Mercurial > repos > pjbriggs > pal_finder
annotate pal_finder_wrapper.sh @ 14:3f8bf1a0403b draft
Uploaded version with bad primer ranger detection (WIP).
| author | pjbriggs |
|---|---|
| date | Thu, 22 Mar 2018 07:21:26 -0400 |
| parents | d26fb5260c67 |
| children | a3af1ff4cad1 |
| rev | line source |
|---|---|
| 0 | 1 #!/bin/sh |
| 2 # | |
| 3 # pal_finder_wrapper.sh: run pal_finder perl script as a Galaxy tool | |
| 4 # | |
| 5 # Usage: run_palfinder.sh FASTQ_R1 FASTQ_R2 MICROSAT_SUMMARY PAL_SUMMARY FILTERED_MICROSATS [OPTIONS] | |
| 6 # run_palfinder.sh --454 FASTA MICROSAT_SUMMARY PAL_SUMMARY [OPTIONS] | |
| 7 # | |
| 8 # Options: | |
| 9 # | |
| 10 # --primer-prefix PREFIX: prefix added to the beginning of all primer names (prPrefixName) | |
| 11 # --2merMinReps N: miniumum number of 2-mer repeat units to detect (0=ignore units of this size) | |
| 12 # --3merMinReps N | |
| 13 # --4merMinReps N | |
| 14 # --5merMinReps N | |
| 15 # --6merMinReps N | |
| 16 # --primer-mispriming-library FASTA: specify a Fasta file with sequences to avoid amplifying | |
| 17 # --primer-opt-size VALUE: optimum primer length | |
| 18 # --primer-min-size VALUE: minimum acceptable primer length | |
| 19 # --primer-max-size VALUE: maximum acceptable primer length | |
| 20 # --primer-min-gc VALUE: minimum allowable percentage of Gs and Cs in any primer | |
| 21 # --primer-max-gc VALUE: maximum allowable percentage of Gs and Cs | |
| 22 # --primer-gc-clamp VALUE: number of consecutive Gs and Cs at 3' end of both left and right primer | |
| 23 # --primer-max-end-gc VALUE: max number of Gs or Cs in last five 3' bases of left or right primer | |
| 24 # --primer-min-tm VALUE: minimum acceptable melting temperature (Celsius) for a primer oligo | |
| 25 # --primer-max-tm VALUE: maximum acceptable melting temperature (Celsius) | |
| 26 # --primer-opt-tm VALUE: optimum melting temperature (Celsius) | |
| 27 # --primer-pair-max-diff-tm VALUE: max difference between melting temps of left & right primers | |
| 28 # --output_config_file FNAME: write a copy of the config.txt file to FNAME | |
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29 # --bad_primer_ranges FNAME: write a list of the read IDs generating bad primer ranges to FNAME |
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30 # --filter_microsats FNAME: write output of filter options to FNAME |
| 3 | 31 # -assembly FNAME: run the 'assembly' filter option and write to FNAME |
| 32 # -primers: run the 'primers' filter option | |
| 33 # -occurrences: run the 'occurrences' filter option | |
| 34 # -rankmotifs: run the 'rankmotifs' filter option | |
| 0 | 35 # |
| 36 # pal_finder is available from http://sourceforge.net/projects/palfinder/ | |
| 37 # | |
| 38 # primer3 is available from http://primer3.sourceforge.net/releases.php | |
| 39 # (nb needs version 2.0.0-alpha) | |
| 40 # | |
| 41 # Explicitly set the locations of the pal_finder script, data files and the primer3 | |
| 42 # executable by setting the following variables in the environment: | |
| 43 # | |
| 44 # * PALFINDER_SCRIPT_DIR: location of the pal_finder Perl script (defaults to | |
| 45 # /usr/bin) | |
| 46 # * PALFINDER_DATA_DIR: location of the pal_finder data files (specifically | |
| 47 # config.txt and simple.ref; defaults to /usr/share/pal_finder_v0.02.04) | |
