Latest version processed -w options as -i options

[hepcat72]

featureProximity.pl -i Caulobacter_spp.basil.filtered.vcf.ins_coords.tab -f Caulobacter_segnis_strain_ATCC_21756.gff3 -c 4 -a 1 -b 5 -j 4 -e 6 -k 5 -o .annot -l -g -v -w '4 5 7 9'

The above generates these errors:

ERROR1:featureProximity.pl: Unable to open input file: [4].  No such file or directory
WARNING12541:featureProximity.pl: Only 1 output handle can be selected at a time.
                                  Supply --extended for additional details.
ERROR2:featureProximity.pl: Unable to open input file: [5].  No such file or directory
WARNING12542:featureProximity.pl: Only 1 output handle can be selected at a time.
                                  Supply --extended for additional details.
ERROR3:featureProximity.pl: Unable to open input file: [7].  No such file or directory
WARNING12543:featureProximity.pl: Only 1 output handle can be selected at a time.
                                  Supply --extended for additional details.
ERROR4:featureProximity.pl: Unable to open input file: [9].  No such file or directory

It was also producing output files: 4.annot 5.annot 7.annot and 9.annot. These are all the values supplied to the -w flag (4 5 7 9).

Not sure why that's happening. I recently swapped out the template with the CommandLineInterface module. I suspect there must be something going on with that. The CLI version installed at the time was 4.135.

[hepcat72]

I created a 'tmp' directory in the repo and copied files there to run this test command:

gen-rl-imac[2019-03-29 16:40:40]:~/pub/featureProximity/tmp>../src/featureProximity.pl -i Caulobacter_crescentus_strain_CB15.basil.filtered.vcf.ins_coords.tab -f CB15_reference.gff3 -c 4 -a 1 -b 5 -j 4 -e 6 -k 5 -o .annot -l -g -v -w '4 5 7 9' --verbose --outdir . --overwrite
[CB15_reference.gff3] Opened input file.
WARNING1: Skipping redundant feature found in feature file: [CB15_reference.gff3]: [NC_002696.2:160-1107].
WARNING2: Skipping redundant feature found in feature file: [CB15_reference.gff3]: [NC_002696.2:1104-1703].
WARNING3: Skipping redundant feature found in feature file: [CB15_reference.gff3]: [NC_002696.2:1700-2557].
WARNING4: Skipping redundant feature found in feature file: [CB15_reference.gff3]: [NC_002696.2:2490-3158].
WARNING5: Skipping redundant feature found in feature file: [CB15_reference.gff3]: [NC_002696.2:3190-3903].
WARNING5: NOTE: Further warnings of this type will be suppressed.
WARNING5: Set --error-limit to 0 to turn off error suppression
[CB15_reference.gff3] Input file done.  Time taken: [1 Seconds].
[./Caulobacter_crescentus_strain_CB15.basil.filtered.vcf.ins_coords.tab.annot] Opened output file.
[Caulobacter_crescentus_strain_CB15.basil.filtered.vcf.ins_coords.tab] Opened input file.
[Caulobacter_crescentus_strain_CB15.basil.filtered.vcf.ins_coords.tab] Input file done.  Time taken: [0 Seconds].
WARNING3853: These sequence IDs in the feature file [CB15_reference.gff3] were not found in the data file [Caulobacter_crescentus_strain_CB15.basil.filtered.vcf.ins_coords.tab]: [NC_002696.2].
[./Caulobacter_crescentus_strain_CB15.basil.filtered.vcf.ins_coords.tab.annot] Output file done.  Time taken: [0 Seconds].
[./4.annot] Opened output file.
ERROR1: Unable to open input file: [4].  No such file or directory
WARNING3854: Only 1 output handle can be selected at a time.
             Supply --extended for additional details.
[./5.annot] Opened output file.
ERROR2: Unable to open input file: [5].  No such file or directory
WARNING3855: Only 1 output handle can be selected at a time.
             Supply --extended for additional details.
[./7.annot] Opened output file.
ERROR3: Unable to open input file: [7].  No such file or directory
WARNING3856: Only 1 output handle can be selected at a time.
             Supply --extended for additional details.
[./9.annot] Opened output file.
ERROR4: Unable to open input file: [9].  No such file or directory

Done.  STATUS: [EXIT-CODE: 0 ERRORS: 4 WARNINGS: 3856 TIME: 1s] SUMMARY:
	4 ERRORS LIKE: [ERROR1: Unable to open input file: [4].  No such file or directory]
	3852 WARNINGS LIKE: [WARNING1: Skipping redundant feature found in feature file: [CB15_reference.gff3]: [NC_002696.2:160-...]
	1 WARNING LIKE: [WARNING3853: These sequence IDs in the feature file [CB15_reference.gff3] were not found in the data...]
	3 WARNINGS LIKE: [WARNING3854: Only 1 output handle can be selected at a time. Supply --extended for additional detail...]
	Scroll up to inspect full errors/warnings in-place.

