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Implement mixture model compatibility in full pipeline #155

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dd6f113
Add makeCB option to all dunk
isaacvock May 1, 2024
6b5bfc7
Fix T overcounting bug
isaacvock May 2, 2024
97746a5
Make cB header consistent with _tcount.tsv header
isaacvock May 2, 2024
4b97031
Changes to be thrown out
isaacvock May 6, 2024
27dc665
Count total number of ref Ts and TC mutations
isaacvock May 6, 2024
d648cb3
Don't double count TC mismatches in nT
isaacvock May 6, 2024
51d369a
Remove unnecessary files from local install
isaacvock May 6, 2024
e529e77
Update comments
isaacvock May 11, 2024
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23 changes: 15 additions & 8 deletions slamdunk/dunks/tcounter.py
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Original file line number Diff line number Diff line change
Expand Up @@ -24,7 +24,6 @@
import os
import re

### NEW CODE
import csv

from os.path import basename
Expand Down Expand Up @@ -151,11 +150,10 @@ def computeTconversions(ref, bed, snpsFile, bam, maxReadLength, minQual, outputC
print("#annotation:", os.path.basename(bed), bedMD5, sep="\t", file=fileCSV)
print(SlamSeqInterval.Header, file=fileCSV)

### NEW CODE
## Create cB output file if necessary
if (makeCB):

header = ['chromosome', 'UTR_name', 'UTR_start', 'UTR_end', 'UTR_strand', 'TC', 'nT', 'n']
header = ['Chromosome', 'Name', 'Start', 'End', 'Strand', 'TC', 'nT', 'n']
fileCB = open(outputCB, 'w')
wr = csv.writer(fileCB)
wr.writerow(header)
Expand Down Expand Up @@ -216,7 +214,6 @@ def computeTconversions(ref, bed, snpsFile, bam, maxReadLength, minQual, outputC
multiMapFwd = 0
multiMapRev = 0

### NEW CODE
## Dictionary to track number of unique combos
## of T-to-C counts and T counts
if (makeCB):
Expand All @@ -225,6 +222,12 @@ def computeTconversions(ref, bed, snpsFile, bam, maxReadLength, minQual, outputC

for read in readIterator:

# Total number of T-to-C mutations in the read
totalTCcnt = read.tcCount

# Total number of reference Ts overlapped (minus those mutated to something other than C)
totalTcnt = read.getTcount()

# Overwrite any conversions for non-TC reads (reads with < 2 TC conversions)
if (not read.isTcRead) :
read.tcCount = 0
Expand Down Expand Up @@ -255,13 +258,17 @@ def computeTconversions(ref, bed, snpsFile, bam, maxReadLength, minQual, outputC
if(mismatch.referencePosition >= 0 and mismatch.referencePosition < utr.getLength()):
if(mismatch.isT(read.direction == ReadDirection.Reverse)):
testN += 1
totalTcnt += 1
if(mismatch.isTCMismatch(read.direction == ReadDirection.Reverse)):
testk += 1
else:
if(mismatch.isT(read.direction == ReadDirection.Reverse)):
totalTcnt += 1

### NEW CODE
# Increment TC and nT counts for cB
if (makeCB):

key = (testk, testN)
key = (totalTCcnt, totalTcnt)

if key in cB:
cB[key] += 1
Expand All @@ -278,7 +285,7 @@ def computeTconversions(ref, bed, snpsFile, bam, maxReadLength, minQual, outputC
if(i >= 0 and i < utr.getLength()):
coverageUtr[i] += 1

### NEW CODE
# Write to cB file
if (makeCB):

for (tc, nt), count in cB.items():
Expand Down Expand Up @@ -365,7 +372,7 @@ def computeTconversions(ref, bed, snpsFile, bam, maxReadLength, minQual, outputC
fileBedgraphPlus.close()
fileBedgraphMinus.close()

### NEW CODE
# Close cB file connection
if (makeCB):

fileCB.close()
Expand Down
1 change: 1 addition & 0 deletions slamdunk/slamdunk.py
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Expand Up @@ -430,6 +430,7 @@ def run():
allparser.add_argument('-st', "--sampleTime", type=int, dest="sampleTime", required = False, default = 0, help="Use this sample time for all supplied samples")
allparser.add_argument("-i", "--sample-index", type=int, required=False, default=-1, dest="sampleIndex", help="Run analysis only for sample <i>. Use for distributing slamdunk analysis on a cluster (index is 1-based).")
allparser.add_argument("-ss", "--skip-sam", action='store_true', dest="skipSAM", help="Output BAM while mapping. Slower but, uses less hard disk.")
allparser.add_argument('-cb', "--makeCB", action='store_true', dest="makeCB", help="Make cB file that can be used for mixture modeling")

args = parser.parse_args()

Expand Down