coalispr.resources.constant¶

Module with constants.

Notes

This file constant.py is actually a link/shortcut to coalispr.resources.constant_out.constant_{EXP}.py, for EXP as defined in this file.

For notes on file naming and experiment descriptors in this file see howtoguides.html#Configuration in the documentation.

Attributes¶

`SHARED`
`EXPTXT`	Begin `constant_in/2_shared.txt` (CONFFOLDER / SHARED)
`p`
`PRGNAM`
`DESCRIPTION`
`DATASTOR`
`INFOREGS`
`INPUTRCS`
`LOGMAX`
`MPLDEBUG`
`NEGCTL`
`POSCTL`
`UNSPECIFIC`
`SPECIFIC`
`MUTANT`
`REFERENCE`
`METHOD`
`CONDITION`
`COLLAPSED`
`UNCOLLAPSED`
`UNSEL`
`DISCARD`
`FRACTION`
`INTR`
`FIGXLABEL`
`FIGYLABEL`
`TRACKLABEL`
`PERC`
`PLOTALL`
`PLOTSPEC`
`PLOTUNSP`
`PLOTLEN`
`PLOTINTRLEN`
`PLOTLIB`
`PLOTPERC`
`MEAN`
`PLOTMEAN`
`MEDIAN`
`PLOTMEDIAN`
`PLOTRAW`
`PLOTSTRT`
`PLOTFREQ`
`PLOTMMAP`
`NONCAPT`
`RCOL`
`UCOL`
`SCOL`
`MCOL`
`NCOL`
`DCOL`
`ACOL`
`AEC`
`ALC`
`METHCOL`
`AXCOL`
`AXCOL2`
`BCKGRCOL`
`FIGCOL`
`CKEY1`
`CKEY2`
`CKEY3`
`CKEY4`
`CVAL1`
`CVAL2`
`CVAL3`
`CVAL4`
`XGRID`
`ALPH`
`HIGHALPH`
`ANNOTALPH`
`HIGHLEG`
`LOWLEG`
`THISALPH`
`LINEW`
`HIGHLINEW`
`LEGNCOL`
`CSFONTSZ`
`SNSFNTSZ`
`SGFONTSZ`
`SGHEIGHT`
`SGWIDTH`
`TXTALIAS`
`GRIDSTYLE`
`CONTEXT`
`PALETTE`
`GRIDALPHA`
`GRIDCOLOR`
`GRIDAXIS`
`GRIDWHICH`
`GRID`
`SNSFNTFAM`
`LOGLIM`
`LINLIM`
`AXLIMS`
`FIGFORMAT`
`TAGCOLL`
`TAGUNCOLL`
`TSV`
`BAK`
`TMP`
`PNG`
`SVG`
`PDF`
`JPG`
`DPI`
`P2TDELIM`
`MULMAPCOLL`
`MULMAPUNCOLL`
`NH`
`HI`
`TSTREGIONS`
`REGS`
`TRSHLD`
`CIGFM`
`CIGPD`
`NM`
`MAXMM`
`TOTINPUT`
`SAMPLE`
`INMAPUNCOLL`
`UNMAP`
`INMAPCOLL`
`TOTALS`
`READCOUNTS`
`SHOWDISC`
`CORB`
`MUNR`
`COMBI`
`UNIQ`
`XTRA`
`ALL`
`COU`
`LIBR`
`COLLR`
`SKIP`
`LENCOUNTS`
`RLENCOUNTS`
`MULMAP`
`BCO`
`LOWR`
`UPPR`
`SPAN`
`SEGSUM`
`LEN`
`REPS`
`LENMER`
`REGI`
`BINN`
`BREG`
`CNTLABELS`
`CNTREAD`
`CNTCDNA`
`CNTGAP`
