Scripts and what they eat
I will be recording my workflow-walkthrough on khmer here. I will be walking through the following tutorials in order:
- 2013 MSU Assembly Workshop
- Eel-pond Tutorial
- Kalamazoo Metagenome Tutorial
For each, I will go step-by-step, pick up the python scripts used and follow their dependencies until I reach the core logic. For each interface, I will list the input parameters it takes and my proposed error handling messages.
split-pe.py 1 inPrm, accepts and adds '.1' and '.2' to the value, no error checking right now, Need to handle: No input file )maybe nest reading in a try-except block?
interleave.py 2 inPrms, error handling + argparse implemented, moving on!
strip-and-split-for-assembly.py 1 mandatory inPrm, 1 optional outPrm, no error checking done for inPrm, basic file existence check needed.
assemstats3.py No of args check done, first arg int check done, file existence check on sys.argv[2:] advisable
No new scripts
No khmer scripts involved
interleave-reads.py extract-paired-reads.py
normalize-by-median.py filter-abund.py
split-paired-reads.py
No khmer scripts involved
do-partition.py
No new khmer scripts used
readstats.py
extract-partitions.py sweep-reads3.py
extract-long-sequences.py
make-coverage.py