def sra__dump( uri, # level=2, silent=1, baseFile=0): uri = pyext.base__file(uri, baseFile=baseFile) # head,tail = pyext.splitPath(uri) CMD = 'fastq-dump --split-files {uri} 2>LOG'.format(**locals()) res = pysh.shellexec(CMD, silent=silent) return res
#!/usr/bin/env python # -*- coding: utf-8 -*- NCORE = 10 import pymisca.ext as pyext execfile(pyext.base__file('headers/header__import.py')) figs = pyutil.collections.OrderedDict() # execfile('/home/feng/meta/header_0903.py') keyDF = pyutil.readBaseFile('headers/key_brachy.csv') tks = pyutil.readBaseFile( 'results/0130__makeTracks-Brachy/tracks.npy').tolist() # execfile("/home/feng/envs/Fig_Brachy/loadRNA_Bd.py") # figs = pyutil.collections.OrderedDict() plt.rcParams['font.size'] = 14. plt.rcParams['xtick.labelsize'] = 16. plt.rcParams['axes.titlepad'] = 24. figsize = [14, 10] panel_kw = dict( figsize=figsize, show_axa=1, show_axc=0, showGrid=0, width_ratios=[1, 14, 0.], tickMax=10, # title= '', # height_ratios = [1,3,3,3,1], ) NCORE = 1
#!/usr/bin/env python2 # -*- coding: utf-8 -*- import pymisca.ext as pyext execfile(pyext.base__file('headers/header__import.py')) figs = pyutil.collections.OrderedDict() # execfile('/home/feng/meta/header_0903.py') keyDF = pyutil.readBaseFile('headers/key_brachy.csv') tks = pyutil.readBaseFile( 'results/0427B__makeTracks-Brachy/tracks.npy').tolist() # execfile("/home/feng/envs/Fig_Brachy/loadRNA_Bd.py") # figs = pyutil.collections.OrderedDict() plt.rcParams['font.size'] = 14. plt.rcParams['xtick.labelsize'] = 16. plt.rcParams['axes.titlepad'] = 24. figsize = [14, 10] panel_kw = dict( figsize=figsize, show_axa=1, show_axc=0, showGrid=0, width_ratios=[1, 14, 0.], tickMax=10, # title= '', # height_ratios = [1,3,3,3,1], ) NCORE = 1
import pymisca.ext as pyext pyext.base__check() suc, res = pyext.job__script( pyext.base__file('BrachyPhoton/0131__dumpDataRNA__Brachy.py'), # env=env, ) assert suc, res suc, res = pyext.job__script( pyext.base__file('BrachyPhoton/0130__makeTracks-Brachy.py'), # env=env, ) assert suc, res
#!/usr/bin/env python # -*- coding: utf-8 -*- NCORE=6 import pymisca.ext as pyext execfile(pyext.base__file('headers/header__import.py')) figs = pyutil.collections.OrderedDict() # execfile('/home/feng/meta/header__script2figure.py') # import synotil.chipShot keyDF = pyutil.readBaseFile('headers/key_brachy.csv') # gconf = pyutil.envSource('/home/feng/ref/config/config_Bd21-3.sh',silent=1); # gconf = pyutil.util_obj(**gconf) # peak2gene = pyutil.readData('/home/feng/envs/Fig_Brachy/peak2gene.tsv') plt.rcParams['font.size'] = 20. plt.rcParams['xtick.labelsize'] = 22. plt.rcParams['ytick.labelsize'] = 22. plt.rcParams['axes.titlepad'] = 24. plt.rcParams['legend.fontsize'] = 22. # bwCurr = bwMeta.query('runID=="182C"').query('bamFinal.str.contains("TAIR10")') # bwCurr = bwMeta # bwCurr.bname=bwCurr.bname.str.split('_').str.get(0) # bwCurr['bnameShort']=bwCurr.bname.str.split('_').str.get(0) # bwCurr = bwCurr.query('runID=="188CR"') # #####