`CNTSKIP`
`LENREAD`
`LENCDNA`
`LENGAP`
`REGCNTRS`
`STOREPICKLE`
`SAVETSV`
`SAVEBAM`
`PKL2TSV`
`TSV2PKL`
`CLUSTVIS`
`CLUSTGR`
`COSEQ`
`STEM`
`PROPR`
`SRCNDIRLEVEL`
`HOME`
`CWD`
`SRCPRGNAM`
`NOCHOICE`
`CONFBASE`
`CONFFOLDER`
`LOGS`
`LOGFILNAM`
`DATA`
`DWNLDS`
`FIGS`
`SAVEPNG`
`SAVESVG`
`SAVEPDF`
`SAVEJPG`
`CHROMFIG`
`LENCNTS`
`LIBCNTS`
`REGCNTS`
`UNSELFIG`
`GROUPAVG`
`SUBFIGS`
`OUTPUTS`
`SOURCE`
`GTFS`
`FASTA`	End `constant_in/2_shared.txt` (CONFFOLDER / SHARED)
`EXP`
`CONFNAM`
`EXPNAM`
`EXPDISP`
`TAG`
`TAGSEG`
`TAGBAM`
`BINSTEP`
`UNSPECLOG10`
`UNSPECTST`
`LOG2BG`
`LOG2BGTST`
`USEGAPS`
`UNSPCGAPS`
`UGAPSTST`
`MIRNAPKBUF`
`CIGARCHK`
`NRMISM`
`MININTRON`
`CNTRS`
`LENCNTRS`
`MMAPCNTRS`
`BINS`
`BAMLOW`
`BAMHIGH`
`BAMPEAK`
`BAMSTART`
`BAM2BGNAM`
`BAM2BG`
`CHROMLBL`
`BACKEND`
`MINGAP`
`MAXGAP`
`INTSTEP`
`SKIPINT`
`XLIM0`
`XLIM1`
`XLIM00`
`XLIM11`
`XLIMMIN`
`XLIMMAX`
`XLIMR0`
`XLIMR1`
`CPPHFAC`
`LPPHFAC`
`MAXROW`
`SETBASE`
`MUTNO`
`SRCFLDR`
`REFS`
`BEDGRAPH`
`BAM`
`PLUS`
`MINUS`
`PLUSIN`
`MINUSIN`
`PL`
`MI`
`SAMBAM`
`UNMAPPEDFIL`
`UNMAPTYPE`
`UNMAPCOLLTP`
`EXPFILNAM`
`FILEKEY`
`SHORT`
`CATEGORY`
`EXPERIMENT`
`GROUP`
`READDENS`
`CAT_R`
`CAT_U`
`CAT_S`
`CAT_M`
`CAT_D`
`TOTAL`
`RIP1`
`RIP2`
`NOTAGIP`
`OTHR`
`REPAIR`
`STARV`
`DENSE`
`REST`
`WCE`
`NUCLEO`
`NUCL`
`CYTO`
`MITOCH`
`MEMBR`
`VACUOL`
`GRANUL`
`ENDRET`
`EXCELL`
`MUTGROUPS`
`CONDITIONS`
`METHODS`
`FRACTIONS`
`UNSPECIFICS`
`MUTANTS`
`LENGTHSNAM`
`DNAXTRNAM`
`LENXTRFILNAM`
`LENXTRA`
`CHRXTRA`
`GTFSPECNAM`
`GTFUNSPNAM`
`GTFREFNAM`
`GTFXTRANAM`
`GTFUNXTNAM`
`GTFEXON`
`GTFFEAT`
`BASEDIR`
`SAVEIN`
`CONFIG`
`LENGTHSFILE`
`DNAXTRA`
`LENXTRAFILE`
`EXPFILE`
`CONFPATH`
`CONFFILE`
`OUTPATH`
`STOREPATH`
`SRCDIR`
`REFDIR`
`REFNDIRLEVEL`
`GTFSPEC`
`GTFUNSP`
`GTFREF`
`GTFXTRA`
`GTFUNXTR`
`FIGDIRSVG`
`FIGDIRPNG`
`FIGDIRPDF`
`FIGDIRJPG`
`FIGDIR`
`LOGFIL`

