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| def | common.Misc.FileType (pathname) |
| | Low level compression determination. More...
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| def | common.Misc.OpenFile4Reading (pathname, mode="r") |
| | Opens file for reading. More...
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| def | common.Misc.TypeConvert (value, toType, warn=True) |
| | Data conversion with error logging. More...
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| def | common.Misc.GetGRChVersion (dver) |
| | Get the human Genome Reference Consortium genome build version used by Ensembl. More...
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| def | common.Misc.SplitGenomicCoord (coord, dver, warn=True, retainBuild=False) |
| | Splits a standard string for genomic location. More...
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| def | common.Misc.SplitSNPGenomicCoord (coord, dver, warn=True) |
| | Splits genomic coordinates from a SNP. More...
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| def | common.Misc.GetGenomicCoordinateString (build, chromosome, startPos, endPos=None, warn=True) |
| | Create the Genomic Coordinate string in the format Build:Chromosome:Start -End or Build:Chromosome:Start (in the case where start and end are equal). More...
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| def | common.Misc.ComplementaryDNA (seq, reverse=False) |
| | Compute the complementary DNA sequence of a given sequence string. More...
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| def | common.Misc.WCheckInputColumns (writer, cols, line, lineNr, permissiveness, warn=True, exitCode=1, index0=True) |
| | Check applicability of column indices and apply permissiveness mode. More...
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| def | common.Misc.CheckInputColumns (cols, nrCols, lineNr, stop, warn=True, exitCode=1, index0=True, lastLen=None) |
| | Check applicability of column indices. More...
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| def | common.Misc.CheckInputLengths (len, lastLen, lineNr, warn=True) |
| | Check the length of an input line by comparing it to the last line. More...
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| def | common.Misc.ConvertInputIndices (cols, warn=True, exit=False) |
| | Convert input column(s) to table indices. More...
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