python-scripts/get_strandedness.py at master · Bioinformatics-Support-Unit/python-scripts · GitHub

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importpysam
importargparse

#chromosomal locations of gene in different annotations
#currently, Ensembl human annotation...
gapdh_location= {'grch37': ("12", 6643093, 6647481, '+'),
'grch38': ("12", 6533927, 6538374, '+'),
'hg19': ("chr12", 6643585, 6647537, '+'),}

defmain(sam, genome):
"""Finds the strandedness of an RNA-Seq sample based on the reads
 that are mapped to the GAPDH gene in a range of supported annotation."""
location=gapdh_location[genome]
#assumes coordinate-sorted BAM file with index(!)
samfile=pysam.AlignmentFile(sam, "rb")
#fetch the GAPDH reads
itersam=samfile.fetch(location[0], location[1], location[2])
#counters for different read types
f1, f2, r1, r2, other=0, 0, 0, 0, 0
forreadinitersam:
ifread.flag&208==80: #first in pair, reverse
r1+=1
elifread.flag&208==64: #first in pair, forward
f1+=1
elifread.flag&208==144: #second in pair, reverse
r2+=1
elifread.flag&208==128: #first in pair, forward
f2+=1
else:
other+=1# should never get here (as all reads are mapped)
total=float(r1+r2+f1+f2)
iflocation[3] =='+':
percent_firststrand= ((r1+f2)/total)*100
percent_secondstrand= ((r2+f1)/total)*100
eliflocation[3] =='-':
percent_firststrand= ((f1+r2)/total)*100
percent_secondstrand= ((f2+r1)/total)*100
ifpercent_firststrand>99:
print("First Stranded")
elifpercent_secondstrand>99:
print("Second Stranded")
else:
print("Unstranded")
print("Percent of reads supporting FR-firststrand (1=AS, 2=S): {0}".format(str(percent_firststrand)))
print("Percent of reads supporting FR-secondstrand (1=S, 2=AS): {0}".format(str(percent_secondstrand)))

if__name__=="__main__":
parser=argparse.ArgumentParser(description='Determine RNA-Seq Strandedness from an indexed BAM file')
parser.add_argument('genome', type=str,
help='Reference genome of alignment, choose from: {0}'.format(', '.join(gapdh_location.keys())))
parser.add_argument('bamfile', type=str,
help='BAM file of aligned RNA-Seq reads (must be coordinate sorted and indexed)')
args=parser.parse_args()
ifargs.genomenotingapdh_location.keys():
print("Error: Unsupported genome")
parser.print_help()
exit()
main(args.bamfile, args.genome)
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importpysam
importargparse

#chromosomal locations of gene in different annotations
#currently, Ensembl human annotation...
gapdh_location= {'grch37': ("12", 6643093, 6647481, '+'),
'grch38': ("12", 6533927, 6538374, '+'),
'hg19': ("chr12", 6643585, 6647537, '+'),}

defmain(sam, genome):
"""Finds the strandedness of an RNA-Seq sample based on the reads
 that are mapped to the GAPDH gene in a range of supported annotation."""
location=gapdh_location[genome]
#assumes coordinate-sorted BAM file with index(!)
samfile=pysam.AlignmentFile(sam, "rb")
#fetch the GAPDH reads
itersam=samfile.fetch(location[0], location[1], location[2])
#counters for different read types
f1, f2, r1, r2, other=0, 0, 0, 0, 0
forreadinitersam:
ifread.flag&208==80: #first in pair, reverse
r1+=1
elifread.flag&208==64: #first in pair, forward
f1+=1
elifread.flag&208==144: #second in pair, reverse
r2+=1
elifread.flag&208==128: #first in pair, forward
f2+=1
else:
other+=1# should never get here (as all reads are mapped)
total=float(r1+r2+f1+f2)
iflocation[3] =='+':
percent_firststrand= ((r1+f2)/total)*100
percent_secondstrand= ((r2+f1)/total)*100
eliflocation[3] =='-':
percent_firststrand= ((f1+r2)/total)*100
percent_secondstrand= ((f2+r1)/total)*100
ifpercent_firststrand>99:
print("First Stranded")
elifpercent_secondstrand>99:
print("Second Stranded")
else:
print("Unstranded")
print("Percent of reads supporting FR-firststrand (1=AS, 2=S): {0}".format(str(percent_firststrand)))
print("Percent of reads supporting FR-secondstrand (1=S, 2=AS): {0}".format(str(percent_secondstrand)))