| 48 # * PRIMER3_CORE_EXE: name of the primer3_core program, which should include the | |
| 49 # full path if it's not on the Galaxy user's PATH (defaults to primer3_core) | |
| 50 # | |
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51 echo "### $(basename $0) ###" |
| 0 | 52 echo $* |
| 53 # | |
| 8 | 54 # Maximum size reporting log file contents |
| 55 MAX_LINES=500 | |
| 56 # | |
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57 # Get helper functions |
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58 . $(dirname $0)/pal_finder_wrapper_utils.sh |
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59 # |
| 0 | 60 # Initialise locations of scripts, data and executables |
| 61 # | |
| 62 # Set these in the environment to overide at execution time | |
| 63 : ${PALFINDER_SCRIPT_DIR:=/usr/bin} | |
| 64 : ${PALFINDER_DATA_DIR:=/usr/share/pal_finder_v0.02.04} | |
| 65 : ${PRIMER3_CORE_EXE:=primer3_core} | |
| 66 # | |
| 67 # Filter script is in the same directory as this script | |
| 5 | 68 PALFINDER_FILTER=$(dirname $0)/pal_filter.py |
| 3 | 69 if [ ! -f $PALFINDER_FILTER ] ; then |
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70 fatal No $PALFINDER_FILTER script |
| 0 | 71 fi |
| 72 # | |
| 73 # Check that we have all the components | |
| 74 if [ "$(have_program $PRIMER3_CORE_EXE)" == "no" ] ; then | |
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75 fatal "primer3_core missing: ${PRIMER3_CORE_EXE} not found" |
| 0 | 76 fi |
| 77 if [ ! -f "${PALFINDER_DATA_DIR}/config.txt" ] ; then | |
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78 fatal "pal_finder config.txt not found in ${PALFINDER_DATA_DIR}" |
| 0 | 79 fi |
| 80 if [ ! -f "${PALFINDER_SCRIPT_DIR}/pal_finder_v0.02.04.pl" ] ; then | |
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81 fatal "pal_finder_v0.02.04.pl not found in ${PALFINDER_SCRIPT_DIR}" |
| 0 | 82 fi |
| 83 # | |
| 84 # Initialise parameters used in the config.txt file | |
| 85 PRIMER_PREFIX="test" | |
| 86 MIN_2_MER_REPS=6 | |
| 87 MIN_3_MER_REPS=0 | |
| 88 MIN_4_MER_REPS=0 | |
| 89 MIN_5_MER_REPS=0 | |
| 90 MIN_6_MER_REPS=0 | |
| 91 PRIMER_MISPRIMING_LIBRARY=$PALFINDER_DATA_DIR/simple.ref | |
| 92 PRIMER_OPT_SIZE= | |
| 93 PRIMER_MAX_SIZE= | |
| 94 PRIMER_MIN_SIZE= | |
| 95 PRIMER_MAX_GC= | |
| 96 PRIMER_MIN_GC= | |
| 97 PRIMER_GC_CLAMP= | |
| 98 PRIMER_MAX_END_GC= | |
| 99 PRIMER_OPT_TM= | |
| 100 PRIMER_MAX_TM= | |
| 101 PRIMER_MIN_TM= | |
| 102 PRIMER_PAIR_MAX_DIFF_TM= | |
| 103 OUTPUT_CONFIG_FILE= | |
| 3 | 104 OUTPUT_ASSEMBLY= |
| 0 | 105 FILTERED_MICROSATS= |
| 3 | 106 FILTER_OPTIONS= |
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107 BAD_PRIMER_RANGES= |
| 0 | 108 # |
| 109 # Collect command line arguments | |
| 110 if [ $# -lt 2 ] ; then | |
| 111 echo "Usage: $0 FASTQ_R1 FASTQ_R2 MICROSAT_SUMMARY PAL_SUMMARY [OPTIONS]" | |
| 112 echo " $0 --454 FASTA MICROSAT_SUMMARY PAL_SUMMARY [OPTIONS]" | |
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113 fatal "Bad command line" |
| 0 | 114 fi |
| 115 if [ "$1" == "--454" ] ; then | |
| 116 PLATFORM="454" | |
| 117 FNA=$2 | |
| 118 else | |
| 119 PLATFORM="Illumina" | |
| 120 FASTQ_R1=$1 | |
| 121 FASTQ_R2=$2 | |
| 122 fi | |
| 123 MICROSAT_SUMMARY=$3 | |
