notes.txt 10.3 KB
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To-do:
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* TRY: BGCorrect edits to get rid of overcorrection of singletons:
  * Round final output to nearest integer; halves away from zero.
  * Clip deviations of less than 1 read to zero while iterating.
  * Both.
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* Samplevis:
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  * Add option to truncate long allele names.
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  * Sort STR alleles by length by default.
  * Option to adjust the sorting.
  * Option to choose complete table download.
  * When we have them, add default values to table filtering (for reference).
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  * Some of the media query breakpoints overlap, fix this.
  * Perhaps it is desirable to be able to request a list of 'Other sequences'.
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* Additions needed for publication:
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  * [If not too difficult to implement] BGEstimate should start with homozygous
    samples and add heterozygous samples later to optimise correction.
  * Summary statistics for BGEstimate based on top N genotypes per marker,
    which is the highest percentage remaining background in reference database
    (maybe also additional value for confidence interval).
  * Visualisation to display highest remaining background (positive and
    negative) in known samples after BGCorrect analysis.
* Add options to Libconvert to generate a template for STR or non-STR markers.
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* Add plotting of raw data points to StuttermodelVis.
* Add a print stylesheet for the other visualisations (only Samplevis has one).
* Add visualisation with all markers in one graph ("samplesummaryvis"?).
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* Allow loading multiple files into HTML visualisations and provide prev/next
  buttons to browse them.
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* Samplevis HTML visualisations in IE11:
  * Printing striped table rows does not seem to work, though this might be an
    NFI-specific issue.
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  * Tables are not perfectly aligned with the graphs (graphs render slightly
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    differently). Firefox is just 1px off (using em units for positioning now).
  * When printing, IE11 respects the pagebreak hints. Chrome and FF are bugged!
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* [Known bug]: pattern_longest_match does not give the longest match if a
  shorter match is possible and found earlier at the same position.
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* Add tool that takes a configuration file and runs a pipeline of other tools.
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* Add "allow_N" flag to [no_repeat] markers.  If the flag is specified, the
  reference sequence may contain Ns.  People might need this for the rCRS mtDNA
  reference sequence.
* Adjust BGEstimate so that it computes forward and reverse in one go.  To do
  this, double the number of columns in P and C and put the forward profile in
  the left half and the reverse profile in the right half.  The benefit of this
  is that this ensures the same A is used for both strands, that is, the
  estimated allele balance is the same.
* Adjust BGEstimate so that it takes strand bias in the allele itself into
  account as well.
* Perhaps there should be a version of BGEstimate that makes a profile for each
  genotype instead of each allele.  This allows for the detection of hybrids.
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* Add tool to summarise various statistics about the entire analysis pipeline:
  (TODO: Write this list)
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Open Vega issues:
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* Lookup transform only takes simple field names for the onKey parameter.
  https://github.com/vega/vega/issues/526
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* Sorting is broken.
  https://github.com/vega/vega/issues/509
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* Feature request: Id-based refs for Force transform's source and target.
  https://github.com/vega/vega/issues/471
* Tick labels of log scale axes don't respect number formatting.
  https://github.com/vega/vega/issues/470
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* Legend and axis corruption on signal changes.
  https://github.com/vega/vega/issues/446
* Feature request for lines (or arbitrary shapes) for legend items.
  https://github.com/vega/vega/issues/408
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Inclusion of tools developed during the project into FDSTools:
PRIO    OLD TOOL NAME       DESCRIPTION
------- ------------------- ---------------------------------------------------
LOW     distance-plot       Check stability of profiles by subsampling
LOW     qq-plot             Draw Q-Q plot vs normal/lognormal distributions
LOW     stuttercheck        Sort-of stuttermodel using profiles as input
LOW     substitutioncheck   Sort-of substitutionmodel using profiles as input
DONE    gen-allele-names    Convert TSSV-style sequences to allelenames
DONE    stuttermark         Mark stutter products in sample
DONE    analyze-background  BGEstimate: generate background profiles
DONE    profilemark         BGCorrect: find and correct for noise in samples
DONE    gen-bg-profiles     Compute statistics on noise in homozygous samples
DONE    blame               Find dirty samples in the reference database
DONE    allelenames-update  Convert allele names from one library to another
DONE    polyfit-repeat-len  Stuttermodel: predict stutter from sequence
DONE    common-background   Compute noise ratios in homozygous samples
DROP    alleles-convert     Convert allele names using lookup table
DROP    block-dedup         Remove duplicate blocks in TSSV-style sequences
DROP    graphgen            Create bar graph from a sample's data
DROP    find-true-alleles   Check whether the true alleles are detected
DROP    allele-graph        Create a graph of allele co-occurrence
DROP    ambiguity           Find potentially ambiguous allele combinations
DROP    strandbias          Find strand bias in the data
DROP    annotate-alleles    Annotate true alleles in sample based on allelelist

