IBD_Kmer_Analysis
Python Implementaion - Thanks Rob!
The python kmerbias should function the same as the perl kmerbias, both depend on the output from GetNucFrequency_PerSeq_varK.pl (GCF_000403175.4mers is an example output file)
python3 kmerbias.py -f GCF_000403175.4mers -k GGCC,GCGC -v > pyout
perl kmerbias.pl GCF_000403175.4mers "GGCC,GCGC" > plout
plout and pyout are not identical because of the floating point math, but they are close to several significant digits.
Perl Version
The code should be able to run the code like this:
perl GetNucFrequency_PerSeq_varK.pl ./GCF_000403175.fna 4 > GCF_000403175.4mers
and then you can count the bias:
perl kmerbias.pl GCF_000403175.4mers "GGCC,GGCG,GGGC"
The first output file is GCF_00403175.4mers
The second command should output:
| Matrix | NZ_KE159482.1 | NZ_KE159483.1 | NZ_KE159484.1 | NZ_KE159485.1 | NZ_KE159486.1 | NZ_KE159487.1 | NZ_KE159488.1 | NZ_KE159489.1 | NZ_KE159490.1 | NZ_KE159491.1 | NZ_KE159492.1 |
|---|---|---|---|---|---|---|---|---|---|---|---|
| GGCC | 0.72379167166026 | 0.564725231578111 | 1.06033886652903 | 0.700487472590855 | 0.722849965243236 | 0.744502198607545 | 0.718905768185197 | 0.627581109687921 | 0.638351277899619 | 0.907762632169645 | 0 |
| GGCG | 1.02371445359977 | 1.01361527445047 | 0.880629901562083 | 1.01214386205571 | 0.99189604408644 | 1.00392096757395 | 1.01391615871228 | 1.03649903331046 | 1.03819590211593 | 0.875969559120189 | 0.934879508443214 |
| GGGC | 1.09172008969991 | 1.11655103110103 | 0.956758304197849 | 1.10617995726091 | 1.08601140376983 | 1.09210234817395 | 1.10214747927039 | 1.15141594439126 | 1.21693684689459 | 1.09103255691336 | 1.22430819416776 |