| 124 PAL_SUMMARY=$4 | |
| 125 shift; shift; shift; shift | |
| 126 # | |
| 127 # Collect command line options | |
| 128 while [ ! -z "$1" ] ; do | |
| 129 case "$1" in | |
| 130 --primer-prefix) | |
| 131 shift | |
| 3 | 132 # Convert all non-alphanumeric characters to underscores in prefix |
| 133 PRIMER_PREFIX=$(echo -n $1 | tr -s -c "[:alnum:]" "_") | |
| 0 | 134 ;; |
| 135 --2merMinReps) | |
| 136 shift | |
| 137 MIN_2_MER_REPS=$1 | |
| 138 ;; | |
| 139 --3merMinReps) | |
| 140 shift | |
| 141 MIN_3_MER_REPS=$1 | |
| 142 ;; | |
| 143 --4merMinReps) | |
| 144 shift | |
| 145 MIN_4_MER_REPS=$1 | |
| 146 ;; | |
| 147 --5merMinReps) | |
| 148 shift | |
| 149 MIN_5_MER_REPS=$1 | |
| 150 ;; | |
| 151 --6merMinReps) | |
| 152 shift | |
| 153 MIN_6_MER_REPS=$1 | |
| 154 ;; | |
| 155 --primer-mispriming-library) | |
| 156 shift | |
| 157 PRIMER_MISPRIMING_LIBRARY=$1 | |
| 158 ;; | |
| 159 --primer-opt-size) | |
| 160 shift | |
| 161 PRIMER_OPT_SIZE=$1 | |
| 162 ;; | |
| 163 --primer-max-size) | |
| 164 shift | |
| 165 PRIMER_MAX_SIZE=$1 | |
| 166 ;; | |
| 167 --primer-min-size) | |
| 168 shift | |
| 169 PRIMER_MIN_SIZE=$1 | |
| 170 ;; | |
| 171 --primer-max-gc) | |
| 172 shift | |
| 173 PRIMER_MAX_GC=$1 | |
| 174 ;; | |
| 175 --primer-min-gc) | |
| 176 shift | |
| 177 PRIMER_MIN_GC=$1 | |
| 178 ;; | |
| 179 --primer-gc-clamp) | |
| 180 shift | |
| 181 PRIMER_GC_CLAMP=$1 | |
| 182 ;; | |
| 183 --primer-max-end-gc) | |
| 184 shift | |
| 185 PRIMER_MAX_END_GC=$1 | |
| 186 ;; | |
| 187 --primer-opt-tm) | |
| 188 shift | |
| 189 PRIMER_OPT_TM=$1 | |
| 190 ;; | |
| 191 --primer-max-tm) | |
| 192 shift | |
| 193 PRIMER_MAX_TM=$1 | |
| 194 ;; | |
| 195 --primer-min-tm) | |
| 196 shift | |
| 197 PRIMER_MIN_TM=$1 | |
| 198 ;; | |
| 199 --primer-pair-max-diff-tm) | |
| 200 shift | |
| 201 PRIMER_PAIR_MAX_DIFF_TM=$1 | |
| 202 ;; | |
| 203 --output_config_file) | |
| 204 shift | |
| 205 OUTPUT_CONFIG_FILE=$1 | |
| 206 ;; | |
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207 --bad_primer_ranges) |
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208 shift |
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209 BAD_PRIMER_RANGES=$1 |
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210 ;; |
| 0 | 211 --filter_microsats) |
| 212 shift | |
| 213 FILTERED_MICROSATS=$1 | |
| 214 ;; | |
| 3 | 215 -primers|-occurrences|-rankmotifs) |
| 216 FILTER_OPTIONS="$FILTER_OPTIONS $1" | |
| 217 ;; | |
| 218 -assembly) | |
| 219 FILTER_OPTIONS="$FILTER_OPTIONS $1" | |
| 220 shift | |
| 221 OUTPUT_ASSEMBLY=$1 | |
| 222 ;; | |
| 0 | 223 *) |
| 224 echo Unknown option: $1 >&2 | |
| 225 exit 1 | |
| 226 ;; | |
| 227 esac | |
| 228 shift | |
| 229 done | |
| 230 # | |
| 231 # Check that primer3_core is available | |
| 232 got_primer3=`which $PRIMER3_CORE_EXE 2>&1 | grep -v "no primer3_core in"` | |
| 233 if [ -z "$got_primer3" ] ; then | |
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234 fatal "primer3_core not found" |
| 0 | 235 fi |
| 236 # | |
| 237 # Set up the working dir | |
| 238 if [ "$PLATFORM" == "Illumina" ] ; then | |
| 239 # Paired end Illumina data as input | |
| 240 if [ $FASTQ_R1 == $FASTQ_R2 ] ; then | |
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241 fatal ERROR R1 and R2 fastqs are the same file |
| 0 | 242 fi |
