nopaste

~/nextstrain/all/mers-beast-tutorial ~/nextstrain/all ~/nextstrain/all
~/nextstrain/all/documentation ~/nextstrain/all ~/nextstrain/all
~/nextstrain/all/phyloTree ~/nextstrain/all ~/nextstrain/all
~/nextstrain/all/react-sidebar ~/nextstrain/all ~/nextstrain/all
~/nextstrain/all/auctor ~/nextstrain/all ~/nextstrain/all
~/nextstrain/all/sphinx-theme ~/nextstrain/all ~/nextstrain/all
~/nextstrain/all/forecasts-ncov ~/nextstrain/all ~/nextstrain/all
~/nextstrain/all/sacra ~/nextstrain/all ~/nextstrain/all
~/nextstrain/all/mumps ~/nextstrain/all ~/nextstrain/all
~/nextstrain/all/project-board ~/nextstrain/all ~/nextstrain/all
~/nextstrain/all/ncov-simple ~/nextstrain/all ~/nextstrain/all
scripts/mask-alignment.py:5:1:from augur.io import open_file, read_sequences, write_sequences
scripts/mutation_summary.py:2:1:from augur.io import open_file
~/nextstrain/all/nextstrain.org ~/nextstrain/all ~/nextstrain/all
~/nextstrain/all/auspice ~/nextstrain/all ~/nextstrain/all
~/nextstrain/all/nextfrequencies ~/nextstrain/all ~/nextstrain/all
~/nextstrain/all/rsv-old ~/nextstrain/all ~/nextstrain/all
~/nextstrain/all/simplest-build ~/nextstrain/all ~/nextstrain/all
~/nextstrain/all/inrb-drc-private ~/nextstrain/all ~/nextstrain/all
~/nextstrain/all/chateau ~/nextstrain/all ~/nextstrain/all
~/nextstrain/all/augur ~/nextstrain/all ~/nextstrain/all
augur/curate/__init__.py:11:1:from augur.io.json import dump_ndjson, load_ndjson
augur/curate/__init__.py:12:1:from augur.io.metadata import read_table_to_dict, read_metadata_with_sequences, write_records_to_tsv
augur/curate/__init__.py:13:1:from augur.io.sequences import write_records_to_fasta
augur/io/metadata.py:10:1:from augur.io.print import print_err
augur/titer_model.py:10:1:from augur.io.file import open_file
augur/utils.py:15:1:from augur.io.file import open_file
tests/io/test_file.py:1:1:import augur.io.file
tests/io/test_metadata.py:7:1:from augur.io.metadata import read_table_to_dict, read_metadata_with_sequences, write_records_to_tsv
tests/io/test_sequences.py:13:1:import augur.io.sequences
tests/io/test_shell_command_runner.py:5:1:from augur.io.shell_command_runner import ShellCommandRunner
tests/io/test_vcf.py:2:1:import augur.io.vcf
tests/test_filter.py:17:1:from augur.io.metadata import read_metadata
~/nextstrain/all/ncov-africa-cdc ~/nextstrain/all ~/nextstrain/all
~/nextstrain/all/test-github-actions ~/nextstrain/all ~/nextstrain/all
~/nextstrain/all/standard-RAxML ~/nextstrain/all ~/nextstrain/all
~/nextstrain/all/community-test ~/nextstrain/all ~/nextstrain/all
~/nextstrain/all/ncov-preprocess ~/nextstrain/all ~/nextstrain/all
~/nextstrain/all/translations ~/nextstrain/all ~/nextstrain/all
~/nextstrain/all/xopen ~/nextstrain/all ~/nextstrain/all
~/nextstrain/all/monkeypox ~/nextstrain/all ~/nextstrain/all
ingest/bin/fasta-to-ndjson:16:1:from augur.io import read_sequences
scripts/construct-recency-from-submission-date.py:3:1:from augur.io import read_metadata
scripts/update_colours.py:3:1:from augur.io import read_metadata
~/nextstrain/all/tb ~/nextstrain/all ~/nextstrain/all
~/nextstrain/all/narratives ~/nextstrain/all ~/nextstrain/all
~/nextstrain/all/conda ~/nextstrain/all ~/nextstrain/all
~/nextstrain/all/private ~/nextstrain/all ~/nextstrain/all
~/nextstrain/all/docker-base ~/nextstrain/all ~/nextstrain/all
~/nextstrain/all/conda-base ~/nextstrain/all ~/nextstrain/all
~/nextstrain/all/yellow-fever ~/nextstrain/all ~/nextstrain/all
~/nextstrain/all/measles ~/nextstrain/all ~/nextstrain/all
~/nextstrain/all/bioconda-recipes ~/nextstrain/all ~/nextstrain/all
~/nextstrain/all/zika ~/nextstrain/all ~/nextstrain/all
~/nextstrain/all/ncov-ingest ~/nextstrain/all ~/nextstrain/all
