Bugfix/gaas maker merge outputs from datastore

[nylander]

The following warning messages where observed:

$ ~/git/NBIS/GAAS/annotation/tools/maker/gaas_maker_merge_outputs_from_datastore.pl \
   -i genome.maker.output_mixabinitio_abinitio_pacbio/ \
   -o genome.maker.output_mixabinitio_abinitio_pacbio_output_processed

[...]
Now save a copy of the Maker option files ...
Copy failed: No such file or directory genome.maker.output_mixabinitio_abinitio_pacbio_output_processed/maker_opts.ctl
Copy failed: No such file or directory genome.maker.output_mixabinitio_abinitio_pacbio_output_processed/maker_exe.ctl
Copy failed: No such file or directory genome.maker.output_mixabinitio_abinitio_pacbio_output_processed/maker_evm.ctl
Copy failed: No such file or directory genome.maker.output_mixabinitio_abinitio_pacbio_output_processed/maker_bopts.ctl

Now protecting the maker_annotation.gff annotation by making it readable only...

Now performing the statistics of the annotation file genome.maker.output_mixabinitio_abinitio_pacbio_output_processed/maker_ann
otation.gff...
WARNING get_longest_cds_level2: NO exon or cds to select the longest l2 for evm-000115f-processed-gene-1.0 l1 ! We will take on
e randomly ! @

There are possibly two kinds of errors observed here. First is the failure of copying control files.

The second is the warning from get_longest_cds_level2. This have not yet been addressed.

One issue related to the error with paths and folders is that the script
searches for output folders from Maker ending in maker.output (line #59), but the case I
was given have folders ending in something else.

Suggested changes

1. Change the regex to allow maker.output in the folder name (see also nr 3. below)

2. Add another option, -c or --ctlfolder, where the folder (or path) to the
   location of the Maker control files are located. The default value is the
   current working directory -- just as the current behaviour -- so no need to
   change a workflow. The logic here is that the current working directory
   may have several Maker output folders, and the same control files may, or
   may not, be applicable to all of them (an assumption from my side). A user
   may now, with the extra option -c, specify exactly where the control files
   are located, and to which Maker input and output folders they should be
   associated with (using the -i and -o options).

3. The routine for searching for Maker output files is now changed, where we
   now search for any folder with the string maker.output, but excluding
   those with the string processed. One complication is that the script does
   not halt if existing output folders are present (in case it would have been
   simpler to handle), but does continue. And since there is an --output option
   where the user can specify any name, the filtering on processed may not be
   sufficient. One may need to use other indicators to test if an older output
   folder is present, perhaps look for specific output files?

4. Multiple changes where made regarding code formatting. I tried to be consistent.

[Juke34]

Sounds good.

[nylander]

@Juke34
Jaques! Should I go through with this PR or do you have more to add (I'm thinking of your comment on #46)?

[Juke34]

Go ahead you can merge the PR