| 243 ln -s $FASTQ_R1 | |
| 244 ln -s $FASTQ_R2 | |
| 245 fastq_r1=$(basename $FASTQ_R1) | |
| 246 fastq_r2=$(basename $FASTQ_R2) | |
| 247 else | |
| 248 # 454 data as input | |
| 249 ln -s $FNA | |
| 250 fna=$(basename $FNA) | |
| 251 fi | |
| 252 ln -s $PRIMER_MISPRIMING_LIBRARY | |
| 253 PRIMER_MISPRIMING_LIBRARY=$(basename $PRIMER_MISPRIMING_LIBRARY) | |
| 254 mkdir Output | |
| 255 # | |
| 256 # Copy in the default config.txt file | |
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257 echo "### Creating config.txt file for pal_finder run ###" |
| 0 | 258 /bin/cp $PALFINDER_DATA_DIR/config.txt . |
| 259 # | |
| 260 # Update the config.txt file with new values | |
| 261 # Input files | |
| 262 set_config_value platform $PLATFORM config.txt | |
| 263 if [ "$PLATFORM" == "Illumina" ] ; then | |
| 264 set_config_value inputFormat fastq config.txt | |
| 265 set_config_value pairedEnd 1 config.txt | |
| 266 set_config_value inputReadFile $fastq_r1 config.txt | |
| 267 set_config_value pairedReadFile $fastq_r2 config.txt | |
| 268 else | |
| 269 set_config_value inputFormat fasta config.txt | |
| 270 set_config_value pairedEnd 0 config.txt | |
| 271 set_config_value input454reads $fna config.txt | |
| 272 fi | |
| 273 # Output files | |
| 274 set_config_value MicrosatSumOut Output/microsat_summary.txt config.txt | |
| 275 set_config_value PALsummaryOut Output/PAL_summary.txt config.txt | |
| 276 # Microsat info | |
| 277 set_config_value 2merMinReps $MIN_2_MER_REPS config.txt | |
| 278 set_config_value 3merMinReps $MIN_3_MER_REPS config.txt | |
| 279 set_config_value 4merMinReps $MIN_4_MER_REPS config.txt | |
| 280 set_config_value 5merMinReps $MIN_5_MER_REPS config.txt | |
| 281 set_config_value 6merMinReps $MIN_6_MER_REPS config.txt | |
| 282 # Primer3 settings | |
| 283 set_config_value primer3input Output/pr3in.txt config.txt | |
| 284 set_config_value primer3output Output/pr3out.txt config.txt | |
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285 set_config_value keepPrimer3files 1 config.txt |
| 0 | 286 set_config_value primer3executable $PRIMER3_CORE_EXE config.txt |
| 287 set_config_value prNamePrefix ${PRIMER_PREFIX}_ config.txt | |
| 288 set_config_value PRIMER_MISPRIMING_LIBRARY "$PRIMER_MISPRIMING_LIBRARY" config.txt | |
| 289 set_config_value PRIMER_OPT_SIZE "$PRIMER_OPT_SIZE" config.txt | |
| 290 set_config_value PRIMER_MIN_SIZE "$PRIMER_MIN_SIZE" config.txt | |
| 291 set_config_value PRIMER_MAX_SIZE "$PRIMER_MAX_SIZE" config.txt | |
| 292 set_config_value PRIMER_MIN_GC "$PRIMER_MIN_GC" config.txt | |
| 293 set_config_value PRIMER_MAX_GC "$PRIMER_MAX_GC" config.txt | |
| 294 set_config_value PRIMER_GC_CLAMP "$PRIMER_GC_CLAMP" config.txt | |
| 295 set_config_value PRIMER_MAX_END_GC "$PRIMER_MAX_END_GC" config.txt | |
| 296 set_config_value PRIMER_MIN_TM "$PRIMER_MIN_TM" config.txt | |
| 297 set_config_value PRIMER_MAX_TM "$PRIMER_MAX_TM" config.txt | |
| 298 set_config_value PRIMER_OPT_TM "$PRIMER_OPT_TM" config.txt | |
| 299 set_config_value PRIMER_PAIR_MAX_DIFF_TM "$PRIMER_PAIR_MAX_DIFF_TM" config.txt | |
| 300 # | |
| 301 # Run pal_finder | |
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302 echo "### Running pal_finder ###" |
| 8 | 303 perl $PALFINDER_SCRIPT_DIR/pal_finder_v0.02.04.pl config.txt 1>pal_finder.log 2>&1 |
