Skip to content

Fixed Alignment issues #3

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
rvanroey wants to merge 1 commit into
base: dev
Choose a base branch
from
Open

Fixed Alignment issues #3

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
30 changes: 19 additions & 11 deletions bin/GetReadCounts.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -105,17 +105,25 @@ def CountReads(sample):
print('Loading alignment ...')
# CLASSIFY ALIGNMENTS
# os.chdir(AlnDir)
sam_file = ReadsFilename0 + '.sam'
sam_file_present = path.exists(sam_file)
bam_file = ReadsFilename0 + '.bam'
bam_file_present = path.exists(bam_file)
if sam_file_present:
sam_file = sam_file
elif bam_file_present:
os.system('samtools view -h '+bam_file+' > '+sam_file)
else:
#sam_file = ReadsFilename0 + '.sam'
#sam_file_present = path.exists(sam_file)
#bam_file = ReadsFilename0 + '.bam'
#bam_file_present = path.exists(bam_file)
#if sam_file_present:
# sam_file = sam_file
#elif bam_file_present:
# os.system('samtools view -h '+bam_file+' > '+sam_file)
#else:
# print('### ERROR: No alignment file present ###')
#bw2sam = pysam.AlignmentFile(sam_file,'rb')
if bam_file_present == False:
print('### ERROR: No alignment file present ###')
bw2sam = pysam.AlignmentFile(sam_file,'rb')
BFS = str("bam_file_sorted")
pysam.sort("-o", BFS + ".bam", bam_file )
pysam.index(BFS + ".bam")
bw2sam = pysam.AlignmentFile(BFS + ".bam",'rb')


print('Applying matching threshold ...')
print('Applying ambiguity threshold ...')
NFail = 0; NUnique = 0; NTol = 0; NAmb = 0
Expand Down Expand Up @@ -313,4 +321,4 @@ def CountReads(sample):

if __name__ == "__main__":
input1 = sys.argv[1]
CountReads(input1)
CountReads(input1)