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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,51 +1,106 @@ | ||
| # This file holds some global variables for some of the input options. | ||
| # Global variables are exclusively read only -- they are not modified anywhere else in the code except when reading the input options. | ||
|
|
||
| import timeit, lib.refcore as RC | ||
| import timeit, sys, lib.refcore as RC | ||
|
|
||
| def init(): | ||
| globs = { | ||
| 'version' : '1.1.2', | ||
| 'releasedate' : 'September 27, 2019', | ||
| 'version' : '1.2', | ||
| 'releasedate' : 'August 08, 2020', | ||
| 'doi' : 'https://doi.org/10.1093/gbe/evz088', | ||
| 'http' : 'https://gwct.github.io/referee/', | ||
| 'github' : 'https://github.com/gwct/referee/issues', | ||
| 'starttime' : timeit.default_timer(), | ||
| 'startdatetime' : RC.getOutTime(), | ||
| 'infile' : "", | ||
| 'intype' : "", | ||
| 'out' : "", | ||
| 'outdir' : "", | ||
| 'reffile' : "", | ||
| 'ref' : "", | ||
| # Meta info | ||
|
|
||
| 'pyver' : ".".join(map(str, sys.version_info[:3])), | ||
| # System info | ||
|
|
||
| 'call' : "", | ||
| # Script call info | ||
|
|
||
| 'in-file' : "", | ||
| 'in-type' : "", | ||
| 'ref-file' : "", | ||
| 'ref-index' : False, | ||
| 'num-procs' : 1, | ||
| 'fastq' : False, | ||
| 'fastq-len' : 100, | ||
| 'bed' : False, | ||
| 'beddir' : False, | ||
| 'lines-per-proc' : 100000, | ||
| 'chunk-size' : "NA", | ||
| # Input locations | ||
|
|
||
| 'pileup-opt' : False, | ||
| 'haploid-opt' : False, | ||
| 'mapq-opt' : False, | ||
| 'reader' : open, | ||
| "read-mode" : "r", | ||
| 'lread' : RC.readLine, | ||
| # Input options | ||
|
|
||
| 'out-prefix' : "", | ||
| 'out-dir' : "", | ||
| 'out-tab' : "", | ||
| 'out-fq' : "", | ||
| 'bed-dir' : "", | ||
| # Output locations | ||
|
|
||
| 'fastq-opt' : False, | ||
|
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| 'bed-opt' : False, | ||
| 'correct-opt' : False, | ||
| 'raw-opt' : False, | ||
| 'log-v' : 1, | ||
| 'mapped' : False, | ||
| 'stats' : True, | ||
| 'allcalc' : False, | ||
| 'pileup' : False, | ||
| 'haploid' : False, | ||
| 'mapq' : False, | ||
| 'mapped-only-opt' : False, | ||
| 'allcalc-opt' : False, | ||
| # Output options | ||
|
|
||
| 'ref' : "", | ||
| 'scaff-lens' : {}, | ||
| 'genotypes' : ["AA", "AC", "AG", "AT", "CC", "CG", "CT", "GG", "GT", "TT"], | ||
| 'haploid-gt' : ["A","T","C","G"], | ||
|
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||
| 'cur-fastq-seq' : "", | ||
| 'cur-fastq-scores' : "", | ||
| 'cur-fastq-len' : 0, | ||
| 'fastq-line-len' : 100, | ||
| # Seq info | ||
|
|
||
| 'bed-template' : { | ||
| 'out' : '', 'scaff' : '', 'scaff-start' : 0, 'scaff-len' : '', | ||
| 'bins' : | ||
| { | ||
| 1 : { 'name' : '<=0', 'rgb' : "165,0,38", 'num-chunks' : 1, 'chunk-sizes' : ["0"], 'chunk-starts' : ["0"], 'last-pos' : 0, 'first-pos' : 0, 'shade' : 1000 }, | ||