Module Contents¶

coalispr.resources.constant.SHARED = '2_shared.txt'¶

coalispr.resources.constant.EXPTXT = '3_EXP.txt'¶: Begin constant_in/2_shared.txt (CONFFOLDER / SHARED)

coalispr.resources.constant.p¶

coalispr.resources.constant.PRGNAM = 'Coalispr'¶

coalispr.resources.constant.DESCRIPTION = 'COunt ALIgned SPecified Reads'¶

coalispr.resources.constant.DATASTOR = '`coalispr storedata -d {1,2} -t {1,2}`'¶

coalispr.resources.constant.INFOREGS = '`coalispr info -r1`'¶

coalispr.resources.constant.INPUTRCS = '`coalispr countbams -rc {1,2}`'¶

coalispr.resources.constant.LOGMAX = 10000000¶

coalispr.resources.constant.MPLDEBUG = False¶

coalispr.resources.constant.NEGCTL = 'Negative'¶

coalispr.resources.constant.POSCTL = 'Positive'¶

coalispr.resources.constant.UNSPECIFIC = 'Unspecific'¶

coalispr.resources.constant.SPECIFIC = 'Specific'¶

coalispr.resources.constant.MUTANT = 'Mutant'¶

coalispr.resources.constant.REFERENCE = 'Reference'¶

coalispr.resources.constant.METHOD = 'Method'¶

coalispr.resources.constant.CONDITION = 'Condition'¶

coalispr.resources.constant.COLLAPSED = 'Collapsed'¶

coalispr.resources.constant.UNCOLLAPSED = 'Uncollapsed'¶

coalispr.resources.constant.UNSEL = 'Unselected'¶

coalispr.resources.constant.DISCARD = 'Not used'¶

coalispr.resources.constant.FRACTION = 'Fraction'¶

coalispr.resources.constant.INTR = 'intron'¶

coalispr.resources.constant.FIGXLABEL = '{} position; scale 1:{} (bin size)'¶

coalispr.resources.constant.FIGYLABEL = 'Bedgraph values; summed/bin'¶

coalispr.resources.constant.TRACKLABEL = 'segm.'¶

coalispr.resources.constant.PERC = '%'¶

coalispr.resources.constant.PLOTALL = 'All reads'¶

coalispr.resources.constant.PLOTSPEC = 'Specific reads'¶

coalispr.resources.constant.PLOTUNSP = 'Unspecific, discarded reads'¶

coalispr.resources.constant.PLOTLEN = 'length (nt)'¶

coalispr.resources.constant.PLOTINTRLEN = 'intron length (nt)'¶

coalispr.resources.constant.PLOTLIB = 'Library counts'¶

coalispr.resources.constant.PLOTPERC = '% reads'¶

coalispr.resources.constant.MEAN = 'mean'¶

coalispr.resources.constant.PLOTMEAN¶

coalispr.resources.constant.MEDIAN = 'median'¶

coalispr.resources.constant.PLOTMEDIAN¶

coalispr.resources.constant.PLOTRAW = 'Raw counts'¶

coalispr.resources.constant.PLOTSTRT = "5' nt"¶

coalispr.resources.constant.PLOTFREQ = 'number of hits'¶

coalispr.resources.constant.PLOTMMAP = '% multimappers'¶

coalispr.resources.constant.NONCAPT = ['cDNA', 'gRNA', 'lncRNA', 'miRNA', 'mRNA', 'ncRNA', 'piRNA', 'rRNA', 'sRNA', 'siRNA', 'snRNA',...¶

