[1] "------> start of PWY TABLE COLLATION <------"
[1] "------> docopt settings ------"
[1] "Usage: my_program.R [options] \n --help              show this screen\n --binDIR PATH       hard path to bin dir [default: 'wdir/TEDreadsTAX/bin']\n --sccList NAME      hard path and name of file listing successful sample names [default: 'SccList.txt']\n --outdir NAME       path to & name of output directory to create [default: 'wdir/TEDreadsTAX/merged_tables']\n --genesDIR PATH     hard path to bin dir for KO or EC genes [default: 'wdir/PWYprofiles/keggPWY/genebin']"
Usage: my_program.R [options] 
 --help              show this screen
 --binDIR PATH       hard path to bin dir [default: 'wdir/TEDreadsTAX/bin']
 --sccList NAME      hard path and name of file listing successful sample names [default: 'SccList.txt']
 --outdir NAME       path to & name of output directory to create [default: 'wdir/TEDreadsTAX/merged_tables']
 --genesDIR PATH     hard path to bin dir for KO or EC genes [default: 'wdir/PWYprofiles/keggPWY/genebin']List of 10
 $ --help    : logi FALSE
 $ --binDIR  : chr "/outputs/PWYprofiles/keggPWYs.MP/pwybin/"
 $ --sccList : chr "/outputs/PWYprofiles/keggPWYs.MP/SccList.txt"
 $ --outdir  : chr "/outputs/PWYprofiles/keggPWYs.MP/merged_tables/"
 $ --genesDIR: chr "/outputs/PWYprofiles/keggPWYs.MP/genebin/"
 $ help      : logi FALSE
 $ binDIR    : chr "/outputs/PWYprofiles/keggPWYs.MP/pwybin/"
 $ sccList   : chr "/outputs/PWYprofiles/keggPWYs.MP/SccList.txt"
 $ outdir    : chr "/outputs/PWYprofiles/keggPWYs.MP/merged_tables/"
 $ genesDIR  : chr "/outputs/PWYprofiles/keggPWYs.MP/genebin/"
NULL
[1] "------> naming input files:"
                                                      SRR12904817 
"/outputs/PWYprofiles/keggPWYs.MP/pwybin//SRR12904817_4krona.txt" 
                                                      SRR12904818 
"/outputs/PWYprofiles/keggPWYs.MP/pwybin//SRR12904818_4krona.txt" 
                                                      SRR12904821 
"/outputs/PWYprofiles/keggPWYs.MP/pwybin//SRR12904821_4krona.txt" 
[1] "------> load data from files"
[1] "------> merging PWY data"
[1] "------> exporting PWY data at: /outputs/PWYprofiles/keggPWYs.MP/merged_tables/"
[1] "------> Starting work on genes files:"
[1] "------> load GENE data from gene files"
[1] "------> merging genedata, setting names to samples, replacing NAs with 0s, and removing rowSum==0s"
[1] "------> exporting GENE data"