[hepcat72]

OK. This is definitely an issue created by a later version of CommandLineInterface. If I use the version that comes with this repo, I get errors/warnings, but not the ones in question:

gen-rl-imac[2019-03-29 16:41:15]:~/pub/featureProximity/tmp>perl -I ../lib ../src/featureProximity.pl -i Caulobacter_crescentus_strain_CB15.basil.filtered.vcf.ins_coords.tab -f CB15_reference.gff3 -c 4 -a 1 -b 5 -j 4 -e 6 -k 5 -o .annot -l -g -v -w '4 5 7 9' --verbose --outdir . --overwrite
...
ERROR10: Unrecognized hash key(s) encountered in parameters passed to addArrayOption: [DELIMITER].
WARNING1: The --overwrite flag will not empty or delete existing output directories.  If you wish to delete existing output directories, you must do it manually.
[CB15_reference.gff3] Opened input file.
WARNING2: Skipping redundant feature found in feature file: [CB15_reference.gff3]: [NC_002696.2:160-1107].
WARNING3: Skipping redundant feature found in feature file: [CB15_reference.gff3]: [NC_002696.2:1104-1703].
WARNING4: Skipping redundant feature found in feature file: [CB15_reference.gff3]: [NC_002696.2:1700-2557].
WARNING5: Skipping redundant feature found in feature file: [CB15_reference.gff3]: [NC_002696.2:2490-3158].
WARNING6: Skipping redundant feature found in feature file: [CB15_reference.gff3]: [NC_002696.2:3190-3903].
WARNING6: NOTE: Further warnings of this type will be suppressed.
WARNING6: Set --error-type-limit to 0 to turn off error suppression
Negative repeat count does nothing at ../lib/CommandLineInterface.pm line 7226.
...
Negative repeat count does nothing at ../lib/CommandLineInterface.pm line 7238.
[CB15_reference.gff3] Input file done.  Time taken: [1 Seconds].
[./Caulobacter_crescentus_strain_CB15.basil.filtered.vcf.ins_coords.tab.annot] Opened output file.
WARNING3930: Runtime warning: [Use of uninitialized value in concatenation (.) or string at ../lib/CommandLineInterface.pm line 10561.].
[Caulobacter_crescentus_strain_CB15.basil.filtered.vcf.ins_coords.tab] Opened input file.
[Caulobacter_crescentus_strain_CB15.basil.filtered.vcf.ins_coords.tab] Input file done.  Time taken: [0 Seconds].
WARNING3931: These sequence IDs in the feature file [CB15_reference.gff3] were not found in the data file [Caulobacter_crescentus_strain_CB15.basil.filtered.vcf.ins_coords.tab]: [NC_002696.2].
[./Caulobacter_crescentus_strain_CB15.basil.filtered.vcf.ins_coords.tab.annot] Output file done.  Time taken: [0 Seconds].

Done.  STATUS: [EXIT-CODE: 0 ERRORS: 10 WARNINGS: 3931 TIME: 1s] SUMMARY:
	1 ERROR LIKE: [ERROR1: Unrecognized hash key(s) encountered in parameters passed to addArrayOption: [DELIMITER].]
...
	1 ERROR LIKE: [ERROR10: Unrecognized hash key(s) encountered in parameters passed to addArrayOption: [DELIMITER].]
	1 WARNING LIKE: [WARNING1: The --overwrite flag will not empty or delete existing output directories.  If you wish to...]
	3928 WARNINGS LIKE: [WARNING2: Skipping redundant feature found in feature file: [CB15_reference.gff3]: [NC_002696.2:160-...]
	1 WARNING LIKE: [WARNING3930: Runtime warning: [Use of uninitialized value in concatenation (.) or string at ../lib/C...]
	1 WARNING LIKE: [WARNING3931: These sequence IDs in the feature file [CB15_reference.gff3] were not found in the data...]
	Scroll up to inspect full errors/warnings in-place.

The "Negative repeat count" error is a perl version thing that is a separate issue which I think has been resolved elsewhere. The "uninitialized value" warning is something I've fixed in the latest CLI. The complaint about the "DELIMITER" hash key is an addition I made for CLI 4.135 that doesn't exist yet in the CLI that comes with this script. It's version is:

perl -I../lib -e 'use CommandLineInterface;print("$CommandLineInterface::VERSION\n")'
4.107

So it looks like this issue is specific to CLI 4.135. Let me see if the latest stable version of CLI fixes this...