Verify input file existence on all Python scripts

[RamRS]

a. Check for existence of command line arg values
b. Check that the value is indeed a file

(The above could be solved by using argparse, I think)

[mr-c]

@RamRS How so?

[RamRS]

@mr-c : This is applicable only to files that use sys.argv[]. We check if all required args were passed, and if any arg is a filename, we check os.path.isfile() so we know it is a file.

Or, we use argparse.

[mr-c]

Yep, all scripts should be using argparse

[RamRS]

All under scripts/ already use argparse + file_api. Only sandbox scripts need our attention.

[RamRS]

There are 124 files under sandbox that use sys.argv[]. I have a list if anyone wants it!

[RamRS]

Here's a list of all sandbox scripts mentioned in open issues:
`

1. calc-best-assembly.py (script to calculate best assembly from a list of contig/scaffold files #198)
2. make-coverage.py (script to calculate best assembly from a list of contig/scaffold files #198)
3. multi-rename.py (script to calculate best assembly from a list of contig/scaffold files #198)
4. remove-N.py (script to calculate best assembly from a list of contig/scaffold files #198)
5. sweep-reads3.py (move sweep-reads3.py and assemstats3.py into scripts/ #187)
6. assemtstats3.py (move sweep-reads3.py and assemstats3.py into scripts/ #187)
7. filter-below-abund.py (move sweep-reads3.py and assemstats3.py into scripts/ #187)
8. fastq-to-fasta.py (move sweep-reads3.py and assemstats3.py into scripts/ #187)
9. calc-median-distribution.py (updates to calc-median-distribution in sandbox/ #184)
10. ident.py (Prototype threaded writing interface and code for diginorm and filter-abund. #92)
11. identpair.py (Prototype threaded writing interface and code for diginorm and filter-abund. #92)
12. thread-rw.py (Prototype threaded writing interface and code for diginorm and filter-abund. #92)
    `

[RamRS]

And oh boy, so many results from https://github.com/ngs-docs/edda ! Link: https://github.com/ctb/edda/search?q=sandbox&type=Code

Note: Search is from under ctb/edda because github cannot search forked repos.

[RamRS]

sandbox scripts referenced in edda:
interleave.py strip-and-split-for-assembly.py assemstats3.py extract-long-sequences.py filter-below-abund.py extract-single-partition.py split-pe.py strip-partition.py multi-rename.py make-coverage.py readstats.py multi-velvet.py sweep-reads3.py

Next step: check these lists for scripts that use sys.argv[].

[mr-c]

Great list, have any of these already been migrated?

On Wed, Mar 5, 2014 at 1:00 PM, Ram RS notifications@github.com wrote:

sandbox scripts referenced in edda:

interleave.py
strip-and-split-for-assembly.py
assemstats3.py
extract-long-sequences.py
filter-below-abund.py
extract-single-partition.py
split-pe.py
strip-partition.py
multi-rename.py
make-coverage.py
readstats.py
multi-velvet.py
sweep-reads3.py

Next step: check these lists for scripts that use sys.argv[].

Reply to this email directly or view it on GitHubhttps://github.com//issues/147#issuecomment-36772673
.

[RamRS]

Not sure, @mr-c. My next step is to check this against my list of 120+
scripts (the one that has all current sandbox scripts that use sys.argv). I
guess this step would answer both our questions.

Ram

On Wed, Mar 5, 2014 at 1:03 PM, Michael R. Crusoe
notifications@github.comwrote:

Great list, have any of these already been migrated?

On Wed, Mar 5, 2014 at 1:00 PM, Ram RS notifications@github.com wrote:

sandbox scripts referenced in edda:

interleave.py
strip-and-split-for-assembly.py
assemstats3.py
extract-long-sequences.py
filter-below-abund.py
extract-single-partition.py
split-pe.py
strip-partition.py
multi-rename.py
make-coverage.py
readstats.py
multi-velvet.py
sweep-reads3.py

Next step: check these lists for scripts that use sys.argv[].

Reply to this email directly or view it on GitHub<
https://github.com/ged-lab/khmer/issues/147#issuecomment-36772673>

.

Reply to this email directly or view it on GitHubhttps://github.com//issues/147#issuecomment-36772900
.

[RamRS]

Surprisingly, none of the scripts from the two lists displayed above use sys.srgv[]. Also, no matches to any of the files under scripts/ as well.

[mr-c]

Okay, should we close this issue then?

[RamRS]

Sure, but should we wait until #270 is closed? There are a bunch of issues linked to it and we can close all of them at once.