mhh-rcug / heatmaps Goto Github PK

Create heatmaps/correlation heatmaps and dendrograms generated from csv
files that are generated from wochenende pipeline. Those files should be filtered, sorted and be into a csv format as the above.

Example: MCF01_S7_R1.ndp.lc.trm.s.mq30.01mm.dup.calmd.bam.txt.filt.sort.csv

20+ bam.txt

Hi Konstantinos, could you please include documentation on packages and versions needed (that can be added to the wochenende env -already has numpy, matplotlib, pandas) to run heatmap script.
ex. seaborn package, scipy.cluster etc

https://github.com/MHH-RCUG/Heatmaps/tree/master/eg1_sepsis_minion

I added a very limited public sample, but this needs a lot more data to make sense. I'll look for others next week

Hi,

I have tried to run some test and had a lot of trouble with the huge amount of memory that is needed.

@konnosif which settings do you use?

Maybe we could think about making the settings with the least memory usage default and add a comment that other settings take a lot of memory

Hi @konnosif

probably due to data but these commands all throw an error with the sample data :

 1883  python3 heat5.py --batch_files eg1_sepsis_minion/sample.txt --filter_sTF 0 --filter_sStart 0 --filter_sEnd 4 --suffix_label A --genus 1 --corr 0
 1884  python3 heat5.py --batch_files eg1_sepsis_minion/sample.txt --filter_sTF 0 --filter_sStart 0 --filter_sEnd 4 --suffix_label A --genus 0 --corr 0
 1885  python3 heat5.py --batch_files eg1_sepsis_minion/sample.txt --filter_sTF 0 --filter_sStart 0 --filter_sEnd 4 --genus 0 --corr 0
 1886  python3 heat5.py --batch_files eg1_sepsis_minion/sample.txt


Error 

python3 heat5.py --batch_files eg1_sepsis_minion/sample.txt
####Current directory is : /mnt/ngsnfs/tools/dev/Heatmaps
####Current file.txt with filenames to open is:eg1_sepsis_minion/sample.txt
Traceback (most recent call last):
  File "heat5.py", line 189, in <module>
    left3=left2.split("_")[0]+"_"+left2.split("_")[1]+"_"+left2.split("_")[2]
IndexError: list index out of range

I learned this trick very recently to avoid malformed csvs on the command line (yay, avoid xlsx and libreoffice).

• Add this to your .bashrc or globalenv

# Functions

#view csv nicely
function pcsv {
    column -t -s, -n "$@" | less -F -S -X -K
}

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• view file
  pcsv some.csv