| 304 echo "### pal_finder finished ###" | |
| 305 # | |
| 306 # Handlers the pal_finder log file | |
| 307 echo "### Output from pal_finder ###" | |
| 308 if [ $(wc -l pal_finder.log | cut -d" " -f1) -gt $MAX_LINES ] ; then | |
| 309 echo WARNING output too long, truncated to last $MAX_LINES lines: | |
| 310 echo ... | |
| 311 fi | |
| 312 tail -$MAX_LINES pal_finder.log | |
| 0 | 313 # |
| 314 # Check that log ends with "Done!!" message | |
| 315 if [ -z "$(tail -n 1 pal_finder.log | grep Done!!)" ] ; then | |
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316 fatal ERROR pal_finder failed to complete successfully |
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317 fi |
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318 echo "### pal_finder finished ###" |
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319 # |
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320 # Check for errors in pal_finder output |
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321 echo "### Checking for errors ###" |
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322 if [ ! -z "$(grep 'primer3_core: Illegal element in PRIMER_PRODUCT_SIZE_RANGE' pal_finder.log)" ] ; then |
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323 echo WARNING primer3 terminated prematurely due to bad product size ranges |
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324 if [ -z "$BAD_PRIMER_RANGES" ] ; then |
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325 # No output file so report to stderr |
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326 cat >&2 <<EOF |
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327 ERROR primer3 terminated prematurely due to bad product size ranges |
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328 |
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329 Pal_finder generated bad ranges for the following read IDs: |
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330 EOF |
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331 echo $(find_bad_primer_ranges Output/pr3in.txt) >&2 |
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332 cat >&2 <<EOF |
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333 |
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334 This error can occur when input data contains short R1 reads and has |
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335 has not been properly trimmed and filtered. |
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336 |
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337 EOF |
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338 else |
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339 # Dump bad ranges to file |
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340 echo "### Writing read IDs with bad primer ranges ###" |
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341 echo $(find_bad_primer_ranges Output/pr3in.txt) >"$BAD_PRIMER_RANGES" |
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342 fi |
| 0 | 343 fi |
| 344 # | |
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345 # Sort microsat_summary output |
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346 echo "### Sorting microsat summary output ###" |