#!/usr/bin/env python # -*- coding: utf-8 -*- NCORE = 6 import pymisca.ext as pyext execfile(pyext.base__file('headers/header__import.py')) figs = pyutil.collections.OrderedDict() keyDF = pyutil.readBaseFile('headers/key_brachy.csv') GSIZE = pyext.base__file('ref/Brachypodium_Bd21_v3-1/genome.sizes') peak2geneFile = 'results/0130__makePeakWindows__Brachy-ELF3/peak2geneFile.tsv' peak2gene = pyutil.readBaseFile(peak2geneFile) # keyDF = pyutil.readData('/home/feng/meta/key_brachy.csv') # peak2gene = pyutil.readData('/home/feng/envs/Fig_Brachy/peak2gene.tsv') plt.rcParams['font.size'] = 20. plt.rcParams['xtick.labelsize'] = 22. plt.rcParams['axes.titlepad'] = 24. ##### rnaScore = pyutil.readBaseFile( 'results/0205__interpAUC__Brachy/score__rnaseq__AUC.csv') xlab = 'transcriptionally perturbed\n over day-night cycle' query = 'score__rnaseq__AUC>1.0' ind1 = rnaScore.query(query).index chipClu = pyutil.readBaseFile( 'results/0130__callDiffTarg__Brachy-ELF3/clu.csv') chipClu.columns = ['clu'] chipDF = pyutil.readBaseFile(
#!/usr/bin/env python import pymisca.ext as pyext execfile(pyext.base__file('headers/header__import.py')) figs = pyutil.collections.OrderedDict() # './headers/header__import.py') NBNAME="1024__chipTarg__ELF3" # DIR = pyext.base__file('.') keyDF = pyutil.readData( pyext.base__file('./headers/key_brachy.csv') ) # BED_FILE = bedFile = DIR + '/bedFile.bed' # bed = sdio.extract_peak(bedFile) # peak2gene = pyutil.readData('%s/peak2gene.tsv' % DIR) # chipRel = pyutil.readData('%s/1018__chip-rel.pk'% DIR) # peak2gene = pyutil.readData('%s/peak2gene.tsv' % DIR) peak2gene = pyutil.readData( 'results/0130__makePeakWindows__Brachy-ELF3/peak2geneFile.tsv',baseFile=1) chipRel = pyutil.readData( 'results/0130__chipSummary__Brachy-ELF3/bwAvg.pk',baseFile=1, callback=scount.countMatrix) peaks0 = peaks = peak2gene.merge(keyDF,right_index=True,left_on="feat_acc") #### QC plot sutil.qc_Sort(df=chipRel); figs['qcPlot'] = plt.gcf()
#!/usr/bin/env python # -*- coding: utf-8 -*- NCORE = 6 import pymisca.ext as pyext execfile(pyext.base__file('headers/header__import.py')) figs = pyutil.collections.OrderedDict() gconf = pyutil.util_obj(**pyutil.envSource( pyext.base__file('ref/config/config_Bd21-3.sh'), silent=1)) keyDF = pyutil.readBaseFile('headers/key_brachy.csv') anno = pyutil.readBaseFile(gconf.ANNOINFO) dfc = pyutil.readBaseFile(gconf.ANNOINFO, comment=None) dfc = dfc.sort_values('transcriptName') dfc = dfc.query('~locusName.duplicated()').set_index('locusName') dfc = dfc['Best-hit-arabi-name,arabi-symbol,arabi-defline'.split(',')] gconf.defline = defline = dfc # Best-hit-arabi-name arabi-symbol arabi-defline # defline = pyutil.readData(gconf.DEFLINE,header = None) # defline.index = defline.index.str.split('.',1).str.get(0) # defline = defline[[2]].rename(columns = {2:'defline'}) # defline = defline.query('~index.duplicated()') # gconf.defline = defline gene2name = dfc = pyutil.readBaseFile(gconf.GENE2NAME, header=None, names=list(range(3))) ### patch rid = ~dfc[2].isnull() dfcc = dfc.loc[rid]
import pymisca.ext as pyext; pyext.base__check() # pyext.os.environ['BASE'] = '/home/feng/work' suc,res = pyext.job__script( pyext.base__file('BrachyPhoton/0129__cluster__Brachy-RNA-all.py'), # env=env, ) assert suc,res suc,res = pyext.job__script( pyext.base__file('BrachyPhoton/0129__showCluster__Brachy-RNA-all.py'), # env=env, ) assert suc,res suc,res = pyext.job__script( pyext.base__file('BrachyPhoton/0128__heatmap__Brachy.py'), # env=env, ) assert suc,res