if__name__=="__main__":
parser=argparse.ArgumentParser(description='Determine RNA-Seq Strandedness from an indexed BAM file')
parser.add_argument('genome', type=str,
help='Reference genome of alignment, choose from: {0}'.format(', '.join(gapdh_location.keys())))
parser.add_argument('bamfile', type=str,
help='BAM file of aligned RNA-Seq reads (must be coordinate sorted and indexed)')
args=parser.parse_args()
ifargs.genomenotingapdh_location.keys():
print("Error: Unsupported genome")
parser.print_help()
exit()
main(args.bamfile, args.genome)
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importpysam
importargparse

#chromosomal locations of gene in different annotations
#currently, Ensembl human annotation...
gapdh_location= {'grch37': ("12", 6643093, 6647481, '+'),
'grch38': ("12", 6533927, 6538374, '+'),
'hg19': ("chr12", 6643585, 6647537, '+'),}

defmain(sam, genome):
"""Finds the strandedness of an RNA-Seq sample based on the reads
 that are mapped to the GAPDH gene in a range of supported annotation."""
location=gapdh_location[genome]
#assumes coordinate-sorted BAM file with index(!)
samfile=pysam.AlignmentFile(sam, "rb")
#fetch the GAPDH reads
itersam=samfile.fetch(location[0], location[1], location[2])
#counters for different read types
f1, f2, r1, r2, other=0, 0, 0, 0, 0
forreadinitersam:
ifread.flag&208==80: #first in pair, reverse
r1+=1
elifread.flag&208==64: #first in pair, forward
f1+=1
elifread.flag&208==144: #second in pair, reverse
r2+=1
elifread.flag&208==128: #first in pair, forward
f2+=1
else:
other+=1# should never get here (as all reads are mapped)
total=float(r1+r2+f1+f2)
iflocation[3] =='+':
percent_firststrand= ((r1+f2)/total)*100
percent_secondstrand= ((r2+f1)/total)*100
eliflocation[3] =='-':
percent_firststrand= ((f1+r2)/total)*100
percent_secondstrand= ((f2+r1)/total)*100
ifpercent_firststrand>99:
print("First Stranded")
elifpercent_secondstrand>99:
print("Second Stranded")
else:
print("Unstranded")
print("Percent of reads supporting FR-firststrand (1=AS, 2=S): {0}".format(str(percent_firststrand)))
print("Percent of reads supporting FR-secondstrand (1=S, 2=AS): {0}".format(str(percent_secondstrand)))

if__name__=="__main__":
parser=argparse.ArgumentParser(description='Determine RNA-Seq Strandedness from an indexed BAM file')
parser.add_argument('genome', type=str,
help='Reference genome of alignment, choose from: {0}'.format(', '.join(gapdh_location.keys())))
parser.add_argument('bamfile', type=str,
help='BAM file of aligned RNA-Seq reads (must be coordinate sorted and indexed)')
args=parser.parse_args()
ifargs.genomenotingapdh_location.keys():
print("Error: Unsupported genome")
parser.print_help()
exit()
main(args.bamfile, args.genome)
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importpysam
importargparse

