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1 #!/bin/bash
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2
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3 # FASTX-toolkit - FASTA/FASTQ preprocessing tools.
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4 # Copyright (C) 2009 A. Gordon (gordon@cshl.edu)
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5 #
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6 # This program is free software: you can redistribute it and/or modify
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7 # it under the terms of the GNU Affero General Public License as
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8 # published by the Free Software Foundation, either version 3 of the
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9 # License, or (at your option) any later version.
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10 #
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11 # This program is distributed in the hope that it will be useful,
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12 # but WITHOUT ANY WARRANTY; without even the implied warranty of
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13 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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14 # GNU Affero General Public License for more details.
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15 #
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16 # You should have received a copy of the GNU Affero General Public License
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17 # along with this program. If not, see <http://www.gnu.org/licenses/>.
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18
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19 #
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20 #This is a shell script wrapper for 'fastx_barcode_splitter.pl'
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21 #
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22 # 1. Output files are saved at the dataset's files_path directory.
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23 #
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24 # 2. 'fastx_barcode_splitter.pl' outputs a textual table.
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25 # This script turns it into pretty HTML with working URL
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26 # (so lazy users can just click on the URLs and get their files)
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27
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28 BARCODE_FILE="$1"
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29 FASTQ_FILE="$2"
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30 LIBNAME="$3"
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31 OUTPUT_PATH="$4"
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32 shift 4
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33 # The rest of the parameters are passed to the split program
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34
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35 if [ "$OUTPUT_PATH" == "" ]; then
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36 echo "Usage: $0 [BARCODE FILE] [FASTQ FILE] [LIBRARY_NAME] [OUTPUT_PATH]" >&2
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37 exit 1
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38 fi
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39
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40 #Sanitize library name, make sure we can create a file with this name
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41 LIBNAME=${LIBNAME//\.gz/}
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42 LIBNAME=${LIBNAME//\.txt/}
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43 LIBNAME=${LIBNAME//[^[:alnum:]]/_}
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44
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45 if [ ! -r "$FASTQ_FILE" ]; then
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46 echo "Error: Input file ($FASTQ_FILE) not found!" >&2
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47 exit 1
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48 fi
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49 if [ ! -r "$BARCODE_FILE" ]; then
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50 echo "Error: barcode file ($BARCODE_FILE) not found!" >&2
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51 exit 1
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52 fi
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53 mkdir -p "$OUTPUT_PATH"
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54 if [ ! -d "$OUTPUT_PATH" ]; then
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55 echo "Error: failed to create output path '$OUTPUT_PATH'" >&2
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56 exit 1
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57 fi
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58
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59 PUBLICURL=""
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60 BASEPATH="$OUTPUT_PATH/"
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61 #PREFIX="$BASEPATH"`date "+%Y-%m-%d_%H%M__"`"${LIBNAME}__"
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62 PREFIX="$BASEPATH""${LIBNAME}__"
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63 SUFFIX=".txt"
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64
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65 RESULTS=`zcat -f "$FASTQ_FILE" | fastx_barcode_splitter.pl --bcfile "$BARCODE_FILE" --prefix "$PREFIX" --suffix "$SUFFIX" "$@"`
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66 if [ $? != 0 ]; then
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67 echo "error"
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68 fi
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69
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70 #
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71 # Convert the textual tab-separated table into simple HTML table,
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72 # with the local path replaces with a valid URL
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73 echo "<html><body><table border=1>"
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74 echo "$RESULTS" | sed -r "s|$BASEPATH(.*)|<a href=\"\\1\">\\1</a>|" | sed '
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75 i<tr><td>
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76 s|\t|</td><td>|g
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77 a<\/td><\/tr>
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78 '
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79 echo "<p>"
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80 echo "</table></body></html>"
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