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annotate summarize_unique_barcodes.sh @ 24:431aebd93843 draft default tip

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Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
author nikos
date Wed, 05 Aug 2015 09:21:02 -0400
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24
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
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1 #!/bin/bash
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
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2
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
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3 ####################################################################################################
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
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4 #Copyright (C) 2014 Lukasz Kielpinski, Nikos Sidiropoulos
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
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5
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
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6 #This program is free software: you can redistribute it and/or modify it under the terms of the
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
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7 #GNU General Public License as published by the Free Software Foundation, either version 3 of the
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
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8 #License, or (at your option) any later version.
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
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9
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
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10 #This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
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11 #even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
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12 #GNU General Public License for more details (http://www.gnu.org/licenses/).
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
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13 ####################################################################################################
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
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14
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
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15 function print_help {
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
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16 cat <<End-of-message
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
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17 Summarize Unique Barcodes.
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
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18 Counts the number of unique random barcodes and reads associated with each sequenced fragment.
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
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19 -------------------------------------
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
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20 Input arguments:
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
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21 -h: Help
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
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22 -f: Aligned reads in BAM format.
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
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23 -b: Barcode file (optional).
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
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24 -p: Set priming position to a fixed value.
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
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25 -t: Trim untemplated nucleotides.
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
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26 -k: Produce k2n file. Warning: Can be sloooow!
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
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27 -r: Rscript path
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
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28 -o: Output folder (default: "output_dir")
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
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29 -------------------------------------
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
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30 Usage : summarize_unique_barcodes.sh -f <BAM_file> -b <BARCODES> -p <PRIMING_POSITION> -t -k -r <R_SCRIPT_PATH>
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
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31 End-of-message
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
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32 exit
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
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33 }
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
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34
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
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35 #defaults
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
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36 output_dir="output_dir"
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
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37 trim_flag="False"
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
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38
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
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39 #parse input
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
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40 while getopts hf:b::p:o:ktr: myarg
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
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41 do case "$myarg" in
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
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42 h) print_help
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
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43 exit ;;
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
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44 f) bamfile="$OPTARG" ;; #required
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
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45 b) barcodes="$OPTARG" ;; #optional
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
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46 t) trim_flag="True" ;;
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
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47 k) k2n="True" ;;
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
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48 p) priming_pos="$OPTARG" ;;
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
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49 o) output_dir="$OPTARG" ;;
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
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50 r) R_SCRIPT_PATH="$OPTARG" ;; #required
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
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51 [?]) echo "ERROR: Unknown parameter"
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
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52 print_help
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
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53 exit 1 ;;
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
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54 esac
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
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55 done
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
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56
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
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57 ###### Sanity checks ######
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
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58 if [ -z $bamfile ]; then
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
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59 echo "Error: Aligned reads file is missing!"
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
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60 print_help
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
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61 exit 1
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
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62 fi
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
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63
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
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64 if [ "$barcodes" == "None" ] && [ "$k2n" == "True" ]; then
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
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65 echo "Error: k2n file cannot be produced without a barcode file!"
