option in depletion to revert tags in aligned files #751
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The desire is to revert the bam to unaligned state. Tags from
representative bams listed via: samtools view input.bam | cut -f 12- |
tr '\t' '\n' | cut -d ':' -f 1 | awk '{ if(!x[$1]++) { print }}'
the DX web interface does not seem to render a UI element for Array[String]?
taxon_filter.py
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| help='When supplying an aligned input file, clear the per-read attribute tags') | ||
| parser.add_argument("--tagsToClear", type=str, nargs='+', dest="tags_to_clear", default=["XT", "X0", "X1", "XA", | ||
| "AM", "SM", "BQ", "CT", "XN", "OC", "OP"], | ||
| help='blastn chunk size (default: %(default)s)') |
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this argparse help string looks incorrect!
| @@ -7,6 +7,8 @@ task deplete_taxa { | |||
| Array[File]? bmtaggerDbs # .tar.gz, .tgz, .tar.bz2, .tar.lz4, .fasta, or .fasta.gz | |||
| Array[File]? blastDbs # .tar.gz, .tgz, .tar.bz2, .tar.lz4, .fasta, or .fasta.gz | |||
| Int? query_chunk_size | |||
| Boolean? clear_tags = false | |||
| String? tags_to_clear_space_separated | |||
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Array[String]? perhaps? Then further below in the task command section you can use the ${sep=' ' tags_to_clear} WDL string join notation.
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Also, because of the behavior of this pair of parameters, maybe it would be clearer to the user of this workflow if tags_to_clear were actually set to a default list that matches the argparse default in python, otherwise it's not clear that leaving it unspecified actually implies a decent default list (or why this requires two parameters instead of just one).
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I initially had it as Array[String], but DNAnexus rendered a simple text box in the optional settings, and the expected input format was not clear (comma-separated, or space-separated?). Setting a default makes sense though, thanks!
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Ok, sounds like something to ask the dxWDL folks about later on.
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I'll want to run this in DNAnexus prior to merging. |
taxon_filter.py
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| @@ -371,6 +371,7 @@ def multi_db_deplete_bam(inBam, refDbs, deplete_method, outBam, **kwargs): | |||
| for db in refDbs: | |||
| if not samtools.isEmpty(tmpBamIn): | |||
| tmpBamOut = mkstempfname('.bam') | |||
| print("db", db) | |||
Depletion calls RevertSam on already-aligned input. This adds an option to clear tags in the bam file as well, with a default tag list an an optional argument to explicitly specify the tags. These options are passed through to the WDL. Also bugfix blastdb prefix finding for large multipart blastdbs; parallelize mvicuna rmdup by library in response to #754