __eq__ and __le__

    Martin Hunt committed Dec 21, 2015
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  2. Add __eq__ and __le__

    Martin Hunt committed Dec 21, 2015
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  3. Add reference_data module

    Martin Hunt committed Dec 21, 2015
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  4. Add gene checking functionality

    Martin Hunt committed Dec 21, 2015
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  5. Use new reference_data instead of refcheck.Checker

    Martin Hunt committed Dec 21, 2015
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Commits on Dec 22, 2015

  1. Remove refcheck; make card download format match new sequence_metadat… 

    …a format
    Martin Hunt committed Dec 22, 2015
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  2. Fix typo in filename

    Martin Hunt committed Dec 22, 2015
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Commits on Dec 23, 2015

  1. warn with metadata problem instead of die

    Martin Hunt committed Dec 23, 2015
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  2. Add length info to bad genes error message

    Martin Hunt committed Dec 23, 2015
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  3. Track which genes removed, so clearer output for user

    Martin Hunt committed Dec 23, 2015
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  4. Do not try to reverse complement genes

    Martin Hunt committed Dec 23, 2015
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  5. Tidy up log lines of removed sequences

    Martin Hunt committed Dec 23, 2015
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  6. Add method make_catted_fasta

    Martin Hunt committed Dec 23, 2015
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Commits on Jan 4, 2016

  1. Add test files for make_catted_fasta

    Martin Hunt committed Jan 4, 2016
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  2. Change to use ReferenceData

    Martin Hunt committed Jan 4, 2016
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  3. Add method sequence_type

    Martin Hunt committed Jan 4, 2016
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  4. Add methods sequence and sequence_length

    Martin Hunt committed Jan 4, 2016
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  5. Add method has_variant

    Martin Hunt committed Jan 4, 2016
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Commits on Jan 7, 2016

  1. Add method has_variant

    Martin Hunt committed Jan 7, 2016
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Commits on Jan 11, 2016

  1. Split Cluster into several classes. This breaks everything. Now fix i… 

    …t...
    Martin Hunt committed Jan 11, 2016
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  2. Typo fix

    Martin Hunt committed Jan 11, 2016
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  3. typo fix

    Martin Hunt committed Jan 11, 2016
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  4. remove line for now, has syntax error

    Martin Hunt committed Jan 11, 2016
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  5. Tests pass

    Martin Hunt committed Jan 11, 2016
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  6. Tests pass

    Martin Hunt committed Jan 11, 2016
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  7. Add missing modules

    Martin Hunt committed Jan 11, 2016
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  8. Remove unneeded test files

    Martin Hunt committed Jan 11, 2016
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  9. Tests pass

    Martin Hunt committed Jan 11, 2016
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  10. Tests pass

    Martin Hunt committed Jan 11, 2016
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  11. Close file before raising error

    Martin Hunt committed Jan 11, 2016
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  12. Tests pass

    Martin Hunt committed Jan 11, 2016
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Commits on Jan 25, 2016

  1. Fixes so counting reads works

    Martin Hunt committed Jan 25, 2016
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  2. test_init_fail_files_missing passes

    Martin Hunt committed Jan 25, 2016
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  3. Remove commented notes

    Martin Hunt committed Jan 25, 2016
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  4. Fix all_non_wild_type_variants

    Martin Hunt committed Jan 25, 2016
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  5. Implement hash function

    Martin Hunt committed Jan 25, 2016
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  6. Change output to be hash

    Martin Hunt committed Jan 25, 2016
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Commits on Jan 26, 2016

  1. Use lt instead of le for sorting

    Martin Hunt committed Jan 26, 2016
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  2. Use lt instead of le for sorting

    Martin Hunt committed Jan 26, 2016
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  3. Store in dicts for easy lookups later

    Martin Hunt committed Jan 26, 2016
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Commits on Jan 29, 2016

  1. Store self.nucmer_snps_file

    Martin Hunt committed Jan 29, 2016
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  2. Add method get_variants

    Martin Hunt committed Jan 29, 2016
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  3. Rename _nucmer_hits_to_ref_coords nucmer_hits_to_ref_coords

    Martin Hunt committed Jan 29, 2016
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  4. Do not need bam file

    Martin Hunt committed Jan 29, 2016
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  5. Rename _ref_cov_per_contig ref_cov_per_contig

    Martin Hunt committed Jan 29, 2016
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Commits on Feb 1, 2016

  1. Spelling typos fix

    Martin Hunt committed Feb 1, 2016
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  2. Catch when no contigs file written

    Martin Hunt committed Feb 1, 2016
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  3. New flag ref_seq_choose_fail

    Martin Hunt committed Feb 1, 2016
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  4. Add method get_depths_at_position

    Martin Hunt committed Feb 1, 2016
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  5. Add tets files needed for previous commit

    Martin Hunt committed Feb 1, 2016
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  6. nucmer_hits_to_ref_coords return dict; ref_covered_by_complete_contig… 

    …_with_orf was returning not what it should
    Martin Hunt committed Feb 1, 2016
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  7. Bug fixes when doing complete run