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
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66 exit 1
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
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67 fi
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
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68
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
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69
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
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70 mkdir -p $output_dir
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
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71
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
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72 #Check if bamfile contains single or paired-end reads
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
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73 samtools view -f 0x1 $bamfile | head -n 1 > paired
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
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74
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
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75 if [ -s paired ]; then
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
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76 #paired-end
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
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77 samtools view $bamfile | awk 'BEGIN{OFS="\t"}{if(substr($0,1,1)!="@"){print}}' - | awk -v out="${output_dir}/trimming_stats.txt" -v flag="${trim_flag}" 'BEGIN{OFS="\t";counter[0]=0;counter[1]=0;counter[2]=0;counter[3]=0;counter[4]=0}
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
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78 function abs(value){return(value<0?-value:value)}
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
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79 function return_offset(local_offset){print($1, $3, $4+local_offset, $4+abs($9)-1);counter[local_offset]++}
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
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80 ($2 != 99) {next};
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
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81 (flag == "False") {return_offset(0);next};
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
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82 (/[\s\t]MD:Z:/ && !/MD:Z:([012][ACGT])/) {return_offset(0);next};
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
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83 (/[\s\t]MD:Z:0[ACGT]/ && !/MD:Z:0[ACGT][01][ACGT]/ && substr($10,1,1)=="N") {return_offset(0);next};
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
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84 (/[\s\t]MD:Z:0[ACGT]/ && !/MD:Z:0[ACGT][01][ACGT]/) {return_offset(1);next};
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
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85
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
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86 (/[\s\t]MD:Z:1[ACGT]/ && !/MD:Z:1[ACGT]0[ACGT]/ && substr($10,2,1)=="N") {return_offset(0);next};
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
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87 (/[\s\t]MD:Z:1[ACGT]/ && !/MD:Z:1[ACGT]0[ACGT]/) {return_offset(2);next};
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
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88
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
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89 (/MD:Z:0[ACGT]0[ACGT]/ && !/MD:Z:0[ACGT]0[ACGT]0[ACGT]/ && substr($10,1,2)=="NN") {return_offset(0);next};
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
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90 (/MD:Z:0[ACGT]0[ACGT]/ && !/MD:Z:0[ACGT]0[ACGT]0[ACGT]/ && substr($10,1,1)=="N") {return_offset(2);next};
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
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91 (/MD:Z:0[ACGT]0[ACGT]/ && !/MD:Z:0[ACGT]0[ACGT]0[ACGT]/ && substr($10,2,1)=="N") {return_offset(1);next};
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
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92 (/MD:Z:0[ACGT]0[ACGT]/ && !/MD:Z:0[ACGT]0[ACGT]0[ACGT]/) {return_offset(2);next};
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
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93
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
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94 (/[\s\t]MD:Z:1[ACGT]0[ACGT]/ && substr($10,2,2)=="NN") {return_offset(0);next};
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
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95 (/[\s\t]MD:Z:1[ACGT]0[ACGT]/ && substr($10,2,1)=="N") {return_offset(3);next};
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
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96 (/[\s\t]MD:Z:1[ACGT]0[ACGT]/ && substr($10,3,1)=="N") {return_offset(2);next};
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
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97 (/[\s\t]MD:Z:1[ACGT]0[ACGT]/) {return_offset(3);next};
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
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98
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
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99 (/MD:Z:0[ACGT]1[ACGT]/ && substr($10,3,1)=="N" && substr($10,1,1)=="N") {return_offset(0);next};