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347 head -n 7 Output/microsat_summary.txt | sort >microsat_summary.sorted |
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348 grep "^$" Output/microsat_summary.txt>>microsat_summary.sorted |
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349 grep "^Microsat Type" Output/microsat_summary.txt >>microsat_summary.sorted |
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350 tail -n +11 Output/microsat_summary.txt >>microsat_summary.sorted |
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351 mv microsat_summary.sorted Output/microsat_summary.txt |
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352 # |
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353 # Sort PAL_summary output |
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354 echo "### Sorting PAL summary output ###" |
| 3 | 355 head -1 Output/PAL_summary.txt > Output/PAL_summary.sorted.txt |
| 356 if [ "$PLATFORM" == "Illumina" ] ; then | |
| 357 grep -v "^readPairID" Output/PAL_summary.txt | sort -k 1 >> Output/PAL_summary.sorted.txt | |
| 358 else | |
| 359 grep -v "^SequenceID" Output/PAL_summary.txt | sort -k 1 >> Output/PAL_summary.sorted.txt | |
| 360 fi | |
| 361 mv Output/PAL_summary.sorted.txt Output/PAL_summary.txt | |
| 362 # | |
| 363 # Run the filtering & assembly script | |
| 364 if [ ! -z "$FILTERED_MICROSATS" ] || [ ! -z "$OUTPUT_ASSEMBLY" ] ; then | |
| 365 echo "### Running filtering & assembly script ###" | |
| 8 | 366 python $PALFINDER_FILTER -i $fastq_r1 -j $fastq_r2 -p Output/PAL_summary.txt $FILTER_OPTIONS 1>pal_filter.log 2>&1 |
| 367 echo "### Output from pal_filter ###" | |
| 368 if [ $(wc -l pal_filter.log | cut -d" " -f1) -gt $MAX_LINES ] ; then | |
| 369 echo WARNING output too long, truncated to last $MAX_LINES lines: | |
| 370 echo ... | |
| 371 fi | |
| 372 tail -$MAX_LINES pal_filter.log | |
| 0 | 373 if [ $? -ne 0 ] ; then |
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374 fatal $PALFINDER_FILTER exited with non-zero status |
| 3 | 375 elif [ ! -f PAL_summary.filtered ] ; then |
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376 fatal no output from $PALFINDER_FILTER |
| 0 | 377 fi |
| 378 fi | |
| 379 # | |
| 380 # Clean up | |
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381 echo "### Handling output files ###" |
| 0 | 382 if [ -f Output/microsat_summary.txt ] ; then |
| 383 /bin/mv Output/microsat_summary.txt $MICROSAT_SUMMARY | |
| 384 fi | |
| 385 if [ -f Output/PAL_summary.txt ] ; then | |
| 386 /bin/mv Output/PAL_summary.txt $PAL_SUMMARY | |
| 387 fi | |
| 3 | 388 if [ ! -z "$FILTERED_MICROSATS" ] && [ -f PAL_summary.filtered ] ; then |
| 389 /bin/mv PAL_summary.filtered $FILTERED_MICROSATS | |
| 390 fi | |
| 391 if [ ! -z "$OUTPUT_ASSEMBLY" ] ; then | |
| 5 | 392 assembly=${fastq_r1%.*}_pal_filter_assembly_output.txt |
| 3 | 393 if [ -f "$assembly" ] ; then |
| 394 /bin/mv $assembly "$OUTPUT_ASSEMBLY" | |
| 5 | 395 else |
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396 fatal no assembly output found |
| 3 | 397 fi |
| 0 | 398 fi |
| 399 if [ ! -z "$OUTPUT_CONFIG_FILE" ] && [ -f config.txt ] ; then | |
| 400 /bin/mv config.txt $OUTPUT_CONFIG_FILE | |
| 401 fi | |
| 8 | 402 # |
| 403 echo "### Pal_finder tool completed ###" | |
| 0 | 404 ## |
| 405 # |