Script arden_filter |
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# Script arden_filter

Script for filtering alignments with deficient properties (rqs,gaps, mismatches). The script generates a new .SAM file from the input SAM file, where only alignments are contained that fulfill certain quality thresholds. nm = numberOfMisMatches rq = readqualityscore MQ = mappingquality

Functions | [hide private]
writeFilteredReads(iddic, fastqfile, fastqfileoutput) Reads a .fastqfile and filters them for certain quality values. |
getMisGapRQ(alngt) Calculates the number of gaps / mistmatches from an HTSeq alngt. |
FilterSAM(samfile, MISM, GAPS, RQ, fsam) Calculates the number of gaps / mistmatches from an HTSeq alngt. |
readHeader(samfile) Function to retrieve the header from a SAM file. |
filter() Function for filtering a given sam file. |

Variables | [hide private]
| counter1 = `0`
| counter2 = `0`
| __package__ = `None`

Function Details | [hide private]

### writeFilteredReads(iddic, fastqfile, fastqfileoutput) |
Reads a .fastqfile and filters them for certain quality values. If an alignment is equally good or better as the threshold it will be written to the filtered .SAM file. input: fastq file output: fastq dictionary key = readid; value = qualstr Parameters: `iddic` (dictionary) - dictionary containing read ids. `fastqfile` (fastq) - HTSeq readfile object `fastqfileoutput` (fastq) - HTSeq readfile object. Alignments that pass the filter are written to this file.

### getMisGapRQ(alngt) |
Calculates the number of gaps / mistmatches from an HTSeq alngt. object. Parameters: `alngt` (HTSeq alignment object) - Initial SAM file for filtering `gaps`, `mism` - Number of gaps / mistmatches. `gaps,mism` (integer)

### FilterSAM(samfile, MISM, GAPS, RQ, fsam) |
Calculates the number of gaps / mistmatches from an HTSeq alngt. object. Parameters: `alngt` (HTSeq alignment object) - Initial SAM file for filtering `gaps`, `mism` - Number of gaps / mistmatches. `gaps,mism` (integer)

### filter() |
Function for filtering a given sam file. The alignments are evaluated individually in regard to RQS,mismatches and gaps. The input needs to be sorted.