/tools/fastx_toolkit/fastx_barcode_splitter_galaxy_wrapper.sh

https://bitbucket.org/cistrome/cistrome-harvard/ · Shell · 80 lines · 41 code · 9 blank · 30 comment · 7 complexity · 8a923b8288c6cffc061819f0defa6aad MD5 · raw file 

    

  1. #!/bin/bash
    2. 

  2. 

  3. #    FASTX-toolkit - FASTA/FASTQ preprocessing tools.
    4. 

  4. #    Copyright (C) 2009  A. Gordon (gordon@cshl.edu)
    5. 

  5. #
    6. 

  6. #   This program is free software: you can redistribute it and/or modify
    7. 

  7. #   it under the terms of the GNU Affero General Public License as
    8. 

  8. #   published by the Free Software Foundation, either version 3 of the
    9. 

  9. #   License, or (at your option) any later version.
    10. 

  10. #
    11. 

  11. #   This program is distributed in the hope that it will be useful,
    12. 

  12. #   but WITHOUT ANY WARRANTY; without even the implied warranty of
    13. 

  13. #   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
    14. 

  14. #   GNU Affero General Public License for more details.
    15. 

  15. #
    16. 

  16. #    You should have received a copy of the GNU Affero General Public License
    17. 

  17. #    along with this program.  If not, see <http://www.gnu.org/licenses/>.
    18. 

  18. 

  19. #
    20. 

  20. #This is a shell script wrapper for 'fastx_barcode_splitter.pl'
    21. 

  21. #
    22. 

  22. # 1. Output files are saved at the dataset's files_path directory.
    23. 

  23. #    
    24. 

  24. # 2. 'fastx_barcode_splitter.pl' outputs a textual table.
    25. 

  25. #    This script turns it into pretty HTML with working URL
    26. 

  26. #    (so lazy users can just click on the URLs and get their files)
    27. 

  27. 

  28. BARCODE_FILE="$1"
    29. 

  29. FASTQ_FILE="$2"
    30. 

  30. LIBNAME="$3"
    31. 

  31. OUTPUT_PATH="$4"
    32. 

  32. shift 4
    33. 

  33. # The rest of the parameters are passed to the split program
    34. 

  34. 

  35. if [ "$OUTPUT_PATH" == "" ]; then
    36. 

  36. 	echo "Usage: $0 [BARCODE FILE] [FASTQ FILE] [LIBRARY_NAME] [OUTPUT_PATH]" >&2
    37. 

  37. 	exit 1
    38. 

  38. fi
    39. 

  39. 

  40. #Sanitize library name, make sure we can create a file with this name
    41. 

  41. LIBNAME=${LIBNAME//\.gz/}
    42. 

  42. LIBNAME=${LIBNAME//\.txt/}
    43. 

  43. LIBNAME=${LIBNAME//[^[:alnum:]]/_}
    44. 

  44. 

  45. if [ ! -r "$FASTQ_FILE" ]; then
    46. 

  46. 	echo "Error: Input file ($FASTQ_FILE) not found!" >&2
    47. 

  47. 	exit 1
    48. 

  48. fi
    49. 

  49. if [ ! -r "$BARCODE_FILE" ]; then
    50. 

  50. 	echo "Error: barcode file ($BARCODE_FILE) not found!" >&2
    51. 

  51. 	exit 1
    52. 

  52. fi
    53. 

  53. mkdir -p "$OUTPUT_PATH"
    54. 

  54. if [ ! -d "$OUTPUT_PATH" ]; then
    55. 

  55. 	echo "Error: failed to create output path '$OUTPUT_PATH'" >&2
    56. 

  56. 	exit 1
    57. 

  57. fi
    58. 

  58. 

  59. PUBLICURL=""
    60. 

  60. BASEPATH="$OUTPUT_PATH/"
    61. 

  61. #PREFIX="$BASEPATH"`date "+%Y-%m-%d_%H%M__"`"${LIBNAME}__"
    62. 

  62. PREFIX="$BASEPATH""${LIBNAME}__"
    63. 

  63. SUFFIX=".txt"
    64. 

  64. 

  65. RESULTS=`zcat -f "$FASTQ_FILE" | fastx_barcode_splitter.pl --bcfile "$BARCODE_FILE" --prefix "$PREFIX" --suffix "$SUFFIX" "$@"`
    66. 

  66. if [ $? != 0 ]; then
    67. 

  67. 	echo "error"
    68. 

  68. fi
    69. 

  69. 

  70. #
    71. 

  71. # Convert the textual tab-separated table into simple HTML table,
    72. 

  72. # with the local path replaces with a valid URL
    73. 

  73. echo "<html><body><table border=1>"
    74. 

  74. echo "$RESULTS" | sed -r "s|$BASEPATH(.*)|<a href=\"\\1\">\\1</a>|" | sed '
    75. 

  75. i<tr><td>
    76. 

  76. s|\t|</td><td>|g
    77. 

  77. a<\/td><\/tr>
    78. 

  78. '
    79. 

  79. echo "<p>"
    80. 

  80. echo "</table></body></html>"
    81.