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
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100 (/MD:Z:0[ACGT]1[ACGT]/ && substr($10,3,1)=="N") {return_offset(1);next};
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
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101 (/MD:Z:0[ACGT]1[ACGT]/ && substr($10,1,1)=="N") {return_offset(3);next};
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
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102 (/MD:Z:0[ACGT]1[ACGT]/) {return_offset(3);next};
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
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103
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
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104 (/MD:Z:2[ACGT]/ && substr($10,3,1)=="N") {return_offset(0);next};
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
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105 (/MD:Z:2[ACGT]/) {return_offset(3);next};
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
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106
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
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107 (substr($10,3,1)!="N" && /MD:Z:0[ACGT]0[ACGT]0[ACGT]/) {return_offset(3);next};
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
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108 (substr($10,2,1)!="N" && /MD:Z:0[ACGT]0[ACGT]0[ACGT]/) {return_offset(2);next};
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
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109 (substr($10,1,1)!="N" && /MD:Z:0[ACGT]0[ACGT]0[ACGT]/) {return_offset(1);next};
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
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110
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
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111 {return_offset(0);counter[4]++}
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
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112 END{print("No trimming:",counter[0],", out of which not recognized MD field for:",counter[4],"; 1 nt trimmed:", counter[1],"; 2 nt trimmed:", counter[2],"; 3 nt trimmed:",counter[3]) > out}' | sort -S1G -k1,1 | gzip > positions_temp_sorted.gz
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
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113
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
nikos
parents:
diff changeset
114 else
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
nikos
parents:
diff changeset
115 #single-end
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
nikos
parents:
diff changeset
116 samtools view $bamfile | awk 'BEGIN{OFS="\t"}{if(substr($0,1,1)!="@"){print}}' - | awk -v out="${output_dir}/trimming_stats.txt" -v flag="${trim_flag}" 'BEGIN{OFS="\t";counter[0]=0;counter[1]=0;counter[2]=0;counter[3]=0;counter[4]=0}
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
nikos
parents:
diff changeset
117 function abs(value){return(value<0?-value:value)}
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
nikos
parents:
diff changeset
118 function return_offset(local_offset){print($1, $3, $4+local_offset, $4+abs($9)-1);counter[local_offset]++}
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
nikos
parents:
diff changeset
119 ($2 != 0) {next};
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
nikos
parents:
diff changeset
120 (flag == "False") {return_offset(0);next};
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
nikos
parents:
diff changeset
121 (/[\s\t]MD:Z:/ && !/MD:Z:([012][ACGT])/) {return_offset(0);next};
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
nikos
parents:
diff changeset
122 (/[\s\t]MD:Z:0[ACGT]/ && !/MD:Z:0[ACGT][01][ACGT]/ && substr($10,1,1)=="N") {return_offset(0);next};
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
nikos
parents:
diff changeset
123 (/[\s\t]MD:Z:0[ACGT]/ && !/MD:Z:0[ACGT][01][ACGT]/) {return_offset(1);next};
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
nikos
parents:
diff changeset
124
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
nikos
parents:
diff changeset
125 (/[\s\t]MD:Z:1[ACGT]/ && !/MD:Z:1[ACGT]0[ACGT]/ && substr($10,2,1)=="N") {return_offset(0);next};
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
nikos
parents:
diff changeset
126 (/[\s\t]MD:Z:1[ACGT]/ && !/MD:Z:1[ACGT]0[ACGT]/) {return_offset(2);next};
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
nikos
parents:
diff changeset
127
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
nikos
parents:
diff changeset
128 (/MD:Z:0[ACGT]0[ACGT]/ && !/MD:Z:0[ACGT]0[ACGT]0[ACGT]/ && substr($10,1,2)=="NN") {return_offset(0);next};
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
nikos
parents:
diff changeset
129 (/MD:Z:0[ACGT]0[ACGT]/ && !/MD:Z:0[ACGT]0[ACGT]0[ACGT]/ && substr($10,1,1)=="N") {return_offset(2);next};
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
nikos
parents:
diff changeset
130 (/MD:Z:0[ACGT]0[ACGT]/ && !/MD:Z:0[ACGT]0[ACGT]0[ACGT]/ && substr($10,2,1)=="N") {return_offset(1);next};
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
nikos
parents:
diff changeset
131 (/MD:Z:0[ACGT]0[ACGT]/ && !/MD:Z:0[ACGT]0[ACGT]0[ACGT]/) {return_offset(2);next};
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
nikos
parents:
diff changeset
132
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
nikos
parents:
diff changeset