coalispr.resources.constant.RCOL = 'xkcd:almost black'¶

coalispr.resources.constant.UCOL = 'xkcd:dull red'¶

coalispr.resources.constant.SCOL = 'xkcd:cornflower blue'¶

coalispr.resources.constant.MCOL = 'tab:olive'¶

coalispr.resources.constant.NCOL = 'xkcd:pale orange'¶

coalispr.resources.constant.DCOL = 'xkcd:pale magenta'¶

coalispr.resources.constant.ACOL = '#CAD9EF'¶

coalispr.resources.constant.AEC = 'xkcd:slate blue'¶

coalispr.resources.constant.ALC = 'xkcd:slate'¶

coalispr.resources.constant.METHCOL = 'xkcd:cloudy blue'¶

coalispr.resources.constant.AXCOL = 'xkcd:almost black'¶

coalispr.resources.constant.AXCOL2 = 'xkcd:light grey'¶

coalispr.resources.constant.BCKGRCOL = 'w'¶

coalispr.resources.constant.FIGCOL = '#f9f9f9'¶

coalispr.resources.constant.CKEY1 = 'fAGO1'¶

coalispr.resources.constant.CKEY2 = 'no_sRNA'¶

coalispr.resources.constant.CKEY3 = 'fAGO2'¶

coalispr.resources.constant.CKEY4 = 'total_sRNA'¶

coalispr.resources.constant.CVAL1 = '#c7b475'¶

coalispr.resources.constant.CVAL2 = '#8ec1d6'¶

coalispr.resources.constant.CVAL3 = '#597dbf'¶

coalispr.resources.constant.CVAL4 = '#797979'¶

coalispr.resources.constant.XGRID = True¶

coalispr.resources.constant.ALPH = 0.33¶

coalispr.resources.constant.HIGHALPH = 0.7¶

coalispr.resources.constant.ANNOTALPH = 0.9¶

coalispr.resources.constant.HIGHLEG = 0.8¶

coalispr.resources.constant.LOWLEG = 0.3¶

coalispr.resources.constant.THISALPH = 0.8¶

coalispr.resources.constant.LINEW = 1.5¶

coalispr.resources.constant.HIGHLINEW = 2.2¶

coalispr.resources.constant.LEGNCOL = 1¶

coalispr.resources.constant.CSFONTSZ = 12¶

coalispr.resources.constant.SNSFNTSZ = 8¶

coalispr.resources.constant.SGFONTSZ = 11¶

coalispr.resources.constant.SGHEIGHT = 9¶

coalispr.resources.constant.SGWIDTH = 12¶

coalispr.resources.constant.TXTALIAS = True¶

coalispr.resources.constant.GRIDSTYLE = 'whitegrid'¶

coalispr.resources.constant.CONTEXT = 'paper'¶

coalispr.resources.constant.PALETTE = 'muted'¶

coalispr.resources.constant.GRIDALPHA = 0.5¶

coalispr.resources.constant.GRIDCOLOR = 'xkcd:light grey'¶

coalispr.resources.constant.GRIDAXIS = 'y'¶

coalispr.resources.constant.GRIDWHICH = 'major'¶

coalispr.resources.constant.GRID = True¶

coalispr.resources.constant.SNSFNTFAM = 'sans-serif'¶

coalispr.resources.constant.LOGLIM = 20¶

coalispr.resources.constant.LINLIM = 20000¶

coalispr.resources.constant.AXLIMS¶

coalispr.resources.constant.FIGFORMAT = 'svg'¶

coalispr.resources.constant.TAGCOLL = 'collapsed'¶

coalispr.resources.constant.TAGUNCOLL = 'uncollapsed'¶

coalispr.resources.constant.TSV = '.tsv'¶

coalispr.resources.constant.BAK = '.bak'¶

coalispr.resources.constant.TMP = '.tmp'¶

coalispr.resources.constant.PNG = '.png'¶

coalispr.resources.constant.SVG = '.svg'¶

coalispr.resources.constant.PDF = '.pdf'¶

coalispr.resources.constant.JPG = '.jpg'¶

coalispr.resources.constant.DPI = 400¶

coalispr.resources.constant.P2TDELIM = '____'¶

coalispr.resources.constant.MULMAPCOLL = 1¶

coalispr.resources.constant.MULMAPUNCOLL = 1¶

coalispr.resources.constant.NH = 'NH'¶

coalispr.resources.constant.HI = 'HI'¶

coalispr.resources.constant.TSTREGIONS = 'collect'¶

coalispr.resources.constant.REGS = 'Regions'¶

coalispr.resources.constant.TRSHLD = 'Threshold'¶

coalispr.resources.constant.CIGFM = 'fullmatch'¶

coalispr.resources.constant.CIGPD = 'pointdel'¶

coalispr.resources.constant.NM = 'nM'¶

coalispr.resources.constant.MAXMM = 10¶

coalispr.resources.constant.TOTINPUT = 'input_totals'¶

coalispr.resources.constant.SAMPLE = 'Sample'¶

coalispr.resources.constant.INMAPUNCOLL = 'Mapped'¶

coalispr.resources.constant.UNMAP = 'Unmapped'¶

