Mercurial > repos > pjbriggs > pal_finder

comparison pal_finder_wrapper.sh @ 3:1cea7b4b838f draft

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Uploaded version 0.02.04.3.
author pjbriggs
date Fri, 04 Dec 2015 04:36:51 -0500
parents 288a74cd7a8d
children ef95b26a2407
comparison
equal deleted inserted replaced
2:dff26850370b 3:1cea7b4b838f
24 # --primer-min-tm VALUE: minimum acceptable melting temperature (Celsius) for a primer oligo 24 # --primer-min-tm VALUE: minimum acceptable melting temperature (Celsius) for a primer oligo
25 # --primer-max-tm VALUE: maximum acceptable melting temperature (Celsius) 25 # --primer-max-tm VALUE: maximum acceptable melting temperature (Celsius)
26 # --primer-opt-tm VALUE: optimum 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 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 28 # --output_config_file FNAME: write a copy of the config.txt file to FNAME
29 # --filter_microsats FNAME: run Graeme Fox's Perl script to filter and sort the 29 # --filter_microsats FNAME: write output of filter options FNAME
30 # microsatellites from pal_finder and write to FNAME 30 # -assembly FNAME: run the 'assembly' filter option and write to FNAME
31 # -primers: run the 'primers' filter option
32 # -occurrences: run the 'occurrences' filter option
33 # -rankmotifs: run the 'rankmotifs' filter option
31 # 34 #
32 # pal_finder is available from http://sourceforge.net/projects/palfinder/ 35 # pal_finder is available from http://sourceforge.net/projects/palfinder/
33 # 36 #
34 # primer3 is available from http://primer3.sourceforge.net/releases.php 37 # primer3 is available from http://primer3.sourceforge.net/releases.php
35 # (nb needs version 2.0.0-alpha) 38 # (nb needs version 2.0.0-alpha)
53 : ${PALFINDER_SCRIPT_DIR:=/usr/bin} 56 : ${PALFINDER_SCRIPT_DIR:=/usr/bin}
54 : ${PALFINDER_DATA_DIR:=/usr/share/pal_finder_v0.02.04} 57 : ${PALFINDER_DATA_DIR:=/usr/share/pal_finder_v0.02.04}
55 : ${PRIMER3_CORE_EXE:=primer3_core} 58 : ${PRIMER3_CORE_EXE:=primer3_core}
56 # 59 #
57 # Filter script is in the same directory as this script 60 # Filter script is in the same directory as this script
58 PALFINDER_FILTER_PL=$(dirname $0)/pal_finder_filter.pl 61 PALFINDER_FILTER=$(dirname $0)/pal_finder_filter_and_assembly.py
59 if [ ! -f $PALFINDER_FILTER_PL ] ; then 62 if [ ! -f $PALFINDER_FILTER ] ; then
60 echo No pal_finder_filter.pl script >&2 63 echo No $PALFINDER_FILTER script >&2
61 exit 1 64 exit 1
62 fi 65 fi
63 # 66 #
64 # Check that we have all the components 67 # Check that we have all the components
65 function have_program() { 68 function have_program() {
102 PRIMER_OPT_TM= 105 PRIMER_OPT_TM=
103 PRIMER_MAX_TM= 106 PRIMER_MAX_TM=
104 PRIMER_MIN_TM= 107 PRIMER_MIN_TM=
105 PRIMER_PAIR_MAX_DIFF_TM= 108 PRIMER_PAIR_MAX_DIFF_TM=
106 OUTPUT_CONFIG_FILE= 109 OUTPUT_CONFIG_FILE=
110 OUTPUT_ASSEMBLY=
107 FILTERED_MICROSATS= 111 FILTERED_MICROSATS=
112 FILTER_OPTIONS=
108 # 113 #
109 # Collect command line arguments 114 # Collect command line arguments
110 if [ $# -lt 2 ] ; then 115 if [ $# -lt 2 ] ; then
