mhh-rcug / heatmaps Goto Github PK

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

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

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 @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

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 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