miga-base 1.0.5.2 → 1.1.0.0

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Files changed (20) hide show
  1. checksums.yaml +4 -4
  2. data/bin/miga-env +6 -0
  3. data/lib/miga/cli/action/doctor.rb +12 -4
  4. data/lib/miga/cli/action/env.rb +1 -1
  5. data/lib/miga/cli/action/init.rb +1 -1
  6. data/lib/miga/cli/action/ncbi_get/downloads.rb +230 -0
  7. data/lib/miga/cli/action/ncbi_get.rb +9 -217
  8. data/lib/miga/cli/action/wf.rb +7 -3
  9. data/lib/miga/common.rb +12 -11
  10. data/lib/miga/dataset/result.rb +2 -1
  11. data/lib/miga/version.rb +3 -3
  12. data/scripts/essential_genes.bash +7 -11
  13. data/scripts/miga.bash +2 -2
  14. data/test/common_test.rb +7 -7
  15. data/utils/FastAAI/FastAAI +3630 -0
  16. data/utils/FastAAI/{FastAAI → FastAAI-legacy}/FastAAI +1 -1
  17. data/utils/FastAAI/{kAAI_v1.0_virus.py → FastAAI-legacy/kAAI_v1.0_virus.py} +0 -0
  18. data/utils/distance/commands.rb +24 -13
  19. data/utils/requirements.txt +7 -7
  20. metadata +7 -4
data/scripts/essential_genes.bash CHANGED
@@ -36,19 +36,15 @@ HMM.essential.rb \
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  > "${DATASET}.ess/log"
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  # Index for FastAAI
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- NOMULTI=$(miga list_datasets -P "$PROJECT" -D "$DATASET" --no-multi \
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+ NOMULTI=$(miga ls -P "$PROJECT" -D "$DATASET" --no-multi \
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  | wc -l | awk '{print $1}')
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  if [[ "$NOMULTI" -eq "1" ]] ; then
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- if [[ "$FAA" == *.gz ]] ; then
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- gzip -cd "$FAA" > "${DATASET}.faix"
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- else
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- cp "$FAA" "${DATASET}.faix"
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- fi
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- FastAAI --qp "${DATASET}.faix" --output "${DATASET}.faix" \
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- --ext ".faix" --index --input-paths --all-vs-all --threads "$CORES"
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- rm "${DATASET}.faix"
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- rm "${DATASET}.faix.hmm"
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- rm "${DATASET}.faix.hmm.filt"
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+ echo "$FAA" > "$DATASET"
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+ FastAAI build_db --protein_file "$DATASET" \
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+ -o "${DATASET}.faix.d" --threads "$CORES"
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+ rm "$DATASET"
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+ mv "${DATASET}.faix.d/database/FastAAI_database.sqlite.db" "${DATASET}.faix"
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+ rm -r "${DATASET}.faix.d"
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  fi
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  # Reduce files
data/scripts/miga.bash CHANGED
@@ -3,8 +3,8 @@
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  ###
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  # Setup environment
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  set -e
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- eval "$("$MIGA/bin/miga" env)"
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- SCRIPT=${SCRIPT:-$(basename "$0" .bash)}
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+ eval "$("$MIGA/bin/miga-env")"
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+ SCRIPT=${SCRIPT:-"$(basename "$0" .bash)"}
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  ###
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  # Ancillary functions
data/test/common_test.rb CHANGED
@@ -78,21 +78,21 @@ class CommonTest < Test::Unit::TestCase
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  # Check advance when missing total
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  o = capture_stderr { m.advance('x', 0) }.string
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- assert_match(/\] x *\r/, o)
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+ assert_match(%r{\] x *\r}, o)
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  # Initialize advance
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- o = capture_stderr { m.advance('x', 0, 10) }.string
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- assert_match(/\] x 0\.0% \(0\/10\) *\r/, o)
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+ o = capture_stderr { m.advance('x', 0, 1001) }.string
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+ assert_match(%r{\] x 0\.0% \(0/1001\) *\r}, o)
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  # Insufficient data for prediction
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  sleep(1)
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- o = capture_stderr { m.advance('x', 1, 10) }.string
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- assert_match(/\] x 10\.0% \(1\/10\) *\r/, o)
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+ o = capture_stderr { m.advance('x', 1, 1000) }.string
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+ assert_match(%r{\] x 0\.1% \(1/1000\) *\r}, o)
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  # Predict time
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  sleep(1)
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- o = capture_stderr { m.advance('x', 2, 10) }.string
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- assert_match(/\] x 20\.0% \(2\/10\) [7-9]s left *\r/, o)
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+ o = capture_stderr { m.advance('x', 2, 1000) }.string
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+ assert_match(%r{\] x 0\.2% \(2/1000\) 1\d\.\dm left *\r}, o)
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  end
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  def test_num_suffix