#chromosomal locations of gene in different annotations
#currently, Ensembl human annotation...
gapdh_location= {'grch37': ("12", 6643093, 6647481, '+'),
'grch38': ("12", 6533927, 6538374, '+'),
'hg19': ("chr12", 6643585, 6647537, '+'),}

defmain(sam, genome):
"""Finds the strandedness of an RNA-Seq sample based on the reads
 that are mapped to the GAPDH gene in a range of supported annotation."""
location=gapdh_location[genome]
#assumes coordinate-sorted BAM file with index(!)
samfile=pysam.AlignmentFile(sam, "rb")
#fetch the GAPDH reads
itersam=samfile.fetch(location[0], location[1], location[2])
#counters for different read types
f1, f2, r1, r2, other=0, 0, 0, 0, 0
forreadinitersam:
ifread.flag&208==80: #first in pair, reverse
r1+=1
elifread.flag&208==64: #first in pair, forward
f1+=1
elifread.flag&208==144: #second in pair, reverse
r2+=1
elifread.flag&208==128: #first in pair, forward
f2+=1
else:
other+=1# should never get here (as all reads are mapped)
total=float(r1+r2+f1+f2)
iflocation[3] =='+':
percent_firststrand= ((r1+f2)/total)*100
percent_secondstrand= ((r2+f1)/total)*100
eliflocation[3] =='-':
percent_firststrand= ((f1+r2)/total)*100
percent_secondstrand= ((f2+r1)/total)*100
ifpercent_firststrand>99:
print("First Stranded")
elifpercent_secondstrand>99:
print("Second Stranded")
else:
print("Unstranded")
print("Percent of reads supporting FR-firststrand (1=AS, 2=S): {0}".format(str(percent_firststrand)))
print("Percent of reads supporting FR-secondstrand (1=S, 2=AS): {0}".format(str(percent_secondstrand)))

if__name__=="__main__":
parser=argparse.ArgumentParser(description='Determine RNA-Seq Strandedness from an indexed BAM file')
parser.add_argument('genome', type=str,
help='Reference genome of alignment, choose from: {0}'.format(', '.join(gapdh_location.keys())))
parser.add_argument('bamfile', type=str,
help='BAM file of aligned RNA-Seq reads (must be coordinate sorted and indexed)')
args=parser.parse_args()
ifargs.genomenotingapdh_location.keys():
print("Error: Unsupported genome")
parser.print_help()
exit()
main(args.bamfile, args.genome)
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importpysam
importargparse

#chromosomal locations of gene in different annotations
#currently, Ensembl human annotation...
gapdh_location= {'grch37': ("12", 6643093, 6647481, '+'),
'grch38': ("12", 6533927, 6538374, '+'),
'hg19': ("chr12", 6643585, 6647537, '+'),}

defmain(sam, genome):
"""Finds the strandedness of an RNA-Seq sample based on the reads
 that are mapped to the GAPDH gene in a range of supported annotation."""
location=gapdh_location[genome]
#assumes coordinate-sorted BAM file with index(!)
samfile=pysam.AlignmentFile(sam, "rb")
#fetch the GAPDH reads
itersam=samfile.fetch(location[0], location[1], location[2])
#counters for different read types
f1, f2, r1, r2, other=0, 0, 0, 0, 0
forreadinitersam:
ifread.flag&208==80: #first in pair, reverse
r1+=1
elifread.flag&208==64: #first in pair, forward
f1+=1
elifread.flag&208==144: #second in pair, reverse
r2+=1
elifread.flag&208==128: #first in pair, forward
f2+=1
else:
other+=1# should never get here (as all reads are mapped)
total=float(r1+r2+f1+f2)
iflocation[3] =='+':
percent_firststrand= ((r1+f2)/total)*100
percent_secondstrand= ((r2+f1)/total)*100
eliflocation[3] =='-':
percent_firststrand= ((f1+r2)/total)*100
percent_secondstrand= ((f2+r1)/total)*100
ifpercent_firststrand>99:
print("First Stranded")
elifpercent_secondstrand>99:
print("Second Stranded")
else:
print("Unstranded")
print("Percent of reads supporting FR-firststrand (1=AS, 2=S): {0}".format(str(percent_firststrand)))
print("Percent of reads supporting FR-secondstrand (1=S, 2=AS): {0}".format(str(percent_secondstrand)))

if__name__=="__main__":
parser=argparse.ArgumentParser(description='Determine RNA-Seq Strandedness from an indexed BAM file')
parser.add_argument('genome', type=str,
help='Reference genome of alignment, choose from: {0}'.format(', '.join(gapdh_location.keys())))
parser.add_argument('bamfile', type=str,
help='BAM file of aligned RNA-Seq reads (must be coordinate sorted and indexed)')
args=parser.parse_args()
ifargs.genomenotingapdh_location.keys():
print("Error: Unsupported genome")
parser.print_help()
exit()
main(args.bamfile, args.genome)
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importpysam
importargparse

