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        / /_/  >  | \// __ \|  |  / /_/ | |  ||  |  
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              grep rough audit - static analysis tool
                  v2.8 written by @Wireghoul
=================================[justanotherhacker.com]===
seqsero-1.0.1+dfsg/libs/BWA_analysis_H_update_new_family_dependent.py-395-  os.system("samtools view -h -o "+sam+" "+bam)
seqsero-1.0.1+dfsg/libs/BWA_analysis_H_update_new_family_dependent.py:396:  os.system("cat "+sam+"|awk '{if ($5>=0) {print $10}}'>"+database+sam+"_seq.txt")
seqsero-1.0.1+dfsg/libs/BWA_analysis_H_update_new_family_dependent.py:397:  os.system("cat "+sam+"|awk '{if ($5>=0) {print $1}}'>"+database+sam+"_title.txt")
seqsero-1.0.1+dfsg/libs/BWA_analysis_H_update_new_family_dependent.py-398-  file1=open(database+sam+"_title.txt","r")
##############################################
seqsero-1.0.1+dfsg/libs/BWA_analysis_O_new_dependent.py-214-  os.system("samtools view -h -o "+sam+" "+bam)
seqsero-1.0.1+dfsg/libs/BWA_analysis_O_new_dependent.py:215:  os.system("cat "+sam+"|awk '{if ($5>0) {print $10}}'>"+sam+"_seq.txt")
seqsero-1.0.1+dfsg/libs/BWA_analysis_O_new_dependent.py:216:  os.system("cat "+sam+"|awk '{if ($5>0) {print $1}}'>"+sam+"_title.txt")
seqsero-1.0.1+dfsg/libs/BWA_analysis_O_new_dependent.py-217-  file1=open(sam+"_title.txt","r")
##############################################
seqsero-1.0.1+dfsg/libs/deletion_compare.py-80-  os.system("samtools view -h -o "+sam+" "+bam)
seqsero-1.0.1+dfsg/libs/deletion_compare.py:81:  os.system("cat "+sam+"|awk '{if ($5>0) {print $10}}'>"+sam+"_seq.txt")
seqsero-1.0.1+dfsg/libs/deletion_compare.py:82:  os.system("cat "+sam+"|awk '{if ($5>0) {print $1}}'>"+sam+"_title.txt")
seqsero-1.0.1+dfsg/libs/deletion_compare.py-83-  file1=open(sam+"_title.txt","r")
##############################################
seqsero-1.0.1+dfsg/debian/bin/seqsero_batch_pair-end-4-    cat <<EOT
seqsero-1.0.1+dfsg/debian/bin/seqsero_batch_pair-end:5:Usage: `basename $0` <dir_with_sequence_pairs>
seqsero-1.0.1+dfsg/debian/bin/seqsero_batch_pair-end-6-
##############################################
seqsero-1.0.1+dfsg/debian/bin/seqsero_batch_pair-end-18-
seqsero-1.0.1+dfsg/debian/bin/seqsero_batch_pair-end:19:numR1=`ls $1/*_R1_001.fastq.gz 2>/dev/null | wc -l`
seqsero-1.0.1+dfsg/debian/bin/seqsero_batch_pair-end-20-if [ $numR1 -eq 0 ] ; then
##############################################
seqsero-1.0.1+dfsg/debian/bin/seqsero_batch_pair-end-24-
seqsero-1.0.1+dfsg/debian/bin/seqsero_batch_pair-end:25:numR2=`ls $1/*_R2_001.fastq.gz | wc -l`
seqsero-1.0.1+dfsg/debian/bin/seqsero_batch_pair-end-26-if [ $numR1 -ne $numR2 ] ; then
##############################################
seqsero-1.0.1+dfsg/debian/bin/seqsero_batch_pair-end-35-for seq1 in `ls *_R1_001.fastq.gz` ; do
seqsero-1.0.1+dfsg/debian/bin/seqsero_batch_pair-end:36:   seq2=`echo $seq1 | sed 's/_R1_001\.fastq\.gz$/_R2_001.fastq.gz/'`
seqsero-1.0.1+dfsg/debian/bin/seqsero_batch_pair-end-37-   if [ ! -e "$seq2" ] ; then
##############################################
seqsero-1.0.1+dfsg/debian/bin/seqsero_batch_pair-end-39-   else
seqsero-1.0.1+dfsg/debian/bin/seqsero_batch_pair-end:40:      check_old_results=`grep "^Input files:[[:space:]]\+\+$seq1 $seq2$" SeqSero_result*/Seqsero_result.txt`
seqsero-1.0.1+dfsg/debian/bin/seqsero_batch_pair-end-41-      if [ "$check_old_results" != "" ] ; then
seqsero-1.0.1+dfsg/debian/bin/seqsero_batch_pair-end:42:         echo "Calculation for $seq1 was done previously and can be found in `echo $check_old_results | sed 's/:Input files.*//'`"
seqsero-1.0.1+dfsg/debian/bin/seqsero_batch_pair-end-43-      else
##############################################
seqsero-1.0.1+dfsg/.pc/2to3.patch/libs/BWA_analysis_H_update_new_family_dependent.py-395-  os.system("samtools view -h -o "+sam+" "+bam)
seqsero-1.0.1+dfsg/.pc/2to3.patch/libs/BWA_analysis_H_update_new_family_dependent.py:396:  os.system("cat "+sam+"|awk '{if ($5>=0) {print $10}}'>"+database+sam+"_seq.txt")
seqsero-1.0.1+dfsg/.pc/2to3.patch/libs/BWA_analysis_H_update_new_family_dependent.py:397:  os.system("cat "+sam+"|awk '{if ($5>=0) {print $1}}'>"+database+sam+"_title.txt")
seqsero-1.0.1+dfsg/.pc/2to3.patch/libs/BWA_analysis_H_update_new_family_dependent.py-398-  file1=open(database+sam+"_title.txt","r")
##############################################
seqsero-1.0.1+dfsg/.pc/2to3.patch/libs/BWA_analysis_O_new_dependent.py-214-  os.system("samtools view -h -o "+sam+" "+bam)
seqsero-1.0.1+dfsg/.pc/2to3.patch/libs/BWA_analysis_O_new_dependent.py:215:  os.system("cat "+sam+"|awk '{if ($5>0) {print $10}}'>"+sam+"_seq.txt")
seqsero-1.0.1+dfsg/.pc/2to3.patch/libs/BWA_analysis_O_new_dependent.py:216:  os.system("cat "+sam+"|awk '{if ($5>0) {print $1}}'>"+sam+"_title.txt")
seqsero-1.0.1+dfsg/.pc/2to3.patch/libs/BWA_analysis_O_new_dependent.py-217-  file1=open(sam+"_title.txt","r")
##############################################
seqsero-1.0.1+dfsg/.pc/2to3.patch/libs/deletion_compare.py-80-  os.system("samtools view -h -o "+sam+" "+bam)
seqsero-1.0.1+dfsg/.pc/2to3.patch/libs/deletion_compare.py:81:  os.system("cat "+sam+"|awk '{if ($5>0) {print $10}}'>"+sam+"_seq.txt")
seqsero-1.0.1+dfsg/.pc/2to3.patch/libs/deletion_compare.py:82:  os.system("cat "+sam+"|awk '{if ($5>0) {print $1}}'>"+sam+"_title.txt")
seqsero-1.0.1+dfsg/.pc/2to3.patch/libs/deletion_compare.py-83-  file1=open(sam+"_title.txt","r")