coalispr.resources.constant.INMAPCOLL = 'Mapped cDNA'¶

coalispr.resources.constant.TOTALS = 'totals'¶

coalispr.resources.constant.READCOUNTS = 'readcounts'¶

coalispr.resources.constant.SHOWDISC = 'withdiscards'¶

coalispr.resources.constant.CORB = 'corbett'¶

coalispr.resources.constant.MUNR = 'munro'¶

coalispr.resources.constant.COMBI = 'combined'¶

coalispr.resources.constant.UNIQ = 'uniq'¶

coalispr.resources.constant.XTRA = 'extra'¶

coalispr.resources.constant.ALL = 'all'¶

coalispr.resources.constant.COU = '_counts'¶

coalispr.resources.constant.LIBR = 'library'¶

coalispr.resources.constant.COLLR = 'cDNA'¶

coalispr.resources.constant.SKIP = 'skipped'¶

coalispr.resources.constant.LENCOUNTS = 'length_counts'¶

coalispr.resources.constant.RLENCOUNTS = 'readlength_counts'¶

coalispr.resources.constant.MULMAP = 'multimapper'¶

coalispr.resources.constant.BCO = '_bin_counts'¶

coalispr.resources.constant.LOWR = 'lower'¶

coalispr.resources.constant.UPPR = 'upper'¶

coalispr.resources.constant.SPAN = 'span'¶

coalispr.resources.constant.SEGSUM = 'segmentsum'¶

coalispr.resources.constant.LEN = 'length'¶

coalispr.resources.constant.REPS = 'repeats'¶

coalispr.resources.constant.LENMER = 'start length'¶

coalispr.resources.constant.REGI = 'region'¶

coalispr.resources.constant.BINN = 'bin no'¶

coalispr.resources.constant.BREG = 'bin-region'¶

coalispr.resources.constant.CNTLABELS¶

coalispr.resources.constant.CNTREAD¶

coalispr.resources.constant.CNTCDNA¶

coalispr.resources.constant.CNTGAP¶

coalispr.resources.constant.CNTSKIP¶

coalispr.resources.constant.LENREAD¶

coalispr.resources.constant.LENCDNA¶

coalispr.resources.constant.LENGAP¶

coalispr.resources.constant.REGCNTRS¶

coalispr.resources.constant.STOREPICKLE = 'pickled'¶

coalispr.resources.constant.SAVETSV = 'tsvfiles'¶

coalispr.resources.constant.SAVEBAM = 'bamfiles'¶

coalispr.resources.constant.PKL2TSV = 'backup_from_pickled'¶

coalispr.resources.constant.TSV2PKL = 'pickled_from_backup'¶

coalispr.resources.constant.CLUSTVIS = 'clustvis'¶

coalispr.resources.constant.CLUSTGR = 'clustgr'¶

coalispr.resources.constant.COSEQ = 'coseq'¶

coalispr.resources.constant.STEM = 'stem'¶

coalispr.resources.constant.PROPR = 'propr'¶

coalispr.resources.constant.SRCNDIRLEVEL = 2¶

coalispr.resources.constant.HOME = 'home'¶

coalispr.resources.constant.CWD = 'current'¶

coalispr.resources.constant.SRCPRGNAM = 'source'¶

coalispr.resources.constant.NOCHOICE = 'other; cancel'¶

coalispr.resources.constant.CONFBASE = 'config'¶

coalispr.resources.constant.CONFFOLDER = 'constant_in'¶

coalispr.resources.constant.LOGS = 'logs'¶

coalispr.resources.constant.LOGFILNAM = 'run-log.txt'¶

coalispr.resources.constant.DATA = 'data'¶

coalispr.resources.constant.DWNLDS = 'downloads'¶

coalispr.resources.constant.FIGS = 'figures'¶

coalispr.resources.constant.SAVEPNG = 'pngfigures'¶

coalispr.resources.constant.SAVESVG = 'svgfigures'¶

coalispr.resources.constant.SAVEPDF = 'pdfs'¶

coalispr.resources.constant.SAVEJPG = 'jpgfigures'¶

coalispr.resources.constant.CHROMFIG = 'chrom_graphs'¶

coalispr.resources.constant.LENCNTS = 'lengthcounts'¶

coalispr.resources.constant.LIBCNTS = 'libcounts'¶

coalispr.resources.constant.REGCNTS = 'regions'¶

coalispr.resources.constant.UNSELFIG = 'unselected_chrom_graphs'¶

coalispr.resources.constant.GROUPAVG = 'groupaverages'¶

coalispr.resources.constant.SUBFIGS¶

coalispr.resources.constant.OUTPUTS = 'outputs'¶

coalispr.resources.constant.SOURCE = 'source'¶

coalispr.resources.constant.GTFS = 'gtfs'¶

coalispr.resources.constant.FASTA = 'fasta'¶

End constant_in/2_shared.txt (CONFFOLDER / SHARED)

