Slight Error in Pathway Tools input (ptools) in organism-params.dat file

[hallamlab]

/ptools/ input has a slight problem causing the following error in the standard output when creating PGDBs. Here's an example:

Issuing Command : /Users/nielsh/pathway-tools/pathway-tools -patho output/NapDC//NapDC_454/ptools// -no-taxonomic-pruning  -no-web-cel-overview

18. Create PGDB  ......... Error!
;; Optimization settings: safety 1, space 1, speed 3, debug 1.
;; For a complete description of all compiler switches given the
;; current optimization settings evaluate (EXPLAIN-COMPILER-SETTINGS).

*** This Pathway Tools executable built on Fri Mar 30, 2012 at 14:24:35. ***
[Scanning PGDB directories   /Users/nielsh/ptools-local/pgdbs/user/
                             /Users/nielsh/ptools-local/pgdbs/registry/
                             /Users/nielsh/pathway-tools/aic-export/pgdbs/biocyc/   8 PGDBs found]
[Opened acache database /Users/nielsh/pathway-tools/aic-export/pathway-tools/ocelot-acache/, which contains 1 ocelot KBs]

[Processed 3 data rows from file /Users/nielsh/ptools-local/ptools-init.dat]
[Reading existing Pathway Tools init file: "/Users/nielsh/ptools-local/ptools-init.dat" ]
[Start downloading patches... 
If any patches are being installed, they are listed in the terminal window.
Looking for patches in
  http://bioinformatics.ai.sri.com/ptools/16.0/MacOSX/patches/
No patches need to be installed.
... done downloading patches]
[Redirecting standard-output and error-output to output/NapDC/NapDC_454/ptools/pathologic.log]

batch-pathologic: A fatal error occurred for output/NapDC/NapDC_454/ptools/ version 1.0.
See pathologic log file output/NapDC/NapDC_454/ptools/pathologic.log for more details.
sys:libgd.2.0.0.macosx-64.bundle: No such file or directory
sys:libX11.6.dylib: No such file or directory
sys:libXt.6.dylib: No such file or directory
sys:libXm.4.dylib: No such file or directory
Error! : ;; Optimization settings: safety 1, space 1, speed 3, debug 1.
;; For a complete description of all compiler switches given the
;; current optimization settings evaluate (EXPLAIN-COMPILER-SETTINGS).

*** This Pathway Tools executable built on Fri Mar 30, 2012 at 14:24:35. ***
[Scanning PGDB directories   /Users/nielsh/ptools-local/pgdbs/user/
                             /Users/nielsh/ptools-local/pgdbs/registry/
                             /Users/nielsh/pathway-tools/aic-export/pgdbs/biocyc/   8 PGDBs found]
[Opened acache database /Users/nielsh/pathway-tools/aic-export/pathway-tools/ocelot-acache/, which contains 1 ocelot KBs]

[Processed 3 data rows from file /Users/nielsh/ptools-local/ptools-init.dat]
[Reading existing Pathway Tools init file: "/Users/nielsh/ptools-local/ptools-init.dat" ]
[Start downloading patches... 
If any patches are being installed, they are listed in the terminal window.
Looking for patches in
  http://bioinformatics.ai.sri.com/ptools/16.0/MacOSX/patches/
No patches need to be installed.
... done downloading patches]
[Redirecting standard-output and error-output to output/NapDC/NapDC_454/ptools/pathologic.log]

batch-pathologic: A fatal error occurred for output/NapDC/NapDC_454/ptools/ version 1.0.
See pathologic log file output/NapDC/NapDC_454/ptools/pathologic.log for more details.
sys:libgd.2.0.0.macosx-64.bundle: No such file or directory
sys:libX11.6.dylib: No such file or directory
sys:libXt.6.dylib: No such file or directory
sys:libXm.4.dylib: No such file or directory
False False

Looking at the pathologic.log file we see that there is some problem parsing the input file:

more pathologic.log
15-Jan-2013  14:55:21 
Started processing output/NapDC/NapDC_454/ptools/
15-Jan-2013  14:55:21 Fatal error: NIL fell through a ECASE form.  The valid cases were :ORACLE, :MYSQL, :ACACHE, and :FILE.
Evaluation stack:

 ->(SYS::..RUNTIME-OPERATION "applyn" :UNKNOWN-ARGS)
   (TPL:DO-COMMAND "zoom" . #<non-lisp object @ #x7>)

Now looking at the organism-params.dat file we see that the STORAGE file is malformed with an extra name of the sample.annot.gff:

more organism-params.dat
ID      NapDC_454.annot.gff
STORAGE FILE    NapDC_454.annot.gff
NAME    NapDC_454.annot.gff
ABBREV-NAME     NapDC_454.annot.gff
STRAIN  1
RANK    |species|
NCBI-TAXON-ID   12908

Also I don't think it is required to have the extra annot.gff appended. So this issue is two changes to the generation of the organism-params.dat file:

1. remove the extra name from the STORAGE line
2. remove the .annot.gff text appended to the sample name

[hallamlab]

Added few regular expressions to clear up filename and format of organism-params.dat See: libs/python_scripts/MetaPathways_create_genbank_ptinput_sequin.py