~/nextstrain/all/sandbox ~/nextstrain/all ~/nextstrain/all
~/nextstrain/all/janus ~/nextstrain/all ~/nextstrain/all
~/nextstrain/all/auspice.us ~/nextstrain/all ~/nextstrain/all
~/nextstrain/all/ebola ~/nextstrain/all ~/nextstrain/all
~/nextstrain/all/ncov-clades-schema ~/nextstrain/all ~/nextstrain/all
~/nextstrain/all/spheres-augur-build ~/nextstrain/all ~/nextstrain/all
~/nextstrain/all/avian-flu ~/nextstrain/all ~/nextstrain/all
~/nextstrain/all/gates-pgi ~/nextstrain/all ~/nextstrain/all
~/nextstrain/all/nextclade_data ~/nextstrain/all ~/nextstrain/all
~/nextstrain/all/whitepaper ~/nextstrain/all ~/nextstrain/all
~/nextstrain/all/seasonal-flu ~/nextstrain/all ~/nextstrain/all
scripts/calculate_epiweek.py:3:1:from augur.io import read_metadata
scripts/construct-recency-from-submission-date.py:2:1:from augur.io import read_metadata
scripts/generate_locations_file.py:3:1:from augur.io import read_metadata
scripts/select_strains.py:10:1:from augur.io import read_metadata
~/nextstrain/all/docs.nextstrain.org ~/nextstrain/all ~/nextstrain/all
~/nextstrain/all/static ~/nextstrain/all ~/nextstrain/all
~/nextstrain/all/groups-migration ~/nextstrain/all ~/nextstrain/all
~/nextstrain/all/enterovirus_d68 ~/nextstrain/all ~/nextstrain/all
~/nextstrain/all/cli ~/nextstrain/all ~/nextstrain/all
~/nextstrain/all/ncov-tutorial ~/nextstrain/all ~/nextstrain/all
~/nextstrain/all/community-search ~/nextstrain/all ~/nextstrain/all
~/nextstrain/all/dengue ~/nextstrain/all ~/nextstrain/all
~/nextstrain/all/wdl-debug ~/nextstrain/all ~/nextstrain/all
~/nextstrain/all/zika-tutorial-nextflow ~/nextstrain/all ~/nextstrain/all
~/nextstrain/all/nextclade ~/nextstrain/all ~/nextstrain/all
~/nextstrain/all/.github ~/nextstrain/all ~/nextstrain/all
~/nextstrain/all/cov ~/nextstrain/all ~/nextstrain/all
~/nextstrain/all/bioconda-utils ~/nextstrain/all ~/nextstrain/all
~/nextstrain/all/readthedocs-cli ~/nextstrain/all ~/nextstrain/all
~/nextstrain/all/lassa ~/nextstrain/all ~/nextstrain/all
~/nextstrain/all/nextstrain-narratives-demo ~/nextstrain/all ~/nextstrain/all
~/nextstrain/all/rsv ~/nextstrain/all ~/nextstrain/all
ingest/bin/fasta-to-ndjson:16:1:from augur.io import read_sequences
~/nextstrain/all/readthedocs-testbed ~/nextstrain/all ~/nextstrain/all
~/nextstrain/all/ncov ~/nextstrain/all ~/nextstrain/all
scripts/annotate_metadata_with_index.py:4:1:from augur.io import read_metadata
scripts/calculate_epiweek.py:3:1:from augur.io import read_metadata
scripts/combine_metadata.py:2:1:from augur.io import open_file, read_metadata
scripts/construct-recency-from-submission-date.py:3:1:from augur.io import read_metadata
scripts/find_clusters.py:3:1:from augur.io import read_metadata
scripts/get_distance_to_focal_set.py:5:1:from augur.io import read_sequences
scripts/mask-alignment.py:5:1:from augur.io import open_file, read_sequences, write_sequences
scripts/mutation_summary.py:2:1:from augur.io import open_file
scripts/sanitize_metadata.py:2:1:from augur.io import open_file, read_metadata
scripts/sanitize_sequences.py:2:1:from augur.io import open_file, read_sequences, write_sequences
~/nextstrain/all/mers ~/nextstrain/all ~/nextstrain/all
~/nextstrain/all/titer-view ~/nextstrain/all ~/nextstrain/all
~/nextstrain/all/WNV ~/nextstrain/all ~/nextstrain/all
~/nextstrain/all/wiki-redirector ~/nextstrain/all ~/nextstrain/all
~/nextstrain/all/fauna ~/nextstrain/all ~/nextstrain/all
~/nextstrain/all/email ~/nextstrain/all ~/nextstrain/all
~/nextstrain/all/flora ~/nextstrain/all ~/nextstrain/all
~/nextstrain/all/zika-tutorial ~/nextstrain/all ~/nextstrain/all
~/nextstrain/all/augurlinos ~/nextstrain/all ~/nextstrain/all