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Computing amino acid sequence alignments in gene clusters should be parallelized #680

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meren opened this issue Jan 4, 2018 · 1 comment · Fixed by #714
Closed

Computing amino acid sequence alignments in gene clusters should be parallelized #680

meren opened this issue Jan 4, 2018 · 1 comment · Fixed by #714
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@ozcan
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enhancement pangenomic workflow performance
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v4

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@meren
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meren commented Jan 4, 2018

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@meren meren added this to the v4 milestone Jan 4, 2018
meren added a commit that referenced this issue Jan 4, 2018
@meren
fixme. re: #680.
fe47fa0
@ozcan
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ozcan commented Jan 23, 2018 •
edited by meren
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[
  [
    "g01_107",
    "MTLFTTLLVLIFERLFKLGEHWQLDHRLEAFFRRVKHFSLGRTLGMTIIAMGVTFLLLRALQGVLFNVPTLLVWLLIGLLCIGAGKVRLHYHAYLTAASRNDSHARATMAGELTMIHGVPAGCDEREYLRELQNALLWINFRFYLAPLFWLIVGGTWGPVTLMGYAFLRAWQYWLARYQTPHHRLQSGIDAVLHVLDWVPVRLAGVVYALIGHGEKALPAWFASLGDFHTSQYQVLTRLAQFSLAREPHVDKVETPKAAVSMAKKTSFVVVVVIALLTIYGALV"
  ],
  [
    "g02_107",
    "MTLFTTLLVLIFERLFKLGEHWQLDHRLEAFFRRVKHFSLGRTLGMTIIAMGVTFLLLRALQGVLFNVPTLLVWLLIGLLCIGAGKVRLHYHAYLTAASRNDSHARATMAGELTMIHGVPAGCDEREYLRELQNALLWINFRFYLAPLFWLIVGGTWGPVTLMGYAFLRAWQYWLARYQTPHHRLQSGIDAVLHVLDWVPVRLAGVVYALIGHGEKALPAWFASLGDFHTSQYQVLTRLAQFSLAREPHVDKVETPKAAVSMAKKTSFVVVVVIALLTIYGALV"
  ],
  [
    "g03_104",
    "MTLFTTLLVLIFERLFKLGEHWQLDHRLEAFFRRVKHFSLGRTLGMTIIAMGVTFLLLRALQGVLFNVPTLLVWLLIGLLCIGAGKVRLHYHAYLTAASRNDSHARATMAGELTMIHGVPAGCDEREYLRELQNALLWINFRFYLAPLFWLIVGGTWGPVTLMGYAFLRAWQYWLARYQMPHHRLQSGIDAVLHVLDWVPVRLAGVVYALIGHGEKALPAWFASLGDFHTSQYQVLTRLAQFSLAREPHVDKVETPRAAVSMAKKTSFVVVVVIALLTIYGALV"
  ]
]
{'gene_caller_id': 104, 'gene_cluster_id': 'GC_00000112', 'genome_name': 'g03', 'alignment_summary': '.|284'}

hey @meren, what does genome_name means in alignment summary? first dictionary is input to aligner, and the second one is summary. How does it pick the g03?

ozcan added a commit that referenced this issue Jan 24, 2018
@ozcan
parallelize alignments, Related #680
afaf6d3
@meren meren mentioned this issue Jan 24, 2018
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enhancement pangenomic workflow performance
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Parallelizing gene cluster alignments merenlab/anvio
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@meren @ozcan