# HG changeset patch
# User davidvanzessen
# Date 1480001234 18000
# Node ID b360a373835fb238d7afa6f80880785a166e4720
# Parent d3cf09f5a1a65779cc3281b6103bfe7c348dcf01
Uploaded
diff -r d3cf09f5a1a6 -r b360a373835f imgt_concatenate.sh
--- a/imgt_concatenate.sh Mon Aug 29 05:46:28 2016 -0400
+++ b/imgt_concatenate.sh Thu Nov 24 10:27:14 2016 -0500
@@ -32,37 +32,43 @@
indir=$1
outdir=$2
start_line=$3 #line # to start at, 2 to skip header
- cat `find $indir/ -name "1_*"` | tail -n+${start_line} >> "$outdir/1_Summary.txt"
- cat `find $indir/ -name "2_*"` | tail -n+${start_line} >> "$outdir/2_IMGT-gapped-nt-sequences.txt"
- cat `find $indir/ -name "3_*"` | tail -n+${start_line} >> "$outdir/3_Nt-sequences.txt"
- cat `find $indir/ -name "4_*"` | tail -n+${start_line} >> "$outdir/4_IMGT-gapped-AA-sequences.txt"
- cat `find $indir/ -name "5_*"` | tail -n+${start_line} >> "$outdir/5_AA-sequences.txt"
- cat `find $indir/ -name "6_*"` | tail -n+${start_line} >> "$outdir/6_Junction.txt"
- cat `find $indir/ -name "7_*"` | tail -n+${start_line} >> "$outdir/7_V-REGION-mutation-and-AA-change-table.txt"
- cat `find $indir/ -name "8_*"` | tail -n+${start_line} >> "$outdir/8_V-REGION-nt-mutation-statistics.txt"
- cat `find $indir/ -name "9_*"` | tail -n+${start_line} >> "$outdir/9_V-REGION-AA-change-statistics.txt"
- cat `find $indir/ -name "10_*"` | tail -n+${start_line} >> "$outdir/10_V-REGION-mutation-hotspots.txt"
+ id=$4
+ cat `find $indir/ -name "1_*"` | tail -n+${start_line} | awk -v id=$id '{ if($1 !~ /^header/) {$2=$2id; } print}' >> "$outdir/1_Summary.txt"
+ cat `find $indir/ -name "2_*"` | tail -n+${start_line} | awk -v id=$id '{ if($1 !~ /^header/) {$2=$2id; } print}' >> "$outdir/2_IMGT-gapped-nt-sequences.txt"
+ cat `find $indir/ -name "3_*"` | tail -n+${start_line} | awk -v id=$id '{ if($1 !~ /^header/) {$2=$2id; } print}' >> "$outdir/3_Nt-sequences.txt"
+ cat `find $indir/ -name "4_*"` | tail -n+${start_line} | awk -v id=$id '{ if($1 !~ /^header/) {$2=$2id; } print}' >> "$outdir/4_IMGT-gapped-AA-sequences.txt"
+ cat `find $indir/ -name "5_*"` | tail -n+${start_line} | awk -v id=$id '{ if($1 !~ /^header/) {$2=$2id; } print}' >> "$outdir/5_AA-sequences.txt"
+ cat `find $indir/ -name "6_*"` | tail -n+${start_line} | awk -v id=$id '{ if($1 !~ /^header/) {$2=$2id; } print}' >> "$outdir/6_Junction.txt"
+ cat `find $indir/ -name "7_*"` | tail -n+${start_line} | awk -v id=$id '{ if($1 !~ /^header/) {$2=$2id; } print}' >> "$outdir/7_V-REGION-mutation-and-AA-change-table.txt"
+ cat `find $indir/ -name "8_*"` | tail -n+${start_line} | awk -v id=$id '{ if($1 !~ /^header/) {$2=$2id; } print}' >> "$outdir/8_V-REGION-nt-mutation-statistics.txt"
+ cat `find $indir/ -name "9_*"` | tail -n+${start_line} | awk -v id=$id '{ if($1 !~ /^header/) {$2=$2id; } print}' >> "$outdir/9_V-REGION-AA-change-statistics.txt"
+ cat `find $indir/ -name "10_*"` | tail -n+${start_line} | awk -v id=$id '{ if($1 !~ /^header/) {$2=$2id; } print}' >> "$outdir/10_V-REGION-mutation-hotspots.txt"
}
echo "Unpacking IMGT file 1.."
imgt_unpack ${inputs[0]} "$workdir/input1"
echo "Concatenating IMGT file 1..."
-concat_imgt_files "$workdir/input1" "$workdir/output" 1
+id=${inputs[1]}
+concat_imgt_files "$workdir/input1" "$workdir/output" 1 $id
-remaining_inputs=("${inputs[@]:1}")
+remaining_inputs=("${inputs[@]:2}")
-i="2"
-for input in "${remaining_inputs[@]}"
-do
- echo "Unpacking IMGT file $i.."
+i="0"
+while [ $i -lt ${#remaining_inputs[@]} ]; do
+ j=$((i+1))
+ input="${remaining_inputs[$i]}"
+ id="${remaining_inputs[$j]}"
+
+ echo "Unpacking IMGT file $j.."
current_dir="$workdir/input${i}"
imgt_unpack "${input}" "${current_dir}"
echo "Concatenating IMGT file $1..."
- concat_imgt_files "${current_dir}" "$workdir/output" 2
- i=$((i+1))
+ concat_imgt_files "${current_dir}" "$workdir/output" 2 $id
+ i=$((i+2))
done
+
echo "Creating new IMGT zip"
cd "$workdir/output"
tar cfJ "$output" *
@@ -70,3 +76,17 @@
#awk to fix the sequence numbers repeating?
echo "Done"
+
+exit 0
+
+i="1"
+for input in "${remaining_inputs[@]}"
+do
+ echo "Unpacking IMGT file $i.."
+ current_dir="$workdir/input${i}"
+ imgt_unpack "${input}" "${current_dir}"
+ echo "Concatenating IMGT file $1..."
+ concat_imgt_files "${current_dir}" "$workdir/output" 2 $id
+ i=$((i+1))
+done
+
diff -r d3cf09f5a1a6 -r b360a373835f imgt_concatenate.xml
--- a/imgt_concatenate.xml Mon Aug 29 05:46:28 2016 -0400
+++ b/imgt_concatenate.xml Thu Nov 24 10:27:14 2016 -0500
@@ -2,16 +2,40 @@
imgt_concatenate.sh $out_file
-#for $i, $f in enumerate($files)
- "$f.file"
-#end for
+#if str( $with_id.with_id_selector ) == "true":
+ #for $i, $f in enumerate($with_id.files)
+ "$f.file"
+ "$f.id"
+ #end for
+#else
+ #for $i, $f in enumerate($with_id.files)
+ "$f.file"
+ ""
+ #end for
+#end if
-
-
-
+
+
+
+
+
+
+
+
+
+ .+
+
+
+
+
+
+
+
+
+
-
+ .+