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Scheme creation/tree visualization#58

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gcttong wants to merge 72 commits intoscheme-creation/_basephac-nml/biohansel:scheme-creation/_basefrom scheme-creation/tree_visualizationphac-nml/biohansel:scheme-creation/tree_visualizationCopy head branch name to clipboard

+332,950-15

Commits

Commits on Aug 8, 2018

• initial commit of scripts directory

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  ae196e3

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• modified ability to change filter out 2-state SNPS in vcf

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• added the split-genome functionality

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• preliminary files for the pipeline

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  ac9a58d

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• made initial changes on the command-line tool

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• made initial changes on the command-line tool

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  a357f62

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• made adjustments to the pipeline and allowed user to input files

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  e7ff894

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• collecting sequences from local genbank file

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• handled exception for file downloads

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  a80499f

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• added docstrings and modified the function structures

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  b24bf2e

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• finished adding docstrings to files

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• added hiearchical clustering functionality

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  e8a0f9e

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• made changes to main file

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• completed pipeline

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• completed checks for pipelin

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• removed files

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• removed comments

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• smaller changes

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• addressed earlier commits

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  dc1463b

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• fixed the docstring for extract_test_columns

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  6d0d7aa

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• fixed the log debug info for reference groups

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  ce09e25

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• fixed the log debug info for reference groups

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  c292223

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• fixed the log debug info for reference groups

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  d4cd0c9

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• fixed the import structure

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  46ee176

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• added docstrings and separated the findcluster function into smaller functions

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• fixed the thresholds so that the array takes distances between 0.0 and 1.0

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  0e59bdc

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• added the needed command-line arguments

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• merged development branch

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• changed the gitignore file to take out pytest_cache and Jupyter notebooks

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• changed the gitignore file

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• changed gitignore files:

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• changed the gitignore file

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• deleted pytest_cache

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• changed the get-sequence name to write-sequence

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  83aa97c

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• script no longer extracts test columns and modified scheme sequence output format

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  aee9496

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• made some formatting changes

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• fixed the docstring in the write_sequence file

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  4d1d9c5

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• separated the write_sequence function into two distinct functions

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• modifed read_vcf that splits up the two dataframes into binary data and snv data

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  d4ff06c

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• changed the get-sequences return type

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  e8ec3cf

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• fixed the way in which the file path is taken from the reference_genome_name

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  b00437e

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• made the variable names in get_sequence more descriptive

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  957fe54

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• fixed the indentation problem for the tiles file output

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  a386dee

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• changed the name of attribute_value to ratio_value in write_sequence

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• allows for multiple records to be part of the reference genome file

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  f68f6e9

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• allowed for better querying of sequence file by using a dictionary

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  b012ece

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• write_sequence now returns a string for the schema file output

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  bad3a86

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• first initial commit

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  1a71e15

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• fixed return value from compute_distance_matrix

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• allows for other file types in addition to genbank files

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  e98d7b0

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• Merge branch 'scheme-creation/_base' of github.com:phac-nml/biohansel into scheme-creation/initial

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• Merge branch 'scheme-creation/_base' of github.com:phac-nml/biohansel into scheme-creation/newChanges

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  dc053ca

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• added tests and fixed formatting for files

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  a24132d

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• Merge branch 'scheme-creation/initial' of github.com:phac-nml/biohansel into scheme-creation/tree_visualization

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• added description for display_tree

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• removed logging messages

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Commits on Aug 9, 2018

• changed the spacing in cli.py

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  e96e954

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• Merge branch 'scheme-creation/_base' of github.com:phac-nml/biohansel into scheme-creation/tree_visualization

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  bfa947b

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Commits on Aug 10, 2018

• changed file names

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Commits on Aug 13, 2018

• changed name of variable to tile-length and gives options of file formats to user

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• changed command line inputs and added default values

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Commits on Aug 15, 2018

• created a cluster class and added range of integer values as an option

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• took out logging messages

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Commits on Aug 16, 2018

• modified the output format for the phylogenetic tree

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Commits on Aug 21, 2018

• midified the string formatting in scheme creation

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Commits on Aug 30, 2018

• allowed user to specify file format and program also parses file format if none given

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Commits on Sep 4, 2018

• changed fasta sequence file function to generator

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Commits on Sep 5, 2018

• added a funciton that extract snvs from ingroup and outgroup

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  292749a

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• added docstring to new function

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  784a18e

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• modified function in cluster_generator

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• changed expand sets function in cluster generator to have dict comprehension

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Commits on Sep 6, 2018

• refactored the output_flat_clusters function in cluster_generator files

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