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04-stampy-run2.py
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#! /usr/bin/env python
# PBS cluster job submission in Python
# Stampy alignment to Painted Turtle Genome
# By Jean P. Elbers
# Last modified 22 Jan 2015
###############################################################################
Usage = """
04-stampy.py version 1.0
Command:
cd InDir = /work/jelber2/immunome_2014/run2/bwa-alignment
1.Produce only sam header and count number of header lines with wc, also copy
header file to stampy-alignment directory for bam concatenation later
~/bin/samtools-1.1/samtools view -SH \
-o Sample.header.bwa.sam Sample.bwa.sam
export HeadLength_i="$(wc -l < Sample.header.bwa.sam)"
cp Sample.header.bwa.sam ../stampy-alignment/
2.Use awk to remove header based on its length from sam file
awk -v n=$HeadLength_i '1 <= NR && NR <= n {next} {print}' Sample.bwa.sam > Sample.noheader.bwa.sam
3.Split the sam file without a header into 16 equal parts
export NumReads_i="$(wc -l < Sample.noheader.bwa.sam)"
export SplitReads_i="$(echo $[(NumReads_i+15)/16])"
split -d -l $SplitReads_i Sample.noheader.bwa.sam Sample-
4.Add the header back to each split
~/bin/parallel-20150122/src/parallel 'cat Sample.header.bwa.sam {} > {}.sam' ::: Sample-*
5.Convert the split sam files to bam format and remove sam in filename
~/bin/parallel-20150122/src/parallel '~/bin/samtools-1.1/samtools view -Sb \
{} > {}.bwa.bam' ::: Sample-*.sam
~/bin/parallel-20150122/src/parallel 'rename .sam "" {}' ::: Sample-*.sam.bwa.bam
6.Map the bam files using stampy
~/bin/parallel-20150122/src/parallel 'python ~/bin/stampy-1.0.23/stampy.py \
-g RefDir/GCF_000241765.3_Chrysemys_picta_bellii-3.0.3_genomic \
-h RefDir/GCF_000241765.3_Chrysemys_picta_bellii-3.0.3_genomic \
-f sam \
-t 1 \
--bamkeepgoodreads \
-M {} > ../stampy-alignment/{}.stampy.sam' ::: Sample-*.bwa.bam
7.Remove all but original sam file associated with the particular sample from
the bwa-alignment directory
find . -name 'Sample*' -not -name 'Sample.bwa.sam' -type f -delete
8.Rename bwa.bam from Sample-##.bwa.bam.stampy.sam
cd ../stampy-alignment/
~/bin/parallel-20150122/src/parallel 'rename .bwa.bam "" {}' ::: Sample-*.bwa.bam.stampy.sam
9.Convert sam2bam then remove sam from filename
~/bin/parallel-20150122/src/parallel '~/bin/samtools-1.1/samtools view \
-bS \
-t RefDir/GCF_000241765.3_Chrysemys_picta_bellii-3.0.3_genomic.fai {} > {}.bam' ::: Sample-*.stampy.sam
~/bin/parallel-20150122/src/parallel 'rename .sam "" {}' ::: Sample-*stampy.sam.bam
10.Concatenate bam files
~/bin/samtools-1.1/samtools cat \
-h Sample.header.sam \
-o Sample.stampy.bam \
Sample-00.stampy.bam \
Sample-01.stampy.bam \
Sample-02.stampy.bam \
Sample-03.stampy.bam \
Sample-04.stampy.bam \
Sample-05.stampy.bam \
Sample-06.stampy.bam \
Sample-07.stampy.bam \
Sample-08.stampy.bam \
Sample-09.stampy.bam \
Sample-10.stampy.bam \
Sample-11.stampy.bam \
Sample-12.stampy.bam \
Sample-13.stampy.bam \
Sample-14.stampy.bam \
Sample-15.stampy.bam
11.Uses samtools flagstat to get alignment metrics on concatenated aligned sam file
~/bin/samtools-1.1/samtools flagstat \
Sample.stampy.bam > Sample.stampy.bam.flagstat
12.Remove sam files and bam splits associated with the particular sample
in stampy-alignment directory
rm Sample*.sam
rm Sample-*.stampy.bam
Directory info:
InDir = /work/jelber2/immunome_2014/run2/bwa-alignment
Input Files = Sample-singlesANDmerged.bwa.sam
Sample-paired.bwa.sam
OutDir = /work/jelber2/immunome_2014/run2/stampy-alignment
Output Files = Sample-singlesANDmerged.stampy.bam
Sample-singlesANDmerged.stampy.bam.flagstat
Sample-paired.stampy.bam
Sample-paired.stampy.bam.flagstat
Usage (execute following code in InDir):
~/scripts/immunome_2014/04-stampy.py *.bwa.sam
"""
###############################################################################
import os, sys, subprocess, re #imports os, sys, subprocess, re modules
if len(sys.argv)<2:
print Usage
else:
FileList = sys.argv[1:]
RefDir = "/work/jelber2/reference"
InDir = "/work/jelber2/immunome_2014/run2/bwa-alignment"
OutDir = "/work/jelber2/immunome_2014/run2/stampy-alignment"
NewFolderName = "stampy-alignment"
os.chdir(InDir)
os.chdir("..") # go up one directory
if not os.path.exists(NewFolderName):
os.mkdir(NewFolderName) # if NewFolderName does not exist, then make it
os.chdir(InDir)
i=0
for InFileName in FileList: # so stampy processes all bam files
i+=1
FileSuffix = ".bwa.sam" # string to remove suffix from InFileName
Sample = InFileName.replace(FileSuffix,'') # creates Sample (note: Sample = Tort1-paired and/or Tort1-singlesANDmerged not Tort1!!)
