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supported to run ROSE2 in python3 environment #67

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supported to run ROSE2 in python3 environment #67

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344a490
Modified files to fix the issue from python2 to python3
gauravj49 Jul 16, 2019
aa76098
Modified files to fix the issue from python2 to python3
gauravj49 Jul 16, 2019
2a2fd18
added support for ucsc and ensembl files (ex. chr1 vs 1)
gauravj49 Sep 30, 2020
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65 changes: 32 additions & 33 deletions ROSE2_geneMapper.py
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Original file line number Diff line number Diff line change
Expand Up @@ -40,7 +40,7 @@

import os
import subprocess
from string import join
# from string import join

@jdimatteo jdimatteo Mar 18, 2020

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Please delete code instead of commenting it out.


from collections import defaultdict

Expand Down Expand Up @@ -189,14 +189,14 @@ def mapEnhancerToGene(annotFile,enhancerFile,transcribedFile='',uniqueGenes=True
if noFormatTable:

newEnhancerLine = list(line)
newEnhancerLine.append(join(utils.uniquify([startDict[x]['name'] for x in overlappingGenes]),','))
newEnhancerLine.append(join(utils.uniquify([startDict[x]['name'] for x in proximalGenes]),','))
newEnhancerLine.append(','.join(utils.uniquify([startDict[x]['name'] for x in overlappingGenes])))
newEnhancerLine.append(','.join(utils.uniquify([startDict[x]['name'] for x in proximalGenes])))
newEnhancerLine.append(closestGene)

else:
newEnhancerLine = line[0:9]
newEnhancerLine.append(join(utils.uniquify([startDict[x]['name'] for x in overlappingGenes]),','))
newEnhancerLine.append(join(utils.uniquify([startDict[x]['name'] for x in proximalGenes]),','))
newEnhancerLine.append(','.join(utils.uniquify([startDict[x]['name'] for x in overlappingGenes])))
newEnhancerLine.append(','.join(utils.uniquify([startDict[x]['name'] for x in proximalGenes])))
newEnhancerLine.append(closestGene)
newEnhancerLine += line[-2:]

Expand Down Expand Up @@ -238,9 +238,9 @@ def mapEnhancerToGene(annotFile,enhancerFile,transcribedFile='',uniqueGenes=True
proxEnhancers = geneDict['overlapping'][refID]+geneDict['proximal'][refID]

superStatus = max(superDict[refID])
enhancerRanks = join([str(x) for x in rankDict[refID]],',')
enhancerRanks = ','.join([str(x) for x in rankDict[refID]])

newLine = [geneName,refID,join(proxEnhancers,','),enhancerRanks,superStatus]
newLine = [geneName,refID,','.join(proxEnhancers),enhancerRanks,superStatus]
geneToEnhancerTable.append(newLine)

#resort enhancerToGeneTable
Expand Down Expand Up @@ -320,8 +320,7 @@ def mapEnhancerToGeneTop(rankByBamFile, controlBamFile, genome, annotFile, enhan
# matter
tssCollection = utils.LocusCollection(tssLoci, 50)

geneDict = {'overlapping': defaultdict(
list), 'proximal': defaultdict(list)}
geneDict = {'overlapping': defaultdict(list), 'proximal': defaultdict(list)}

# dictionaries to hold ranks and superstatus of gene nearby enhancers
rankDict = defaultdict(list)
Expand All @@ -347,16 +346,13 @@ def mapEnhancerToGeneTop(rankByBamFile, controlBamFile, genome, annotFile, enhan
else:
# set up the output tables
# first by enhancer
enhancerToGeneTable = [
header[0:9] + ['OVERLAP_GENES', 'PROXIMAL_GENES', 'CLOSEST_GENE'] + header[-2:]]
enhancerToGeneTable = [header[0:9] + ['OVERLAP_GENES', 'PROXIMAL_GENES', 'CLOSEST_GENE'] + header[-2:]]

# next by gene
geneToEnhancerTable = [
['GENE_NAME', 'REFSEQ_ID', 'PROXIMAL_ENHANCERS']]
geneToEnhancerTable = [['GENE_NAME', 'REFSEQ_ID', 'PROXIMAL_ENHANCERS']]

# next make the gene to enhancer table
geneToEnhancerTable = [
['GENE_NAME', 'REFSEQ_ID', 'PROXIMAL_ENHANCERS', 'ENHANCER_RANKS', 'IS_SUPER', 'ENHANCER_SIGNAL']]
geneToEnhancerTable = [['GENE_NAME', 'REFSEQ_ID', 'PROXIMAL_ENHANCERS', 'ENHANCER_RANKS', 'IS_SUPER', 'ENHANCER_SIGNAL']]

for line in enhancerTable:
if line[0][0] == '#' or line[0][0] == 'R':
Expand Down Expand Up @@ -405,35 +401,38 @@ def mapEnhancerToGeneTop(rankByBamFile, controlBamFile, genome, annotFile, enhan
distalGenes.remove(refID)

