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annotate pal_finder_wrapper_utils.sh @ 8:4e625d3672ba draft

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Pal_finder tool version 0.02.04.7: add detection/reporting of bad ranges; enable subset of reads to be used; check n-mers.
author pjbriggs
date Wed, 16 May 2018 07:39:16 -0400
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8
4e625d3672ba Pal_finder tool version 0.02.04.7: add detection/reporting of bad ranges; enable subset of reads to be used; check n-mers.
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1 #!/bin/bash
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2 #
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3 # Helper functions for the pal_finder_wrapper.sh script
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4 #
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5 # Utility function for terminating on fatal error
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6 function fatal() {
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7 echo "FATAL $@" >&2
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8 exit 1
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9 }
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10 #
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11 # Check that specified program is available
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12 function have_program() {
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13 local program=$1
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14 local got_program=$(which $program 2>&1 | grep "no $(basename $program) in")
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15 if [ -z "$got_program" ] ; then
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16 echo yes
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17 else
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18 echo no
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19 fi
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20 }
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21 #
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22 # Set the value for a parameter in the pal_finder config file
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23 function set_config_value() {
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24 local key=$1
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25 local value=$2
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26 local config_txt=$3
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27 if [ -z "$value" ] ; then
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28 echo "No value for $key, left as default"
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29 else
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30 echo Setting "$key" to "$value"
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31 sed -i 's,^'"$key"' .*,'"$key"' '"$value"',' $config_txt
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32 fi
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33 }
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34 #
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35 # Identify 'bad' PRIMER_PRODUCT_SIZE_RANGE from pr3in.txt file
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36 function find_bad_primer_ranges() {
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37 # Parses a pr3in.txt file from pal_finder and reports
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38 # sequence ids where the PRIMER_PRODUCT_SIZE_RANGE has
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39 # upper limit which is smaller than lower limit
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40 local pr3in=$1
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41 local outfile=$2
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42 local pattern="^(SEQUENCE_ID|PRIMER_PRODUCT_SIZE_RANGE)"
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43 for line in $(grep -E "$pattern" $pr3in | sed 's/ /^/' | sed 'N;s/\n/*/')
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44 do
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45 # Loop over pairs of SEQUENCE_ID and PRIMER_PRODUCT_SIZE_RANGE
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46 # keywords in the primer3 input
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47 if [ ! -z "$(echo $line | grep ^SEQUENCE_ID)" ] ; then
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48 # Lines look like:
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49 # SEQUENCE_ID=(AT_1_16)(AT_1_16)M00879:99:000000000-AH9KG:1:2107:10006:2535*PRIMER_PRODUCT_SIZE_RANGE=194-329^59-194
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50 local size_range=$(echo $line | cut -d'*' -f2 | cut -d'=' -f2 | tr '^' ' ')
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51 local seq_id=$(echo $line | cut -d'*' -f1 | cut -d'=' -f2)
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52 elif [ ! -z "$(echo $line | grep ^PRIMER_PRODUCT_SIZE_RANGE)" ] ; then
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53 # Lines look like:
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54 # PRIMER_PRODUCT_SIZE_RANGE=194-329^59-194*SEQUENCE_ID=(AT_1_16)(AT_1_16)M00879:99:000000000-AH9KG:1:2107:10006:2535
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55 local size_range=$(echo $line | cut -d'*' -f1 | cut -d'=' -f2 | tr '^' ' ')
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56 local seq_id=$(echo $line | cut -d'*' -f2 | cut -d'=' -f2)
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57 fi
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58 seq_id=$(echo $seq_id | cut -d')' -f3)
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59 # Check the upper and lower limits in each range
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60 # to see if it's okay
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61 local bad_range=
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62 for range in $(echo $size_range) ; do
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63 local lower=$(echo $range | cut -d'-' -f1)
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64 local upper=$(echo $range | cut -d'-' -f2)
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65 if [ "$lower" -gt "$upper" ] ; then
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66 bad_range=yes
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67 break
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68 fi
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69 done
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70 # Report if the range is wrong
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71 if [ ! -z "$bad_range" ] ; then
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72 echo "${seq_id}"$'\t'"(${size_range})" >>$outfile
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73 fi
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74 done
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75 }