133 (/[\s\t]MD:Z:1[ACGT]0[ACGT]/ && substr($10,2,2)=="NN") {return_offset(0);next};
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
nikos
parents:
diff changeset
134 (/[\s\t]MD:Z:1[ACGT]0[ACGT]/ && substr($10,2,1)=="N") {return_offset(3);next};
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
nikos
parents:
diff changeset
135 (/[\s\t]MD:Z:1[ACGT]0[ACGT]/ && substr($10,3,1)=="N") {return_offset(2);next};
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
nikos
parents:
diff changeset
136 (/[\s\t]MD:Z:1[ACGT]0[ACGT]/) {return_offset(3);next};
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
nikos
parents:
diff changeset
137
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
nikos
parents:
diff changeset
138 (/MD:Z:0[ACGT]1[ACGT]/ && substr($10,3,1)=="N" && substr($10,1,1)=="N") {return_offset(0);next};
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
nikos
parents:
diff changeset
139 (/MD:Z:0[ACGT]1[ACGT]/ && substr($10,3,1)=="N") {return_offset(1);next};
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
nikos
parents:
diff changeset
140 (/MD:Z:0[ACGT]1[ACGT]/ && substr($10,1,1)=="N") {return_offset(3);next};
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
nikos
parents:
diff changeset
141 (/MD:Z:0[ACGT]1[ACGT]/) {return_offset(3);next};
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
nikos
parents:
diff changeset
142
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
nikos
parents:
diff changeset
143 (/MD:Z:2[ACGT]/ && substr($10,3,1)=="N") {return_offset(0);next};
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
nikos
parents:
diff changeset
144 (/MD:Z:2[ACGT]/) {return_offset(3);next};
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
nikos
parents:
diff changeset
145
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
nikos
parents:
diff changeset
146 (substr($10,3,1)!="N" && /MD:Z:0[ACGT]0[ACGT]0[ACGT]/) {return_offset(3);next};
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
nikos
parents:
diff changeset
147 (substr($10,2,1)!="N" && /MD:Z:0[ACGT]0[ACGT]0[ACGT]/) {return_offset(2);next};
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
nikos
parents:
diff changeset
148 (substr($10,1,1)!="N" && /MD:Z:0[ACGT]0[ACGT]0[ACGT]/) {return_offset(1);next};
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
nikos
parents:
diff changeset
149
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
nikos
parents:
diff changeset
150 {return_offset(0);counter[4]++}
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
nikos
parents:
diff changeset
151 END{print("No trimming:",counter[0],", out of which not recognized MD field for:",counter[4],"; 1 nt trimmed:", counter[1],"; 2 nt trimmed:", counter[2],"; 3 nt trimmed:",counter[3]) > out}' | sort -S1G -k1,1 | gzip > positions_temp_sorted.gz
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
nikos
parents:
diff changeset
152
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
nikos
parents:
diff changeset
153 fi
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
nikos
parents:
diff changeset
154
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
nikos
parents:
diff changeset
155 #Computing barcode length (Use the first line and compute the string length of the second column)
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
nikos
parents:
diff changeset
156 if [ "$barcodes" != "None" ]; then
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
nikos
parents:
diff changeset
157
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
nikos
parents:
diff changeset
158 TMP=$(for line in `cut -f 2 $barcodes`; do if [ ! -z "$line" ]; then echo $line; break; fi; done)
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
nikos
parents:
diff changeset
159 BAR_LEN=`echo ${#TMP}`
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
nikos
parents:
diff changeset
160
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
nikos
parents:
diff changeset
161 #Remove "@" from barcodes and sort them
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
nikos
parents:
diff changeset
162 sed 's/^.//' $barcodes | sort -k1,1 -S1G | gzip > barcodes_temp_sorted.gz
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
nikos
parents:
diff changeset
163
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
nikos
parents:
diff changeset
164 #Merge poistions and barcodes
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
nikos
parents:
diff changeset
165 join -1 1 <(zcat positions_temp_sorted.gz) <(zcat barcodes_temp_sorted.gz) | cut -f 2,3,4,5 -d " " | awk '{if($4 !~ /N/){print}}' | awk -v bar_len="${BAR_LEN}" '{if(length($4)==bar_len){print}}' | gzip > merged_temp.gz
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
nikos
parents:
diff changeset
166
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
nikos
parents:
diff changeset
167 rm barcodes_temp_sorted.gz
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
nikos
parents:
diff changeset
168
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
nikos
parents:
diff changeset
169 else
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
nikos
parents:
diff changeset
170 zcat positions_temp_sorted.gz | cut -f 2,3,4 | gzip > merged_temp.gz
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
nikos
parents:
diff changeset
171 fi
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
nikos
parents:
diff changeset
172
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
nikos
parents:
diff changeset
173 #If the experiment is single-end set NA values to the priming column.