Visualisations:
LOW     blame               Common alleles
LOW     qqplot              Q-Q plot of normal/lognormal distribution
LOW     stability           Profile distance vs amount of subsampling
DONE    samplevis           Sample data
DONE    profiles            Background profiles
DONE    bg                  Dotplots of noise ratios in homozygous samples
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DONE    trends              Fit repeat length vs stutter amount
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DONE    allelegraph         Homozygosity/heterozygosity
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Argument group order*:
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input file options          bgcorrect,samplestats,seqconvert,stuttermark
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output file options         allelefinder,bgcorrect,bgestimate,bghomraw,bghomstats,bgmerge,blame,samplestats,seqconvert,stuttermark,stuttermodel,tssv
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sample tag parsing options  allelefinder,bgcorrect,bgestimate,bghomraw,bghomstats,blame,samplestats,seqconvert,stuttermark,stuttermodel
allele detection options    bgestimate,bghomraw,bghomstats,blame,stuttermodel
interpretation options      samplestats
filtering options           allelefinder,bgcorrect,bgestimate,bghomraw,bghomstats,bgpredict,blame,samplestats,stuttermark,stuttermodel
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sequence format options     allelefinder,bgcorrect,bgestimate,bghomraw,bghomstats,bgmerge,bgpredict,blame,stuttermark,stuttermodel,tssv
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random subsampling options  bgestimate,bghomstats,stuttermodel
visualisation options       vis
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*tssv has sequence format options before output file options
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Input/output of tools:      INPUT           OUTPUT
allelefinder    list of sample files        *single output + report
bgcorrect       bg file + single sample (b) single sample (batches supported)
bgestimate      list of sample files        single output + report
bghomraw        list of sample files        single output
bghomstats      list of sample files        single output
bgmerge^        list of bg files            single output
bgpredict^      model + seqfile             single output
blame           bg file + list of samples   single output
libconvert^     single input library        single output
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samplestats     single sample file (batch)  single sample (batches supported)
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seqconvert      single sample file (batch)  single sample (batches supported)
stuttermark     single sample file (batch)  single sample (batches supported)
stuttermodel    list of sample files        single output
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tssv            single sample FQ/FA         single output + report
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vis^            single sample (optional)    single output
*TODO: add option to change single output to multi-out (batch_process=True)
^does not use add_args functions (bgmodel/predict use sequence_format_args)

Input/output conventions:
* Write single output to sys.stdout by default, allow changing by -o
* Write report (if applicable) to sys.stderr by default, allow changing by -R
* For multi-in to single-out: list input files as positionals
* For single-in: provide [IN], [OUT] positionals (defaulting IN to sys.stdin)
* Single-in batch support via -i/-o; mutex with positionals!
  (if len(-o) == len(-i), map infile->outfile; if len(-o) == 1,
   map sample->outfile by rewriting tag)
* Multi-in to multi-out: allow multiple values in -o option (currently unused)

Reserved option letters:
-h  Help (used globally)
-v  Version (used globally)
-d  Debug (used globally)
-i  Batch input files
-o  Output files
-R  Report file
-F  Target sequence format
-l  Library
-e  Sample tag extraction pattern
-f  Sample tag format

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Action for special values in sequence columns:
TOOL            'No data'                   'Other sequences'
allelefinder    Not suitable for marker     Treated as single noise sequence
bgcorrect       Transparent                 Transparent
bgestimate      Ignored                     Ignored
bghomraw        Ignored                     Ignored
bghomstats      Ignored                     Ignored
bgmerge         Transparent                 Transparent
bgpredict       Ignored                     Ignored
blame           Ignored                     Ignored
samplestats     Transparent                 Transparent; may remove or add more
seqconvert      Transparent                 Transparent
stuttermark     Marked as 'UNKNOWN'         Marked as 'UNKNOWN'
stuttermodel    Ignored                     Ignored
tssv            May create them             May create them

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Sequence format conversions:
From    To
raw     tssv    OK - Transparent to non-STR markers (have no regex_middle).
raw     name    OK - Uses raw->tssv as a first step.
tssv    raw     OK - Trivial case.
tssv    name    (Implemented as tssv->raw->name)
name    raw     (Implemented as name->tssv->raw)
name    tssv    OK

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