import pymisca.ext as pyext pyext.base__check() # matplotlib.use("Agg") # pyext.os.environ['BASE'] = '/home/feng/work' suc, res = pyext.job__script( pyext.base__file('BrachyPhoton/0130__lineplot__pfr.py'), # env=env, ) assert suc, res
#!/usr/bin/env python # -*- coding: utf-8 -*- NCORE = 6 import pymisca.ext as pyext execfile(pyext.base__file('headers/header__import.py')) figs = pyutil.collections.OrderedDict() gconf = pyutil.util_obj(**pyutil.envSource( pyext.base__file('ref/config/config_Ath_TAIR10.sh'), silent=1)) keyDF = pyutil.readBaseFile('headers/key_ath.csv') if hasattr(keyDF, 'gconf'): anno = pyutil.readBaseFile(gconf.ANNOINFO) dfc = pyutil.readBaseFile(gconf.ANNOINFO, comment=None) dfc = dfc.sort_values('transcriptName') dfc = dfc.query('~locusName.duplicated()').set_index('locusName') dfc = dfc['Best-hit-arabi-name,arabi-symbol,arabi-defline'.split(',')] gconf.defline = defline = dfc # Best-hit-arabi-name arabi-symbol arabi-defline # defline = pyutil.readData(gconf.DEFLINE,header = None) # defline.index = defline.index.str.split('.',1).str.get(0) # defline = defline[[2]].rename(columns = {2:'defline'}) # defline = defline.query('~index.duplicated()') # gconf.defline = defline gene2name = dfc = pyutil.readBaseFile(gconf.GENE2NAME, header=None, names=list(range(3))) ### patch rid = ~dfc[2].isnull()
import pymisca.ext as pyext pyext.base__check() suc, res = pyext.job__script( pyext.base__file('BrachyPhoton/0130__makePeakWindows__Brachy-ELF3.py'), # env=env, ) assert suc suc, res = pyext.job__script( pyext.base__file('BrachyPhoton/0130__chipSummary__Brachy-ELF3.py')) assert suc suc, res = pyext.job__script( pyext.base__file('BrachyPhoton/0130__callDiffTarg__Brachy-ELF3.py')) assert suc
#!/usr/bin/env python # -*- coding: utf-8 -*- import pymisca.ext as pyext execfile(pyext.base__file('headers/header__import.py')) figs = pyutil.collections.OrderedDict() # npkFiles = \ # ['Mapped_data/188CR/S1/64-LD-ZT0-ELF3-OX-RERUN_S1_peaks.narrowPeak', # 'Mapped_data/188CR/S2/64-SD-ZT0-ELF3-OX-RERUN_S2_peaks.narrowPeak', # 'Mapped_data/188CR/S3/64-LL-ZT0-ELF3-OX-RERUN_S3_peaks.narrowPeak', # 'Mapped_data/188CR/S4/64-LD-ZT4-ELF3-OX-RERUN_S4_peaks.narrowPeak', # 'Mapped_data/188CR/S5/64-SD-ZT4-ELF3-OX-RERUN_S5_peaks.narrowPeak', # 'Mapped_data/188CR/S7/64-LD-ZT20-ELF3OX-RERUN_S7_peaks.narrowPeak', # 'Mapped_data/188CR/S8/64-SD-ZT20-ELF3OX-RERUN_S8_peaks.narrowPeak'] # npkFiles = map(pyext.base__file,npkFiles) bwCurr = pyutil.readBaseFile('results/0201__dumpMeta__Brachy/bwCurr.csv') npkFiles = bwCurr.npkFile.map(pyext.base__file) # bwCurr = bwMeta.query("runID=='188CR'") # bwCurr = bwCurr.query('bname.str.contains("ELF3",case=0)') fnames = map( pyutil.functools.partial(pyutil.queryCopy, inplace=False, query='FC>2.0', reader=sdio.extract_peak), npkFiles) peakFile = ofname = sdio.bed__merge( pyutil.file__cat(fnames, ofname='combined__ELF3__peaks.narrowPeak')) print(ofname, pyutil.lineCount(ofname)) windowFile = ofname = sdio.bed__makewindows(peakFile,