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Author: Nilesh Patra <npatra974@gmail.com>
Description: Search for the binary in same location: since both are eventually installed to /usr/bin
Last Changed: Sun Jun 28 2020
--- a/TIDDIT.py
+++ b/TIDDIT.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#! /usr/bin/python3
import argparse
import os
import sys
@@ -60,14 +60,14 @@
print ("error, could not find the bam file")
quit()
- if not os.path.isfile("{}/bin/TIDDIT".format(args.wd)):
+ if not os.path.isfile("{}/TIDDIT".format(args.wd)):
print ("error, could not find the TIDDIT executable file, try rerun the INSTALL.sh script")
quit()
if not args.bam.endswith(".cram"):
- command_str="{}/bin/TIDDIT --sv -b {} -o {} -p {} -r {} -q {} -n {} -s {}".format(args.wd,args.bam,args.o,args.p,args.r,args.q,args.n,args.s)
+ command_str="{}/TIDDIT --sv -b {} -o {} -p {} -r {} -q {} -n {} -s {}".format(args.wd,args.bam,args.o,args.p,args.r,args.q,args.n,args.s)
else:
- command_str="samtools view -hbu {} -T {} | {}/bin/TIDDIT --sv -b /dev/stdin -o {} -p {} -r {} -q {} -n {} -s {}".format(args.bam,args.ref,args.wd,args.o,args.p,args.r,args.q,args.n,args.s)
+ command_str="samtools view -hbu {} -T {} | {}/TIDDIT --sv -b /dev/stdin -o {} -p {} -r {} -q {} -n {} -s {}".format(args.bam,args.ref,args.wd,args.o,args.p,args.r,args.q,args.n,args.s)
if args.i:
@@ -82,9 +82,9 @@
t=time.time()
print ("Generating GC wig file")
if args.ref.endswith(".gz"):
- os.system("zcat {} | {}/bin/TIDDIT --gc -z 50 -o {}".format(args.ref,args.wd,args.o))
+ os.system("zcat {} | {}/TIDDIT --gc -z 50 -o {}".format(args.ref,args.wd,args.o))
else:
- os.system("cat {} | {}/bin/TIDDIT --gc -z 50 -o {}".format(args.ref,args.wd,args.o))
+ os.system("cat {} | {}/TIDDIT --gc -z 50 -o {}".format(args.ref,args.wd,args.o))
print ("Constructed GC wig in {} sec".format(time.time()-t))
if not args.no_cluster:
@@ -108,12 +108,12 @@
quit()
if not args.bam.endswith(".cram"):
- command="{}/bin/TIDDIT --cov -b {} -o {} -z {}".format(args.wd,args.bam,args.o,args.z)
+ command="{}/TIDDIT --cov -b {} -o {} -z {}".format(args.wd,args.bam,args.o,args.z)
else:
if not args.ref:
print("error, missing reference sequence!")
quit()
- command="samtools view -hbu {} -T {} | {}/bin/TIDDIT --cov -b /dev/stdin -o {} -z {}".format(args.bam,args.ref,args.wd,args.o,args.z)
+ command="samtools view -hbu {} -T {} | {}/TIDDIT --cov -b /dev/stdin -o {} -z {}".format(args.bam,args.ref,args.wd,args.o,args.z)
if args.w:
command += " -w"
@@ -124,7 +124,7 @@
if not os.path.isfile(args.bam):
print ("error, could not find the bam file")
quit()
- if not os.path.isfile("{}/bin/TIDDIT".format(args.wd)):
+ if not os.path.isfile("{}/TIDDIT".format(args.wd)):
print ("error, could not find the TIDDIT executable file, try rerun the INSTALL.sh script")
quit()
os.system(command)
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