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grep rough audit - static analysis tool
v2.8 written by @Wireghoul
=================================[justanotherhacker.com]===
dnaclust-3/debian/patches/resolve_name_space_conflict_fastasort.patch-14-@@ -67,8 +67,8 @@ trap "rm -fr $tempdir" EXIT
dnaclust-3/debian/patches/resolve_name_space_conflict_fastasort.patch:15: db_sorted=`basename ${cluster_centers} .fasta`.sorted.fasta
dnaclust-3/debian/patches/resolve_name_space_conflict_fastasort.patch-16- # Reads the sequences from STDIN.
##############################################
dnaclust-3/debian/patches/resolve_name_space_conflict_fastasort.patch-29-@@ -74,8 +74,8 @@ trap "rm -fr $tempdir" EXIT
dnaclust-3/debian/patches/resolve_name_space_conflict_fastasort.patch:30: db_sorted=`basename ${cluster_centers} .fasta`.sorted.fasta
dnaclust-3/debian/patches/resolve_name_space_conflict_fastasort.patch-31- # Reads the sequences from STDIN.
##############################################
dnaclust-3/debian/patches/resolve_name_space_conflict_fastasort.patch-40-@@ -87,7 +87,7 @@ then
dnaclust-3/debian/patches/resolve_name_space_conflict_fastasort.patch:41: unclustered_seq=`basename $input .fasta`.unclustered.fasta
dnaclust-3/debian/patches/resolve_name_space_conflict_fastasort.patch-42- awk '{ for (i = 1; i <= NF; i++) print $i}' $input.db.clusters > $tempdir/clustered_seqs
##############################################
dnaclust-3/debian/patches/resolve_name_space_conflict_fastasort.patch-51-@@ -54,7 +54,7 @@ tempdir=`mktemp -d -p .`
dnaclust-3/debian/patches/resolve_name_space_conflict_fastasort.patch:52: sequences_sorted=`mktemp -p $tempdir`
dnaclust-3/debian/patches/resolve_name_space_conflict_fastasort.patch-53- # Reads the sequences from STDIN.
##############################################
dnaclust-3/debian/patches/resolve_name_space_conflict_fastasort.patch-57-
dnaclust-3/debian/patches/resolve_name_space_conflict_fastasort.patch:58: input_count=`grep -c '^>' $sequences_sorted`
dnaclust-3/debian/patches/resolve_name_space_conflict_fastasort.patch-59- if [ $input_count -le 1 ]
##############################################
dnaclust-3/debian/patches/resolve_name_space_conflict_fastasort.patch-62-
dnaclust-3/debian/patches/resolve_name_space_conflict_fastasort.patch:63: sequences_sorted_head_large_centers=`mktemp -p $tempdir`
dnaclust-3/debian/patches/resolve_name_space_conflict_fastasort.patch-64--"$dnaclust_path/fastaselect" -c -f $sequences_sorted_head < $large_clusters > $sequences_sorted_head_large_centers
##############################################
dnaclust-3/debian/patches/resolve_name_space_conflict_fastasort.patch-66-
dnaclust-3/debian/patches/resolve_name_space_conflict_fastasort.patch:67: sequences_minus_centers=`mktemp -p $tempdir`
dnaclust-3/debian/patches/resolve_name_space_conflict_fastasort.patch-68--"$dnaclust_path/fastaselect" --everything-except -f $sequences_sorted < $large_clusters > $sequences_minus_centers
##############################################
dnaclust-3/debian/patches/resolve_name_space_conflict_fastasort.patch-70-
dnaclust-3/debian/patches/resolve_name_space_conflict_fastasort.patch:71: centers_count=`grep -c '^>' $sequences_sorted_head_large_centers`
dnaclust-3/debian/patches/resolve_name_space_conflict_fastasort.patch-72- print_message "Recruiting from the rest of the sequences, using $centers_count centers."
##############################################
dnaclust-3/debian/patches/resolve_name_space_conflict_fastasort.patch-74-+++ b/star-align
dnaclust-3/debian/patches/resolve_name_space_conflict_fastasort.patch:75:@@ -38,7 +38,7 @@ sequences_fasta=`mktemp -p $tempdir`
dnaclust-3/debian/patches/resolve_name_space_conflict_fastasort.patch-76-
##############################################
dnaclust-3/.pc/resolve_name_space_conflict_fastasort.patch/dnaclust-abun.sh-65-
dnaclust-3/.pc/resolve_name_space_conflict_fastasort.patch/dnaclust-abun.sh:66:#sequences_sorted=`mktemp -p $tempdir`
dnaclust-3/.pc/resolve_name_space_conflict_fastasort.patch/dnaclust-abun.sh:67:db_sorted=`basename ${cluster_centers} .fasta`.sorted.fasta
dnaclust-3/.pc/resolve_name_space_conflict_fastasort.patch/dnaclust-abun.sh-68-# Reads the sequences from STDIN.