| 2 : { 'name' : '1-10', 'rgb' : "221,61,45", 'num-chunks' : 1, 'chunk-sizes' : ["0"], 'chunk-starts' : ["0"], 'last-pos' : 0, 'first-pos' : 0, 'shade' : 900 }, | ||
| 3 : { 'name' : '11-20', 'rgb' : "246,126,75", 'num-chunks' : 1, 'chunk-sizes' : ["0"], 'chunk-starts' : ["0"], 'last-pos' : 0, 'first-pos' : 0, 'shade' : 800 }, | ||
| 4 : { 'name' : '21-30', 'rgb' : "253,179,102", 'num-chunks' : 1, 'chunk-sizes' : ["0"], 'chunk-starts' : ["0"], 'last-pos' : 0, 'first-pos' : 0, 'shade' : 700 }, | ||
| 5 : { 'name' : '31-40', 'rgb' : "254,218,139", 'num-chunks' : 1, 'chunk-sizes' : ["0"], 'chunk-starts' : ["0"], 'last-pos' : 0, 'first-pos' : 0, 'shade' : 600 }, | ||
| 6 : { 'name' : '41-50', 'rgb' : "194,228,239", 'num-chunks' : 1, 'chunk-sizes' : ["0"], 'chunk-starts' : ["0"], 'last-pos' : 0, 'first-pos' : 0, 'shade' : 500 }, | ||
| 7 : { 'name' : '51-60', 'rgb' : "152,202,225", 'num-chunks' : 1, 'chunk-sizes' : ["0"], 'chunk-starts' : ["0"], 'last-pos' : 0, 'first-pos' : 0, 'shade' : 400 }, | ||
| 8 : { 'name' : '61-70', 'rgb' : "110,166,205", 'num-chunks' : 1, 'chunk-sizes' : ["0"], 'chunk-starts' : ["0"], 'last-pos' : 0, 'first-pos' : 0, 'shade' : 300 }, | ||
| 9 : { 'name' : '71-80', 'rgb' : "74,123,183", 'num-chunks' : 1, 'chunk-sizes' : ["0"], 'chunk-starts' : ["0"], 'last-pos' : 0, 'first-pos' : 0, 'shade' : 200 }, | ||
| 10 : { 'name' : '81+', 'rgb' : "54,75,154", 'num-chunks' : 1, 'chunk-sizes' : ["0"], 'chunk-starts' : ["0"], 'last-pos' : 0, 'first-pos' : 0, 'shade' : 100 } | ||
| }, | ||
| 'chunk-start' : 0, 'last-bin' : False, 'cur-bin' : "" | ||
| }, | ||
| 'cur-bed' : "", | ||
| # Bed info | ||
| # https://genome.ucsc.edu/FAQ/FAQformat.html#format1https://genome.ucsc.edu/FAQ/FAQformat.html#format1 | ||
|
|
||
| 'endprog' : False, | ||
| 'quiet' : False, | ||
| 'progstarttime' : 0, | ||
| 'stepstarttime' : 0, | ||
| 'pids' : "", | ||
| 'method' : 1, | ||
| 'genotypes' : ["AA", "AC", "AG", "AT", "CC", "CG", "CT", "GG", "GT", "TT"], | ||
| 'haploid-gt' : ["A","T","C","G"], | ||
| 'psutil' : "", | ||
| 'probs' : "", | ||
| 'debug' : False, | ||
| 'nolog' : False, | ||
| 'maxsize' : 100000000000 | ||
| 'norun' : False, | ||
| 'exit-code' : 0 | ||
| # Internal stuff | ||
| } | ||
|
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| globs['logfilename'] = "referee-" + globs['startdatetime'] + ".log"; | ||
| globs['tmpdir'] = "referee-tmpdir-" + globs['startdatetime'] + "-" + RC.getRandStr(); | ||
| globs['logfilename'] = "referee-" + globs['startdatetime'] + ".errlog"; | ||
| # Temporary logfile for errors that occur before the log file optoins are parsed. | ||
|
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||
| return globs; |
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