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blobtools v0.9.19
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@DRL DRL released this 26 Jul 15:55
· 150 commits to master since this release
v0.9.19
8bad6a5

DOI

Release notes

  • general refactoring
  • version number now printed in all output files

blobtools create

BAM parsing

  • BAM parsing now fast(er)
  • BAM is parsed with samtools view -F 4 -F 1028 -F 256 (only mapped, no optical-dupes, no 2nd-ary)
  • Support for M/X/= in CIGAR string (previously only M's)

BAM/SAM/CAS parsing

  • when parsing mapping files, blobtools automatically writes COV files

Taxonomy calculation

  • if two highest scoring taxonomies for a given contig have EQUAL scores, taxonomy gets set to "unresolved"
  • during plotting, the group "unresolved" gets treated as any other group
  • new flag [--tax_collision_random] allows legacy behaviour (random selection of taxonomy)
  • new argument [--min_diff FLOAT] sets minimal score difference between two highest scoring taxonomies of a contig in order for the contig to not be called "unresolved"

blobtools view

  • refactored and is now fast(er)

supported views

  • default view : table output, taxonomy columns are now numbered (1-based, for cut'ing). Can be turned off with [--notable]
  • [--concoct]: outputs taxonomy and coverage information necessary to run concoct
  • [--cov]: outputs coverage files (for using them in covplots)

blobtools map2cov

  • previously bam2cov
  • now supports BAM, SAM and CAS files (uses parsers in BtIO)
  • implemented, so that one can convert multiple mapping files to lightweight COV format (i.e. using GNU parallel)

blobtools blobplot

Flags and arguments

  • changed behaviour of [--multiplot]. Plots each group separately, then final plot of all groups.
  • new flag [--cumulative]. Analogous to [--multiplot] behaviour in previous versions: incremental addition of groups
  • new flag [--legend]. Plots legend in a separate figure, useful for slides.
  • new argument [--lib LIBNAME]. Allows selecting particular covlib(s) to plot; lists available libraries when no argument is specified.
  • new flag [--filelabel] : labels coverage axis based on coverage file
  • fixed [--exclude], now removes group(s) from plotting and stats
  • changed behaviour of [--colours FILE]. All groups not named in FILE are set to WHITE (for example see test_files/colours.txt)
  • added example file for [--refcov FILE] (test_files/refcov.txt)

Scaling

  • changed scaling of blobs in plots
  • previously, blobs had an area of 65*(length/1,000) pixels^2. But if an assembly had a few very big contigs, these covered the smaller ones.
  • now the scaling is done in the following way:
    • the biggest contig gets plotted as a blob of area 12,500 pixels^2
    • all other contigs get scaled proportionally
    • reference scale shows area of 5%, 10% and 25% length of longest contig

Misc

  • added x-axis minor ticklabels, all ticklabels facing outwards
  • fixed bug causing different plots to share filenames, causing overwriting

blobtools covplot

  • same underlying library as blobplot.
  • coverage axes are labelled based on coverage file
  • axes can be relabelled using [--xlabel XLABEL] and [--ylabel YLABEL]
  • maximal value for x/y-axes can be set using [--max FLOAT]

blobtools sumcov

  • removed

blobtools taxify

  • allows annotating similarity search results (from BLAST or Diamond) with TaxIDs using an ID-mapping-file, or a single TaxID

blobtools seqfilter

  • allows filtering a FASTA file based on a list of headers
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