##############################################
dnaclust-3/.pc/resolve_name_space_conflict_fastasort.patch/dnaclust-ref-72-
dnaclust-3/.pc/resolve_name_space_conflict_fastasort.patch/dnaclust-ref:73:#sequences_sorted=`mktemp -p $tempdir`
dnaclust-3/.pc/resolve_name_space_conflict_fastasort.patch/dnaclust-ref:74:db_sorted=`basename ${cluster_centers} .fasta`.sorted.fasta
dnaclust-3/.pc/resolve_name_space_conflict_fastasort.patch/dnaclust-ref-75-# Reads the sequences from STDIN.
##############################################
dnaclust-3/.pc/resolve_name_space_conflict_fastasort.patch/dnaclust-ref-86- print_message "Run DNACLUST on remaining sequences."
dnaclust-3/.pc/resolve_name_space_conflict_fastasort.patch/dnaclust-ref:87: unclustered_seq=`basename $input .fasta`.unclustered.fasta
dnaclust-3/.pc/resolve_name_space_conflict_fastasort.patch/dnaclust-ref-88- awk '{ for (i = 1; i <= NF; i++) print $i}' $input.db.clusters > $tempdir/clustered_seqs
##############################################
dnaclust-3/.pc/resolve_name_space_conflict_fastasort.patch/find-large-clusters-53-
dnaclust-3/.pc/resolve_name_space_conflict_fastasort.patch/find-large-clusters:54:sequences_sorted=`mktemp -p $tempdir`
dnaclust-3/.pc/resolve_name_space_conflict_fastasort.patch/find-large-clusters-55-# Reads the sequences from STDIN.
##############################################
dnaclust-3/.pc/resolve_name_space_conflict_fastasort.patch/find-large-clusters-58-
dnaclust-3/.pc/resolve_name_space_conflict_fastasort.patch/find-large-clusters:59:input_count=`grep -c '^>' $sequences_sorted`
dnaclust-3/.pc/resolve_name_space_conflict_fastasort.patch/find-large-clusters-60-if [ $input_count -le 1 ]
##############################################
dnaclust-3/.pc/resolve_name_space_conflict_fastasort.patch/find-large-clusters-67-then
dnaclust-3/.pc/resolve_name_space_conflict_fastasort.patch/find-large-clusters:68: sample_count_float=`echo "e(l($input_count)*0.8)" | bc -l`
dnaclust-3/.pc/resolve_name_space_conflict_fastasort.patch/find-large-clusters:69: sample_count=`echo "($sample_count_float * 2 + 1) / 2" | bc`
dnaclust-3/.pc/resolve_name_space_conflict_fastasort.patch/find-large-clusters-70-fi
dnaclust-3/.pc/resolve_name_space_conflict_fastasort.patch/find-large-clusters-71-
dnaclust-3/.pc/resolve_name_space_conflict_fastasort.patch/find-large-clusters:72:sample_lines=`awk --assign=count=$sample_count '/^>/{if (++n > count) {print FNR - 1; exit}}' $sequences_sorted`
dnaclust-3/.pc/resolve_name_space_conflict_fastasort.patch/find-large-clusters-73-
##############################################
dnaclust-3/.pc/resolve_name_space_conflict_fastasort.patch/find-large-clusters-75-print_message "Splitting $input_count input sequences into a sample of size $sample_count, and the rest."
dnaclust-3/.pc/resolve_name_space_conflict_fastasort.patch/find-large-clusters:76:sequences_sorted_head=`mktemp -p $tempdir`
dnaclust-3/.pc/resolve_name_space_conflict_fastasort.patch/find-large-clusters-77-head -n $sample_lines $sequences_sorted > $sequences_sorted_head
dnaclust-3/.pc/resolve_name_space_conflict_fastasort.patch/find-large-clusters-78-
dnaclust-3/.pc/resolve_name_space_conflict_fastasort.patch/find-large-clusters:79:large_clusters=`mktemp -p $tempdir`
dnaclust-3/.pc/resolve_name_space_conflict_fastasort.patch/find-large-clusters-80-print_message "Clustering the set of sample sequences, and extracting centers of large clusters."
##############################################
dnaclust-3/.pc/resolve_name_space_conflict_fastasort.patch/find-large-clusters-83-
dnaclust-3/.pc/resolve_name_space_conflict_fastasort.patch/find-large-clusters:84:sequences_sorted_head_large_centers=`mktemp -p $tempdir`
dnaclust-3/.pc/resolve_name_space_conflict_fastasort.patch/find-large-clusters-85-"$dnaclust_path/fastaselect" -c -f $sequences_sorted_head < $large_clusters > $sequences_sorted_head_large_centers
dnaclust-3/.pc/resolve_name_space_conflict_fastasort.patch/find-large-clusters-86-
dnaclust-3/.pc/resolve_name_space_conflict_fastasort.patch/find-large-clusters:87:sequences_minus_centers=`mktemp -p $tempdir`
dnaclust-3/.pc/resolve_name_space_conflict_fastasort.patch/find-large-clusters-88-"$dnaclust_path/fastaselect" --everything-except -f $sequences_sorted < $large_clusters > $sequences_minus_centers
dnaclust-3/.pc/resolve_name_space_conflict_fastasort.patch/find-large-clusters-89-
dnaclust-3/.pc/resolve_name_space_conflict_fastasort.patch/find-large-clusters:90:centers_count=`grep -c '^>' $sequences_sorted_head_large_centers`
dnaclust-3/.pc/resolve_name_space_conflict_fastasort.patch/find-large-clusters-91-print_message "Recruiting from the rest of the sequences, using $centers_count centers."
