def R_trim(self, outfile_R_ori, outfile_R):
cldict = self.cldict
trim_script = cldict.trim_script
trim_cmd = trim_script + " " + outfile_R_ori
print("trim_cmd: " + trim_cmd + ", outfile_R: " + outfile_R)
exe_command(trim_cmd, outfile_R)
return
def gen_sam_single_bwamem(self, sample_id, ref_acc, read_file, outdir):
cldict = self.cldict
ldelim = cldict.ldelim
bwa_path = cldict.bwa_path
patho_path = self.get_patho_ref_path(ref_acc)
# bwa mem ref.fa reads.fq > aln-se.sam
bwamem_cmd = bwa_path + " mem " + patho_path + " " + read_file
print("Aligning with bwa mem: " + bwamem_cmd)
outsamfile = outdir + ldelim + sample_id + "_" + ref_acc + ".sam"
exe_command(bwamem_cmd, outsamfile)
return outsamfile
def sample_to_sai(self, outdir, sample_id, ref_acc, suf, read_file,
patho_path):
cldict = self.cldict
ldelim = cldict.ldelim
bwa_path = cldict.bwa_path
R_sai = outdir + ldelim + sample_id + "_" + ref_acc + "_" + suf + ".sai"
read_cmd = bwa_path + " aln " + patho_path + " " + read_file
print("bwa aln cmd: " + read_cmd)
exe_command(read_cmd, R_sai)
print("bwa aln cmd done.")
return R_sai
def gen_sam_single(self, sample_id, ref_acc, read_file, suf, outdir):
cldict = self.cldict
ldelim = cldict.ldelim
bwa_path = cldict.bwa_path
samtools_path = cldict.samtools
patho_path = self.get_patho_ref_path(ref_acc)
R_sai = self.sample_to_sai(outdir, sample_id, ref_acc, suf, read_file,
patho_path)
sampecmd = bwa_path + " samse " + patho_path + " " + R_sai + " " + read_file
print("sampe cmd: " + sampecmd)
outsamfile = outdir + ldelim + sample_id + "_" + ref_acc + ".sam"
exe_command(sampecmd, outsamfile)
print("sampe cmd done.")
os.remove(R_sai)
print("removed " + R_sai)
return outsamfile
def gen_sam_paired(self, sample_id, ref_acc, read1_file, read2_file, suf1,
suf2, outdir):
cldict = self.cldict
ldelim = cldict.ldelim
bwa_path = cldict.bwa_path
samtools_path = cldict.samtools
patho_path = self.get_patho_ref_path(ref_acc)
R1_sai = self.sample_to_sai(outdir, sample_id, ref_acc, suf1,
read1_file, patho_path)
R2_sai = self.sample_to_sai(outdir, sample_id, ref_acc, suf2,
read2_file, patho_path)
sampecmd = bwa_path + " sampe " + patho_path + " " + R1_sai + " " + R2_sai +\
" " + read1_file + " " + read2_file
outsamfile = outdir + ldelim + sample_id + "_" + ref_acc + ".sam"
print("bwa sampe cmd: " + sampecmd)
exe_command(sampecmd, outsamfile)
print("bwa sampe cmd done.")
os.remove(R1_sai)
os.remove(R2_sai)
return outsamfile
def sam_to_bam(samtools_path, outsamfile, outbamfile):
bamcmd = samtools_path + ' view -b -S ' + outsamfile
print("sam to bam cmd: " + bamcmd)
exe_command(bamcmd, outbamfile)
print("sam to bam cmd done.")
def bam_to_sam(samtools_path, outbamfile, outsamfile):
samcmd = samtools_path + ' view -h ' + outbamfile
print("Converting bam to sam: " + outbamfile)
print("samcmd: " + samcmd)
exe_command(samcmd, outsamfile)
def sam_to_bam(samtools_path, outsamfile, outbamfile): bamcmd = samtools_path + ' view -b -S ' + outsamfile exe_command(bamcmd, outbamfile)