#chromosomal locations of gene in different annotations
#currently, Ensembl human annotation...
gapdh_location= {'grch37': ("12", 6643093, 6647481, '+'),
'grch38': ("12", 6533927, 6538374, '+'),
'hg19': ("chr12", 6643585, 6647537, '+'),}

defmain(sam, genome):
"""Finds the strandedness of an RNA-Seq sample based on the reads
 that are mapped to the GAPDH gene in a range of supported annotation."""
location=gapdh_location[genome]
#assumes coordinate-sorted BAM file with index(!)
samfile=pysam.AlignmentFile(sam, "rb")
#fetch the GAPDH reads
itersam=samfile.fetch(location[0], location[1], location[2])
#counters for different read types
f1, f2, r1, r2, other=0, 0, 0, 0, 0
forreadinitersam:
ifread.flag&208==80: #first in pair, reverse
r1+=1
elifread.flag&208==64: #first in pair, forward
f1+=1
elifread.flag&208==144: #second in pair, reverse
r2+=1
elifread.flag&208==128: #first in pair, forward
f2+=1
else:
other+=1# should never get here (as all reads are mapped)
total=float(r1+r2+f1+f2)
iflocation[3] =='+':
percent_firststrand= ((r1+f2)/total)*100
percent_secondstrand= ((r2+f1)/total)*100
eliflocation[3] =='-':
percent_firststrand= ((f1+r2)/total)*100
percent_secondstrand= ((f2+r1)/total)*100
ifpercent_firststrand>99:
print("First Stranded")
elifpercent_secondstrand>99:
print("Second Stranded")
else:
print("Unstranded")
print("Percent of reads supporting FR-firststrand (1=AS, 2=S): {0}".format(str(percent_firststrand)))
print("Percent of reads supporting FR-secondstrand (1=S, 2=AS): {0}".format(str(percent_secondstrand)))

if__name__=="__main__":
parser=argparse.ArgumentParser(description='Determine RNA-Seq Strandedness from an indexed BAM file')
parser.add_argument('genome', type=str,
help='Reference genome of alignment, choose from: {0}'.format(', '.join(gapdh_location.keys())))
parser.add_argument('bamfile', type=str,
help='BAM file of aligned RNA-Seq reads (must be coordinate sorted and indexed)')
args=parser.parse_args()
ifargs.genomenotingapdh_location.keys():
print("Error: Unsupported genome")
parser.print_help()
exit()
main(args.bamfile, args.genome)
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importpysam
importargparse

#chromosomal locations of gene in different annotations
#currently, Ensembl human annotation...
gapdh_location= {'grch37': ("12", 6643093, 6647481, '+'),
'grch38': ("12", 6533927, 6538374, '+'),
'hg19': ("chr12", 6643585, 6647537, '+'),}

