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TPRead
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getTPRead(alngt,
compareList,
readdic)
Funtion which transforms an HTSeq alignment to a TPRead class. |
source code
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CustomRead
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getCustomRead(alngt,
compareList,
readdic)
Funtion which transforms an HTSeq alignment to a CustomRead class. |
source code
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dictionary
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GetOrderDictionary(referenceSAM)
Function to get a dictionary containing the rank of a read (given a
sorted samfile by readname, samtools). |
source code
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Readobj
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gaps,mismatches
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(bool,list,bool)
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getAllID(textfile,
read,
compareList,
readdic)
Reads all alignments for the current read which are in the SAM file
(sorted). |
source code
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np.array
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CompareAlignments(reflist,
artlist,
file)
Compares alignments for the reference and artificial reference for a
specific read id. |
source code
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read obj.
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SkipHeader(file,
compareList,
readdic)
Skips the header from a SAM file, but reads the first line of the
alignment section. |
source code
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int,int
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getRanks(RefRead,
ArtRead,
rankdic)
Function which returns the ranks of 2 given readIDs (read from
reference,read from artificial). |
source code
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ranks
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int
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int
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float
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float
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int
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readobj, readname
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isSaneAlignment(alignment,
identifier,
compareList,
readdic)
Checks alignment line for unnecessary informations to skip |
source code
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bool
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int
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getHammingdistance(CompareString,
start,
end)
Computes the number of subsitutions in the artificial reference using
the CompareString. |
source code
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dictionary
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readReadQualities(fastqfile)
Reads a .fastqfile and calculates a defined readscore input: fastq
file output: fastq dictionary key = readid; value = qualstr |
source code
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dictionary
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extendReadDic(readdic)
Extends a given dictionary with KEY = readid and VALUE = qualstr such
that an internal naming is generated which can be used to efficiently
create an numpy array |
source code
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string
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list
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CreateCompareList(Reference,
ARG)
Creates a list which is used for comparisons between aligned reads
(exact number of mismatches) |
source code
|
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read obj.
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readSAMline(alignment,
identifier,
compareList,
readdic)
Function for reading SAM alignment text file (one line) |
source code
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int
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array
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writeToTabRef(RefArray,
outfile,
reverseReadArray,
ReadDic)
Write function for hits ont he reference genome. |
source code
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np.array(obj)
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files
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initOutFiles(controlDic,
mapper,
outpath)
Since we append in the program, we need to make sure no old files
remain... |
source code
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