# Customize your job options here
Queue = "workq"
Allocation = "hpc_gopo02"
Processors = "nodes=1:ppn=16"
WallTime = "08:00:00"
LogOut = OutDir
LogMerge = "oe"
JobName = "stampy-%s" % (Sample)
Command ="""
~/bin/samtools-1.1/samtools view -SH \
-o %s.header.bwa.sam %s.bwa.sam
export HeadLength_%d="$(wc -l < %s.header.bwa.sam)"
cp %s.header.bwa.sam ../stampy-alignment/
awk -v n=$HeadLength_%d '1 <= NR && NR <= n {next} {print}' %s.bwa.sam > %s.noheader.bwa.sam
export NumReads_%d="$(wc -l < %s.noheader.bwa.sam)"
export SplitReads_%d="$(echo $[(NumReads_%d+15)/16])"
split -d -l $SplitReads_%d %s.noheader.bwa.sam %s-
~/bin/parallel-20150122/src/parallel 'cat %s.header.bwa.sam {} > {}.sam' ::: %s-*
~/bin/parallel-20150122/src/parallel '~/bin/samtools-1.1/samtools view -Sb \
{} > {}.bwa.bam' ::: %s-*.sam
~/bin/parallel-20150122/src/parallel 'rename .sam "" {}' ::: %s-*.sam.bwa.bam
~/bin/parallel-20150122/src/parallel 'python ~/bin/stampy-1.0.23/stampy.py \
-g %s/GCF_000241765.3_Chrysemys_picta_bellii-3.0.3_genomic \
-h %s/GCF_000241765.3_Chrysemys_picta_bellii-3.0.3_genomic \
-f sam \
-t 1 \
--bamkeepgoodreads \
-M {} > ../stampy-alignment/{}.stampy.sam' ::: %s-*.bwa.bam
find . -name '%s*' -not -name '%s.bwa.sam' -type f -delete
cd ../stampy-alignment/
~/bin/parallel-20150122/src/parallel 'rename .bwa.bam "" {}' ::: %s-*.bwa.bam.stampy.sam
~/bin/parallel-20150122/src/parallel '~/bin/samtools-1.1/samtools view \
-bS {} > {}.bam' ::: %s-*.stampy.sam
~/bin/parallel-20150122/src/parallel 'rename .sam "" {}' ::: %s-*stampy.sam.bam
~/bin/samtools-1.1/samtools cat \
-h %s.header.bwa.sam \
-o %s.stampy.bam \
%s-00.stampy.bam \
%s-01.stampy.bam \
%s-02.stampy.bam \
%s-03.stampy.bam \
%s-04.stampy.bam \
%s-05.stampy.bam \
%s-06.stampy.bam \
%s-07.stampy.bam \
%s-08.stampy.bam \
%s-09.stampy.bam \
%s-10.stampy.bam \
%s-11.stampy.bam \
%s-12.stampy.bam \
%s-13.stampy.bam \
%s-14.stampy.bam \
%s-15.stampy.bam
~/bin/samtools-1.1/samtools flagstat \
%s.stampy.bam > %s.stampy.bam.flagstat
rm %s*.sam
rm %s-*.stampy.bam""" %\
(Sample, Sample, i, Sample, Sample,
i, Sample, Sample,
i, Sample, i, i, i, Sample, Sample,
Sample, Sample,
Sample, Sample,
RefDir, RefDir, Sample,
Sample, Sample,
Sample,
Sample, Sample,
Sample, Sample, Sample, Sample, Sample, Sample, Sample, Sample, Sample,
Sample, Sample, Sample, Sample, Sample, Sample, Sample, Sample, Sample,
Sample, Sample,
Sample, Sample)
JobString = """
#!/bin/bash
#PBS -q %s
#PBS -A %s
#PBS -l %s
#PBS -l walltime=%s
#PBS -o %s
#PBS -j %s
#PBS -N %s
cd %s
%s\n""" % (Queue, Allocation, Processors, WallTime, LogOut, LogMerge, JobName, InDir, Command)
#Create pipe to qsub
proc = subprocess.Popen(['qsub'], shell=True,
stdin=subprocess.PIPE, stdout=subprocess.PIPE, close_fds=True)
(child_stdout, child_stdin) = (proc.stdout, proc.stdin)
#Print JobString
JobName = proc.communicate(JobString)[0]
print JobString
print JobName