    Martin Hunt committed Feb 1, 2016
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  8. Rewrite of cluster, split into separate modules

    Martin Hunt committed Feb 1, 2016
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  9. Remove uneeded test files

    Martin Hunt committed Feb 1, 2016
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Commits on Feb 2, 2016

  1. Renmove gene_ from flag

    Martin Hunt committed Feb 2, 2016
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  2. Do not give noncoding seqs the compelte_orf flag

    Martin Hunt committed Feb 2, 2016
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  3. Add to_string method

    Martin Hunt committed Feb 2, 2016
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  4. Return variant in a list, for consistency

    Martin Hunt committed Feb 2, 2016
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  5. Bug fixes making noncoding report lines

    Martin Hunt committed Feb 2, 2016
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  6. Return nucletoide change string

    Martin Hunt committed Feb 2, 2016
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  7. bug fix reporting number of assembled bases

    Martin Hunt committed Feb 2, 2016
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  8. Report variant type for noncoding variants

    Martin Hunt committed Feb 2, 2016
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  9. Test all combinations of noncoding snps

    Martin Hunt committed Feb 2, 2016
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  10. Should be same as references.fa in cluster dir

    Martin Hunt committed Feb 2, 2016
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  11. Add tests for noncoding indels

    Martin Hunt committed Feb 2, 2016
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Commits on Feb 3, 2016

  1. List elements should be intervals, not nucmer alignments

    Martin Hunt committed Feb 3, 2016
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  2. Add test full run presence absence cluster

    Martin Hunt committed Feb 3, 2016
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  3. remove keys when values empty

    Martin Hunt committed Feb 3, 2016
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  4. Add tests for variants_only cluster runs

    Martin Hunt committed Feb 3, 2016
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  5. Remove unused imports

    Martin Hunt committed Feb 3, 2016
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  6. Simplify by not renaming, use -d option to cdhit instead

    Martin Hunt committed Feb 3, 2016
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  7. New nethod cluster_with_cdhit

    Martin Hunt committed Feb 3, 2016
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Commits on Feb 4, 2016

  1. Write cluster allocation file

    Martin Hunt committed Feb 4, 2016
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  2. rewrite started. tests pass. write_report fixed

    Martin Hunt committed Feb 4, 2016
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  3. Tidy up getting files from argannot

    Martin Hunt committed Feb 4, 2016
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  4. Tidy up getting files from resfinder

    Martin Hunt committed Feb 4, 2016
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  5. Add author and date to citation

    Martin Hunt committed Feb 4, 2016
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  6. Tidy up getting files from card

    Martin Hunt committed Feb 4, 2016
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  7. More tidy up getting files from card

    Martin Hunt committed Feb 4, 2016
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  8. New task getref

    Martin Hunt committed Feb 4, 2016
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Commits on Feb 5, 2016

  1. Add method write_seqs_to_fasta

    Martin Hunt committed Feb 5, 2016
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  2. Set filehandle to None so pickling works

    Martin Hunt committed Feb 5, 2016
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  3. Smalt no longer used

    Martin Hunt committed Feb 5, 2016
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  4. Set filehandle to None so pickling works

    Martin Hunt committed Feb 5, 2016
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  5. Velvet no longer used

    Martin Hunt committed Feb 5, 2016
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  6. Small fixes so now whole thing runs

    Martin Hunt committed Feb 5, 2016
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  7. Update to reflect rewrite of clusters.py

    Martin Hunt committed Feb 5, 2016
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  8. Bug fix writing report

    Martin Hunt committed Feb 5, 2016
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  9. Use new smatools sort syntax

    Martin Hunt committed Feb 5, 2016
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Commits on Feb 9, 2016

  1. Add method nucmer_hit_containing_reference_position

    Martin Hunt committed Feb 9, 2016
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  2. Add method nucmer_hit_containing_reference_position

    Martin Hunt committed Feb 9, 2016
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  3. Add method nucleotide_range

    Martin Hunt committed Feb 9, 2016
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Commits on Feb 10, 2016

  1. Report read depths etc on variants wild both ref and assembly

    Martin Hunt committed Feb 10, 2016
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  2. Die if input fastas empty

    Martin Hunt committed Feb 10, 2016
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  3. typo bug fix in __lt__

    Martin Hunt committed Feb 10, 2016
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  4. Pass samtools

    Martin Hunt committed Feb 10, 2016
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  5. Skip seqs that did not make cluster

    Martin Hunt committed Feb 10, 2016
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  6. Be verbose, when applicable

    Martin Hunt committed Feb 10, 2016
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  7. Be verbose with cdhit

    Martin Hunt committed Feb 10, 2016
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  8. Put sequence in dummy fa file to stop crashing

    Martin Hunt committed Feb 10, 2016
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  9. Add option to run test data

    Martin Hunt committed Feb 10, 2016
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  10. Tidy up output to log file

    Martin Hunt committed Feb 10, 2016
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  11. Remove unsorted bam