# Now find the closest gene
closestGene = ''
if len(allEnhancerGenes) == 0:
closestGene = ''
else:
# get enhancerCenter
enhancerCenter = (int(line[2]) + int(line[3])) / 2

# get absolute distance to enhancer center
distList = [abs(enhancerCenter - startDict[geneID]['start'][0])
for geneID in allEnhancerGenes]
# get the ID and convert to name
closestGene = startDict[
allEnhancerGenes[distList.index(min(distList))]]['name']
try:
# get absolute distance to enhancer center
distList = [abs(enhancerCenter - list(startDict[geneID]['start'])[0]) for geneID in allEnhancerGenes]

# get the ID and convert to name
closestGene = startDict[allEnhancerGenes[distList.index(min(distList))]]['name']
except:

@vsoch vsoch Mar 18, 2020

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Do you want this to fail silently? Or give some meaningful message to the user? Or catch a specific kind of error that you expect?

pass

# NOW WRITE THE ROW FOR THE ENHANCER TABLE
if noFormatTable:

newEnhancerLine = list(line)
newEnhancerLine.append(
join(utils.uniquify([startDict[x]['name'] for x in overlappingGenes]), ','))
','.join(utils.uniquify([startDict[x]['name'] for x in overlappingGenes])))
newEnhancerLine.append(
join(utils.uniquify([startDict[x]['name'] for x in proximalGenes]), ','))
','.join(utils.uniquify([startDict[x]['name'] for x in proximalGenes])))
newEnhancerLine.append(closestGene)

else:
newEnhancerLine = line[0:9]
newEnhancerLine.append(
join(utils.uniquify([startDict[x]['name'] for x in overlappingGenes]), ','))
','.join(utils.uniquify([startDict[x]['name'] for x in overlappingGenes])))
newEnhancerLine.append(
join(utils.uniquify([startDict[x]['name'] for x in proximalGenes]), ','))
','.join(utils.uniquify([startDict[x]['name'] for x in proximalGenes])))
newEnhancerLine.append(closestGene)
newEnhancerLine += line[-2:]

Expand All @@ -460,14 +459,15 @@ def mapEnhancerToGeneTop(rankByBamFile, controlBamFile, genome, annotFile, enhan

#get the chromLists from the various bams here
cmd = 'samtools idxstats %s' % (rankByBamFile)
idxStats = subprocess.Popen(cmd,stdout=subprocess.PIPE,shell=True)
idxStats= idxStats.communicate()
bamChromList = [line.split('\t')[0] for line in idxStats[0].split('\n')[0:-2]]
idxStats = subprocess.Popen(cmd, stdout=subprocess.PIPE, shell=True,
universal_newlines=True).communicate()[0]

@vsoch vsoch Mar 18, 2020

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Generally it's not good practice to use shell=True, but probably for a small scientific pipeline this would be okay. Here is an example of not using shell=True: https://github.com/HPC-buildtest/buildtest-framework/blob/devel/buildtest/utils/command.py#L55


bamChromList = [bytes(line.split('\t')[0]) for line in idxStats[0].split('\n')[0:-2]]

if len(controlBamFile) > 0:
cmd = 'samtools idxstats %s' % (controlBamFile)
idxStats = subprocess.Popen(cmd,stdout=subprocess.PIPE,shell=True)
idxStats= idxStats.communicate()
idxStats = idxStats.communicate()
bamChromListControl = [line.split('\t')[0] for line in idxStats[0].split('\n')[0:-2]]
bamChromList = [chrom for chrom in bamChromList if bamChromListControl.count(chrom) != 0]

Expand Down Expand Up @@ -572,13 +572,12 @@ def mapEnhancerToGeneTop(rankByBamFile, controlBamFile, genome, annotFile, enhan
refID] + geneDict['proximal'][refID]

superStatus = max(superDict[refID])
enhancerRanks = join([str(x) for x in rankDict[refID]], ',')
enhancerRanks = ','.join([str(x) for x in rankDict[refID]])

enhancerSignal = signalDict[refID]
geneNameSigDict[geneName].append(enhancerSignal)

newLine = [geneName, refID, join(
proxEnhancers, ','), enhancerRanks, superStatus, enhancerSignal]
newLine = [geneName, refID, ','.join(proxEnhancers), enhancerRanks, superStatus, enhancerSignal]
geneToEnhancerTable.append(newLine)
#utils.unParseTable(geneToEnhancerTable,'/grail/projects/newRose/geneMapper/foo.txt','\t')
print('MAKING ENHANCER TO TOP GENE TABLE')
Expand Down Expand Up @@ -711,7 +710,7 @@ def main():
if options.out:
outFolder = utils.formatFolder(options.out, True)
else:
outFolder = join(enhancerFile.split('/')[0:-1], '/') + '/'
outFolder = '/'.join(enhancerFile.split('/')[0:-1]) + '/'

# GETTING BAM INFO
rankByBamFile = options.rankby
Expand Down
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