defmain(sam, genome):
"""Finds the strandedness of an RNA-Seq sample based on the reads
 that are mapped to the GAPDH gene in a range of supported annotation."""
location=gapdh_location[genome]
#assumes coordinate-sorted BAM file with index(!)
samfile=pysam.AlignmentFile(sam, "rb")
#fetch the GAPDH reads
itersam=samfile.fetch(location[0], location[1], location[2])
#counters for different read types
f1, f2, r1, r2, other=0, 0, 0, 0, 0
forreadinitersam:
ifread.flag&208==80: #first in pair, reverse
r1+=1
elifread.flag&208==64: #first in pair, forward
f1+=1
elifread.flag&208==144: #second in pair, reverse
r2+=1
elifread.flag&208==128: #first in pair, forward
f2+=1
else:
other+=1# should never get here (as all reads are mapped)
total=float(r1+r2+f1+f2)
iflocation[3] =='+':
percent_firststrand= ((r1+f2)/total)*100
percent_secondstrand= ((r2+f1)/total)*100
eliflocation[3] =='-':
percent_firststrand= ((f1+r2)/total)*100
percent_secondstrand= ((f2+r1)/total)*100
ifpercent_firststrand>99:
print("First Stranded")
elifpercent_secondstrand>99:
print("Second Stranded")
else:
print("Unstranded")
print("Percent of reads supporting FR-firststrand (1=AS, 2=S): {0}".format(str(percent_firststrand)))
print("Percent of reads supporting FR-secondstrand (1=S, 2=AS): {0}".format(str(percent_secondstrand)))

if__name__=="__main__":
parser=argparse.ArgumentParser(description='Determine RNA-Seq Strandedness from an indexed BAM file')
parser.add_argument('genome', type=str,
help='Reference genome of alignment, choose from: {0}'.format(', '.join(gapdh_location.keys())))
parser.add_argument('bamfile', type=str,
help='BAM file of aligned RNA-Seq reads (must be coordinate sorted and indexed)')
args=parser.parse_args()
ifargs.genomenotingapdh_location.keys():
print("Error: Unsupported genome")
parser.print_help()
exit()
main(args.bamfile, args.genome)
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importpysam
importargparse

#chromosomal locations of gene in different annotations
#currently, Ensembl human annotation...
gapdh_location= {'grch37': ("12", 6643093, 6647481, '+'),
'grch38': ("12", 6533927, 6538374, '+'),
'hg19': ("chr12", 6643585, 6647537, '+'),}

defmain(sam, genome):
"""Finds the strandedness of an RNA-Seq sample based on the reads
 that are mapped to the GAPDH gene in a range of supported annotation."""
location=gapdh_location[genome]
#assumes coordinate-sorted BAM file with index(!)
samfile=pysam.AlignmentFile(sam, "rb")
#fetch the GAPDH reads
itersam=samfile.fetch(location[0], location[1], location[2])
#counters for different read types
f1, f2, r1, r2, other=0, 0, 0, 0, 0
forreadinitersam:
ifread.flag&208==80: #first in pair, reverse
r1+=1
elifread.flag&208==64: #first in pair, forward
f1+=1
elifread.flag&208==144: #second in pair, reverse
r2+=1
elifread.flag&208==128: #first in pair, forward
f2+=1
else:
other+=1# should never get here (as all reads are mapped)
total=float(r1+r2+f1+f2)
iflocation[3] =='+':
percent_firststrand= ((r1+f2)/total)*100
percent_secondstrand= ((r2+f1)/total)*100
eliflocation[3] =='-':
percent_firststrand= ((f1+r2)/total)*100
percent_secondstrand= ((f2+r1)/total)*100
ifpercent_firststrand>99:
print("First Stranded")
elifpercent_secondstrand>99:
print("Second Stranded")
else:
print("Unstranded")
print("Percent of reads supporting FR-firststrand (1=AS, 2=S): {0}".format(str(percent_firststrand)))
print("Percent of reads supporting FR-secondstrand (1=S, 2=AS): {0}".format(str(percent_secondstrand)))

if__name__=="__main__":
parser=argparse.ArgumentParser(description='Determine RNA-Seq Strandedness from an indexed BAM file')
parser.add_argument('genome', type=str,
help='Reference genome of alignment, choose from: {0}'.format(', '.join(gapdh_location.keys())))
parser.add_argument('bamfile', type=str,
help='BAM file of aligned RNA-Seq reads (must be coordinate sorted and indexed)')
args=parser.parse_args()
ifargs.genomenotingapdh_location.keys():
print("Error: Unsupported genome")
parser.print_help()
exit()
main(args.bamfile, args.genome)