    Martin Hunt committed Feb 10, 2016
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  12. Clean files

    Martin Hunt committed Feb 10, 2016
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Commits on Feb 11, 2016

  1. Check assembly dir exists before trying to delete it

    Martin Hunt committed Feb 11, 2016
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  2. unsorted bam already deleted

    Martin Hunt committed Feb 11, 2016
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  3. Remove smalt

    Martin Hunt committed Feb 11, 2016
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  4. Rewrite external_progs module

    Martin Hunt committed Feb 11, 2016
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  5. New always_report column in metadata

    Martin Hunt committed Feb 11, 2016
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  6. Add new always_report column to metadata

    Martin Hunt committed Feb 11, 2016
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  7. Add new always_report column to metadata

    Martin Hunt committed Feb 11, 2016
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  8. Add new always_report column to metadata

    Martin Hunt committed Feb 11, 2016
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  9. Add new always_report column to output tsv

    Martin Hunt committed Feb 11, 2016
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  10. Force getting always_report=Y variants

    Martin Hunt committed Feb 11, 2016
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Commits on Feb 15, 2016

  1. Add test for always_ouput variants

    Martin Hunt committed Feb 15, 2016
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  2. Always report variants_only, even when variant not found

    Martin Hunt committed Feb 15, 2016
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  3. Report variants_only, whenever any reads mapped

    Martin Hunt committed Feb 15, 2016
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  4. Update to report variants_only when variant not there

    Martin Hunt committed Feb 15, 2016
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  5. Write assembled ref seqs to fasta file

    Martin Hunt committed Feb 15, 2016
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  6. Remove commented out code

    Martin Hunt committed Feb 15, 2016
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  7. Remove old refcheck

    Martin Hunt committed Feb 15, 2016
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  8. Remove old refcheck

    Martin Hunt committed Feb 15, 2016
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Commits on Feb 16, 2016

  1. Report rewrite, fewer lines and more columns

    Martin Hunt committed Feb 16, 2016
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Commits on Feb 17, 2016

  1. Change report format. Again.

    Martin Hunt committed Feb 17, 2016
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  2. Add missing comma

    Martin Hunt committed Feb 17, 2016
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  3. Fix missing columns with a . and always assert correct number of columns

    Martin Hunt committed Feb 17, 2016
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  4. Rename cluster_rep column

    Martin Hunt committed Feb 17, 2016
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  5. fix line2dict to work with new report

    Martin Hunt committed Feb 17, 2016
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  6. Make line2dict a classmethod

    Martin Hunt committed Feb 17, 2016
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  7. fix _load_file for new report.tsv format

    Martin Hunt committed Feb 17, 2016
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  8. Store as dict of dicts

    Martin Hunt committed Feb 17, 2016
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  9. refactor _pc_id_of_longest

    Martin Hunt committed Feb 17, 2016
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  10. refactor _to_summary_number -> _to_summary_number_for_seq

    Martin Hunt committed Feb 17, 2016
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  11. Add _to_summary_number_for_variant

    Martin Hunt committed Feb 17, 2016
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  12. fix _gather_output_rows for new report.tsv format

    Martin Hunt committed Feb 17, 2016
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  13. Make filter_output_rows a classmethod

    Martin Hunt committed Feb 17, 2016
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  14. make _write_tsv a classmethod

    Martin Hunt committed Feb 17, 2016
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  15. Convert dict to string for printing

    Martin Hunt committed Feb 17, 2016
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  16. Should be a string

    Martin Hunt committed Feb 17, 2016
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  17. Make classmethod

    Martin Hunt committed Feb 17, 2016
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  18. Make classmethod

    Martin Hunt committed Feb 17, 2016
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  19. Make classmethod

    Martin Hunt committed Feb 17, 2016
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  20. Use classmethods

    Martin Hunt committed Feb 17, 2016
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  21. Update run() to work with previous commits

    Martin Hunt committed Feb 17, 2016
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  22. Update with new column names

    Martin Hunt committed Feb 17, 2016
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  23. Reinstate unit test

    Martin Hunt committed Feb 17, 2016
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Commits on Feb 18, 2016

  1. Add ";var" into column names that are variants

    Martin Hunt committed Feb 18, 2016
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  2. Rename JS candy to phandango

    Martin Hunt committed Feb 18, 2016
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  3. tell phandango to colour columns consistently

    Martin Hunt committed Feb 18, 2016
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  4. Add N in required column

    Martin Hunt committed Feb 18, 2016
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  5. use hit_both_strands flag

    Martin Hunt committed Feb 18, 2016
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  6. Use has_nonsynonymous_variants flag

    Martin Hunt committed Feb 18, 2016
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  7. Bug fix when file not exists

    Martin Hunt committed Feb 18, 2016
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  8. Filter small contigs

    Martin Hunt committed Feb 18, 2016
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  9. Bux fig getting has_nonynonymous_variants flag

    Martin Hunt committed Feb 18, 2016
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  10. Discard read pairs where both reads unmapped

    Martin Hunt committed Feb 18, 2016
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