##############################################
dnaclust-3/.pc/resolve_name_space_conflict_fastasort.patch/star-align-35-
dnaclust-3/.pc/resolve_name_space_conflict_fastasort.patch/star-align:36:center_fasta=`mktemp -p $tempdir`
dnaclust-3/.pc/resolve_name_space_conflict_fastasort.patch/star-align:37:sequences_fasta=`mktemp -p $tempdir`
dnaclust-3/.pc/resolve_name_space_conflict_fastasort.patch/star-align-38-
##############################################
dnaclust-3/dnaclust-abun.sh-65-
dnaclust-3/dnaclust-abun.sh:66:#sequences_sorted=`mktemp -p $tempdir`
dnaclust-3/dnaclust-abun.sh:67:db_sorted=`basename ${cluster_centers} .fasta`.sorted.fasta
dnaclust-3/dnaclust-abun.sh-68-# Reads the sequences from STDIN.
##############################################
dnaclust-3/dnaclust-ref-72-
dnaclust-3/dnaclust-ref:73:#sequences_sorted=`mktemp -p $tempdir`
dnaclust-3/dnaclust-ref:74:db_sorted=`basename ${cluster_centers} .fasta`.sorted.fasta
dnaclust-3/dnaclust-ref-75-# Reads the sequences from STDIN.
##############################################
dnaclust-3/dnaclust-ref-86- print_message "Run DNACLUST on remaining sequences."
dnaclust-3/dnaclust-ref:87: unclustered_seq=`basename $input .fasta`.unclustered.fasta
dnaclust-3/dnaclust-ref-88- awk '{ for (i = 1; i <= NF; i++) print $i}' $input.db.clusters > $tempdir/clustered_seqs
##############################################
dnaclust-3/find-large-clusters-53-
dnaclust-3/find-large-clusters:54:sequences_sorted=`mktemp -p $tempdir`
dnaclust-3/find-large-clusters-55-# Reads the sequences from STDIN.
##############################################
dnaclust-3/find-large-clusters-58-
dnaclust-3/find-large-clusters:59:input_count=`grep -c '^>' $sequences_sorted`
dnaclust-3/find-large-clusters-60-if [ $input_count -le 1 ]
##############################################
dnaclust-3/find-large-clusters-67-then
dnaclust-3/find-large-clusters:68: sample_count_float=`echo "e(l($input_count)*0.8)" | bc -l`
dnaclust-3/find-large-clusters:69: sample_count=`echo "($sample_count_float * 2 + 1) / 2" | bc`
dnaclust-3/find-large-clusters-70-fi
dnaclust-3/find-large-clusters-71-
dnaclust-3/find-large-clusters:72:sample_lines=`awk --assign=count=$sample_count '/^>/{if (++n > count) {print FNR - 1; exit}}' $sequences_sorted`
dnaclust-3/find-large-clusters-73-
##############################################
dnaclust-3/find-large-clusters-75-print_message "Splitting $input_count input sequences into a sample of size $sample_count, and the rest."
dnaclust-3/find-large-clusters:76:sequences_sorted_head=`mktemp -p $tempdir`
dnaclust-3/find-large-clusters-77-head -n $sample_lines $sequences_sorted > $sequences_sorted_head
dnaclust-3/find-large-clusters-78-
dnaclust-3/find-large-clusters:79:large_clusters=`mktemp -p $tempdir`
dnaclust-3/find-large-clusters-80-print_message "Clustering the set of sample sequences, and extracting centers of large clusters."
##############################################
dnaclust-3/find-large-clusters-83-
dnaclust-3/find-large-clusters:84:sequences_sorted_head_large_centers=`mktemp -p $tempdir`
dnaclust-3/find-large-clusters-85-"/usr/lib/dnaclust/fastaselect" -c -f $sequences_sorted_head < $large_clusters > $sequences_sorted_head_large_centers
dnaclust-3/find-large-clusters-86-
dnaclust-3/find-large-clusters:87:sequences_minus_centers=`mktemp -p $tempdir`
dnaclust-3/find-large-clusters-88-"/usr/lib/dnaclust/fastaselect" --everything-except -f $sequences_sorted < $large_clusters > $sequences_minus_centers
dnaclust-3/find-large-clusters-89-
dnaclust-3/find-large-clusters:90:centers_count=`grep -c '^>' $sequences_sorted_head_large_centers`
dnaclust-3/find-large-clusters-91-print_message "Recruiting from the rest of the sequences, using $centers_count centers."
##############################################
dnaclust-3/star-align-35-
dnaclust-3/star-align:36:center_fasta=`mktemp -p $tempdir`
dnaclust-3/star-align:37:sequences_fasta=`mktemp -p $tempdir`
dnaclust-3/star-align-38-