Begin constant_in/3_EXP.txt (CONFFOLDER / EXPTXT)

coalispr.resources.constant.EXP = 'mouse'¶

coalispr.resources.constant.CONFNAM = '3_mouse.txt'¶

coalispr.resources.constant.EXPNAM = 'Mus musculus'¶

coalispr.resources.constant.EXPDISP = '$\\mathit{Mus musculus}$'¶

coalispr.resources.constant.TAG = 'uncollapsed'¶

coalispr.resources.constant.TAGSEG = 'uncollapsed'¶

coalispr.resources.constant.TAGBAM = 'collapsed'¶

coalispr.resources.constant.BINSTEP = 50¶

coalispr.resources.constant.UNSPECLOG10 = 0.905¶

coalispr.resources.constant.UNSPECTST = (0.61, 0.78, 0.905, 1.0, 1.3)¶

coalispr.resources.constant.LOG2BG = 4¶

coalispr.resources.constant.LOG2BGTST = (4, 5, 6, 7, 8, 9, 10)¶

coalispr.resources.constant.USEGAPS = 50¶

coalispr.resources.constant.UNSPCGAPS = 50¶

coalispr.resources.constant.UGAPSTST = (50, 100, 150, 200, 300)¶

coalispr.resources.constant.MIRNAPKBUF = 0.2¶

coalispr.resources.constant.CIGARCHK = 'fullmatch'¶

coalispr.resources.constant.NRMISM = 0¶

coalispr.resources.constant.MININTRON = 20¶

coalispr.resources.constant.CNTRS¶

coalispr.resources.constant.LENCNTRS¶

coalispr.resources.constant.MMAPCNTRS¶

coalispr.resources.constant.BINS = 1¶

coalispr.resources.constant.BAMLOW = 19¶

coalispr.resources.constant.BAMHIGH = 25¶

coalispr.resources.constant.BAMPEAK¶

coalispr.resources.constant.BAMSTART = 'T'¶

coalispr.resources.constant.BAM2BGNAM = 'bm2bg.sh'¶

coalispr.resources.constant.BAM2BG¶

coalispr.resources.constant.CHROMLBL = ''¶

coalispr.resources.constant.BACKEND = 'QtAgg'¶

coalispr.resources.constant.MINGAP = 30¶

coalispr.resources.constant.MAXGAP = 150¶

coalispr.resources.constant.INTSTEP = 10¶

coalispr.resources.constant.SKIPINT = ''¶

coalispr.resources.constant.XLIM0 = 12¶

coalispr.resources.constant.XLIM1 = 40¶

coalispr.resources.constant.XLIM00 = 16¶

coalispr.resources.constant.XLIM11 = 26¶

coalispr.resources.constant.XLIMMIN = 12¶

coalispr.resources.constant.XLIMMAX = 75¶

coalispr.resources.constant.XLIMR0 = 16¶

coalispr.resources.constant.XLIMR1 = 36¶

coalispr.resources.constant.CPPHFAC = 0.125¶

coalispr.resources.constant.LPPHFAC = 0.2¶

coalispr.resources.constant.MAXROW = 30¶

coalispr.resources.constant.SETBASE = '/home/working/DATA_ANALYSIS_2/zenodo/Sarshad-2018'¶

