Daniel:Notebook/Haplotyping/SISSORPipeline/2014-12-3: Difference between revisions
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>Djacobse (Created page with "=Segmentation Analysis Pipeline (Started 12/2/2014)= Back to Calendar ...") |
>Djacobse |
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This doesn't actually need reworking, but I'm having trouble running the command. | This doesn't actually need reworking, but I'm having trouble running the command. | ||
''' | '''Command''' | ||
python varbin.50k.sam.py pgp22_chamber1.BQSR.realigned.sam test.varbin50k.txt test.varbin50k.stats.txt | python varbin.50k.sam.py pgp22_chamber1.BQSR.realigned.sam test.varbin50k.txt test.varbin50k.stats.txt | ||
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ZeroDivisionError: float division by zero | ZeroDivisionError: float division by zero | ||
awk 'BEGIN {OFS = "\t"} $3 = "chr" $3' | I think the problem is the chromosomes in the script are named "chr1","chr2",etc., whereas the chromosomes in my file are named "1","2",etc. This is a common problem I have run in to, and should be addressed. This is an example command to append "chr" to the 3rd column (reference name column) of the output file. | ||
awk 'BEGIN {OFS = "\t"} $3 = "chr" $3' infile.sam > outfile.sam | |||
Repeating the first command now produces a viable result. | |||
===Step 2-Cutoff To Define Initial States=== |
Revision as of 22:32, 3 December 2014
Segmentation Analysis Pipeline (Started 12/2/2014)
Reworking the Analysis Pipeline
Looks like there are many steps to rework the pipeline. I'll start at the beginning.
Step 1-Python Script
This doesn't actually need reworking, but I'm having trouble running the command.
Command
python varbin.50k.sam.py pgp22_chamber1.BQSR.realigned.sam test.varbin50k.txt test.varbin50k.stats.txt
Result
Traceback (most recent call last): File "varbin.50k.sam.py", line 129, in <module> main() File "varbin.50k.sam.py", line 71, in main thisRatio = float(binCounts[i]) / (float(counter) / float(len(bins))) ZeroDivisionError: float division by zero
I think the problem is the chromosomes in the script are named "chr1","chr2",etc., whereas the chromosomes in my file are named "1","2",etc. This is a common problem I have run in to, and should be addressed. This is an example command to append "chr" to the 3rd column (reference name column) of the output file.
awk 'BEGIN {OFS = "\t"} $3 = "chr" $3' infile.sam > outfile.sam
Repeating the first command now produces a viable result.