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
nikos
parents:
diff changeset
174 if [ ! -s paired ]; then
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
nikos
parents:
diff changeset
175 zcat merged_temp.gz | awk '{print $1, $2, "NA", $4, $5}' - > merged_temp2
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
nikos
parents:
diff changeset
176 gzip -c merged_temp2 > merged_temp.gz
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
nikos
parents:
diff changeset
177 rm merged_temp2
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
nikos
parents:
diff changeset
178 fi
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
nikos
parents:
diff changeset
179
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
nikos
parents:
diff changeset
180 #Fix priming position
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
nikos
parents:
diff changeset
181 if [ ! -z $priming_pos ]; then
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
nikos
parents:
diff changeset
182 zcat merged_temp.gz | awk -v pos="${priming_pos}" '{print $1, $2, pos, $4, $5}' - > merged_temp2
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
nikos
parents:
diff changeset
183 gzip -c merged_temp2 > merged_temp.gz
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
nikos
parents:
diff changeset
184 rm merged_temp2
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
nikos
parents:
diff changeset
185 fi
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
nikos
parents:
diff changeset
186
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
nikos
parents:
diff changeset
187 #File summary.txt columns: RNA_ID, Start, End, barcode sequence, sequenced_count[=number of sequenced fragments fulfilling previous requiremnts]
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
nikos
parents:
diff changeset
188
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
nikos
parents:
diff changeset
189 zcat merged_temp.gz | awk '{barcode[$1][$2][$3][$4]++}END{
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
nikos
parents:
diff changeset
190 for(RNA in barcode){
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
nikos
parents:
diff changeset
191 for(start_position in barcode[RNA]){
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
nikos
parents:
diff changeset
192 for(end_position in barcode[RNA][start_position]){
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
nikos
parents:
diff changeset
193 for(barseq in barcode[RNA][start_position][end_position]){print RNA,start_position,end_position,barseq,barcode[RNA][start_position][end_position][barseq]}}}}}' > $output_dir/summary.txt
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
nikos
parents:
diff changeset
194
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
nikos
parents:
diff changeset
195 #File unique_barcodes.txt columns: RNA_ID, Start, End, number of unique barcodes observed for this fragment.
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
nikos
parents:
diff changeset
196
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
nikos
parents:
diff changeset
197 awk '{barcode[$1][$2][$3]++}END{
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
nikos
parents:
diff changeset
198 for(RNA in barcode){
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
nikos
parents:
diff changeset
199 for(start_position in barcode[RNA]){
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
nikos
parents:
diff changeset
200 for(end_position in barcode[RNA][start_position]){print RNA "\t" start_position "\t" end_position "\t" barcode[RNA][start_position][end_position]}}}}' $output_dir/summary.txt > $output_dir/unique_barcodes.txt &
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
nikos
parents:
diff changeset
201
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
nikos
parents:
diff changeset
202 #File read_counts.txt colums: RNA_ID, Start, End, sequenced_count
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
nikos
parents:
diff changeset
203
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
nikos
parents:
diff changeset
204 zcat merged_temp.gz | awk '{barcode[$1][$2][$3]++}END{
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
nikos
parents:
diff changeset
205 for(RNA in barcode){
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
nikos
parents:
diff changeset
206 for(start_position in barcode[RNA]){
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
nikos
parents:
diff changeset
207 for(end_position in barcode[RNA][start_position]){print RNA "\t" start_position "\t" end_position "\t" barcode[RNA][start_position][end_position]}}}}' > $output_dir/read_counts.txt &
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
nikos
parents:
diff changeset
208
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
nikos
parents:
diff changeset
209 wait
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
nikos
parents:
diff changeset
210
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
nikos
parents:
diff changeset
211 #Print the maximum observed barcodes value. Usefull to assess the necessity of producing the k2n file.
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
nikos
parents:
diff changeset
212 if [ "$barcodes" != "None" ]; then
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
nikos
parents:
diff changeset
213
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
nikos
parents:
diff changeset
214 cut -f 4 $output_dir/unique_barcodes.txt | sort -S1G -rn > sorted_bars
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
nikos
parents:
diff changeset
215 max_observed_barcodes=`head -n 1 sorted_bars`
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
nikos
parents:
diff changeset
216
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
nikos
parents:
diff changeset
217 echo "Maximum observed Barcodes = ${max_observed_barcodes}"
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
nikos
parents:
diff changeset
218 rm sorted_bars
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
nikos
parents:
diff changeset
219 fi
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
nikos
parents:
diff changeset
220
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
nikos
parents:
diff changeset
221 #Produce k2n file
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
nikos
parents:
diff changeset
222 if [ "$k2n" == "True" ]; then
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
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223 if [ ! -s paired ]; then
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
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224 Rscript $R_SCRIPT_PATH/k2n.R merged_temp.gz $output_dir/unique_barcodes.txt $output_dir/k2n.txt FALSE
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
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225 else
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
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226 Rscript $R_SCRIPT_PATH/k2n.R merged_temp.gz $output_dir/unique_barcodes.txt $output_dir/k2n.txt TRUE
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
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227 fi
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
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228 fi
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
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229
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
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230 #Remove temp files
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.
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231 rm merged_temp.gz positions_temp_sorted.gz paired