coalispr.resources.constant.MUTNO = '0'¶

coalispr.resources.constant.SRCFLDR = 'STAR-analysis0-mouse_'¶

coalispr.resources.constant.REFS = ''¶

coalispr.resources.constant.BEDGRAPH = '.bedgraph'¶

coalispr.resources.constant.BAM = '.bam'¶

coalispr.resources.constant.PLUS = 'plus'¶

coalispr.resources.constant.MINUS = 'minus'¶

coalispr.resources.constant.PLUSIN = 'plus'¶

coalispr.resources.constant.MINUSIN = 'minus'¶

coalispr.resources.constant.PL = 'p'¶

coalispr.resources.constant.MI = 'm'¶

coalispr.resources.constant.SAMBAM = 'samtoolsAligned.sortedByCoord.out.bam'¶

coalispr.resources.constant.UNMAPPEDFIL = 'Unmapped.out.mate1.gz'¶

coalispr.resources.constant.UNMAPTYPE = 'fastq'¶

coalispr.resources.constant.UNMAPCOLLTP = 'fasta'¶

coalispr.resources.constant.EXPFILNAM = 'GSE108799_Exp.tsv'¶

coalispr.resources.constant.FILEKEY = 'Run'¶

coalispr.resources.constant.SHORT = 'Short'¶

coalispr.resources.constant.CATEGORY = 'Category'¶

coalispr.resources.constant.EXPERIMENT = 'Experiment'¶

coalispr.resources.constant.GROUP = 'Group'¶

coalispr.resources.constant.READDENS = 'Read-density'¶

coalispr.resources.constant.CAT_R = 'R'¶

coalispr.resources.constant.CAT_U = 'U'¶

coalispr.resources.constant.CAT_S = 'S'¶

coalispr.resources.constant.CAT_M = 'M'¶

coalispr.resources.constant.CAT_D = 'D'¶

coalispr.resources.constant.TOTAL = 'total'¶

coalispr.resources.constant.RIP1 = 'rip1'¶

coalispr.resources.constant.RIP2 = 'rip2'¶

coalispr.resources.constant.NOTAGIP = 'rip0'¶

coalispr.resources.constant.OTHR = 'meth'¶

coalispr.resources.constant.REPAIR = 'rep'¶

coalispr.resources.constant.STARV = 'ms0'¶

coalispr.resources.constant.DENSE = 'highOD'¶

coalispr.resources.constant.REST = 'standard'¶

coalispr.resources.constant.WCE = 'WCE'¶

coalispr.resources.constant.NUCLEO = 'Nucleo'¶

coalispr.resources.constant.NUCL = 'Nuc'¶

coalispr.resources.constant.CYTO = 'Total'¶

coalispr.resources.constant.MITOCH = 'Mit'¶

coalispr.resources.constant.MEMBR = 'Mem'¶

coalispr.resources.constant.VACUOL = 'Vac'¶

coalispr.resources.constant.GRANUL = 'P-body'¶

coalispr.resources.constant.ENDRET = 'ER'¶

coalispr.resources.constant.EXCELL = 'Medium'¶

coalispr.resources.constant.MUTGROUPS¶

coalispr.resources.constant.CONDITIONS = ''¶

coalispr.resources.constant.METHODS¶

coalispr.resources.constant.FRACTIONS¶

coalispr.resources.constant.UNSPECIFICS = ['n', 't']¶

coalispr.resources.constant.MUTANTS = ''¶

coalispr.resources.constant.LENGTHSNAM = 'GRCm_genome_fa-chrlengths.tsv'¶

coalispr.resources.constant.DNAXTRNAM = ''¶

coalispr.resources.constant.LENXTRFILNAM = ''¶

coalispr.resources.constant.LENXTRA = ''¶

coalispr.resources.constant.CHRXTRA = ''¶

coalispr.resources.constant.GTFSPECNAM = 'miRNAs.gtf'¶

coalispr.resources.constant.GTFUNSPNAM = 'common_ncRNAs.gtf'¶

coalispr.resources.constant.GTFREFNAM = 'miRNAtargets.gtf'¶

coalispr.resources.constant.GTFXTRANAM = ''¶

coalispr.resources.constant.GTFUNXTNAM = ''¶

coalispr.resources.constant.GTFEXON = 'exon'¶

coalispr.resources.constant.GTFFEAT = 'sirnasegment'¶

coalispr.resources.constant.BASEDIR¶

coalispr.resources.constant.SAVEIN¶

coalispr.resources.constant.CONFIG¶

coalispr.resources.constant.LENGTHSFILE¶

coalispr.resources.constant.DNAXTRA = ''¶

coalispr.resources.constant.LENXTRAFILE = ''¶

coalispr.resources.constant.EXPFILE¶

coalispr.resources.constant.CONFPATH¶

coalispr.resources.constant.CONFFILE¶

coalispr.resources.constant.OUTPATH¶

coalispr.resources.constant.STOREPATH¶

coalispr.resources.constant.SRCDIR¶

coalispr.resources.constant.REFDIR¶

coalispr.resources.constant.REFNDIRLEVEL = 1¶

coalispr.resources.constant.GTFSPEC¶

coalispr.resources.constant.GTFUNSP¶

coalispr.resources.constant.GTFREF¶

coalispr.resources.constant.GTFXTRA = ''¶

coalispr.resources.constant.GTFUNXTR = ''¶

coalispr.resources.constant.FIGDIRSVG¶

coalispr.resources.constant.FIGDIRPNG¶

coalispr.resources.constant.FIGDIRPDF¶

coalispr.resources.constant.FIGDIRJPG¶

coalispr.resources.constant.FIGDIR¶

coalispr.resources.constant.LOGFIL¶