111 echo "Usage: $0 FASTQ_R1 FASTQ_R2 MICROSAT_SUMMARY PAL_SUMMARY [OPTIONS]" 116 echo "Usage: $0 FASTQ_R1 FASTQ_R2 MICROSAT_SUMMARY PAL_SUMMARY [OPTIONS]"
112 echo " $0 --454 FASTA MICROSAT_SUMMARY PAL_SUMMARY [OPTIONS]" 117 echo " $0 --454 FASTA MICROSAT_SUMMARY PAL_SUMMARY [OPTIONS]"
127 # Collect command line options 132 # Collect command line options
128 while [ ! -z "$1" ] ; do 133 while [ ! -z "$1" ] ; do
129 case "$1" in 134 case "$1" in
130 --primer-prefix) 135 --primer-prefix)
131 shift 136 shift
132 # Convert spaces to underscores in prefix 137 # Convert all non-alphanumeric characters to underscores in prefix
133 PRIMER_PREFIX=$(echo $1 | tr " " "_") 138 PRIMER_PREFIX=$(echo -n $1 | tr -s -c "[:alnum:]" "_")
134 ;; 139 ;;
135 --2merMinReps) 140 --2merMinReps)
136 shift 141 shift
137 MIN_2_MER_REPS=$1 142 MIN_2_MER_REPS=$1
138 ;; 143 ;;
205 OUTPUT_CONFIG_FILE=$1 210 OUTPUT_CONFIG_FILE=$1
206 ;; 211 ;;
207 --filter_microsats) 212 --filter_microsats)
208 shift 213 shift
209 FILTERED_MICROSATS=$1 214 FILTERED_MICROSATS=$1
215 ;;
216 -primers|-occurrences|-rankmotifs)
217 FILTER_OPTIONS="$FILTER_OPTIONS $1"
218 ;;
219 -assembly)
220 FILTER_OPTIONS="$FILTER_OPTIONS $1"
221 shift
222 OUTPUT_ASSEMBLY=$1
210 ;; 223 ;;
211 *) 224 *)
212 echo Unknown option: $1 >&2 225 echo Unknown option: $1 >&2
213 exit 1 226 exit 1
214 ;; 227 ;;
307 if [ -z "$(tail -n 1 pal_finder.log | grep Done!!)" ] ; then 320 if [ -z "$(tail -n 1 pal_finder.log | grep Done!!)" ] ; then
308 echo ERROR pal_finder failed to complete successfully >&2 321 echo ERROR pal_finder failed to complete successfully >&2
309 exit 1 322 exit 1
310 fi 323 fi
311 # 324 #
312 # Run the pal_finder_filter.pl script from Graeme Fox 325 # Sort outputs into a consistent order regardless of Perl version
313 if [ ! -z "$FILTERED_MICROSATS" ] ; then 326 echo "### Sorting outputs ###"
314 echo "### Running filtering script ###" 327 head -1 Output/PAL_summary.txt > Output/PAL_summary.sorted.txt
315 perl $PALFINDER_FILTER_PL Output/PAL_summary.txt 2>&1 328 if [ "$PLATFORM" == "Illumina" ] ; then
329 grep -v "^readPairID" Output/PAL_summary.txt | sort -k 1 >> Output/PAL_summary.sorted.txt
330 else
331 grep -v "^SequenceID" Output/PAL_summary.txt | sort -k 1 >> Output/PAL_summary.sorted.txt
332 fi
333 mv Output/PAL_summary.sorted.txt Output/PAL_summary.txt
334 #
335 # Run the filtering & assembly script
336 if [ ! -z "$FILTERED_MICROSATS" ] || [ ! -z "$OUTPUT_ASSEMBLY" ] ; then
337 echo "### Running filtering & assembly script ###"
338 python $PALFINDER_FILTER -i $fastq_r1 -j $fastq_r2 -p Output/PAL_summary.txt $FILTER_OPTIONS 2>&1
316 if [ $? -ne 0 ] ; then 339 if [ $? -ne 0 ] ; then
317 echo ERROR pal_finder_filter.pl exited with non-zero status >&2 340 echo ERROR $PALFINDER_FILTER exited with non-zero status >&2
318 exit 1 341 exit 1
319 elif [ ! -f pal_finder_filter_output.txt ] ; then 342 elif [ ! -f PAL_summary.filtered ] ; then
320 echo ERROR no output from pal_finder_filter.pl >&2 343 echo ERROR no output from $PALFINDER_FILTER >&2
321 exit 1 344 exit 1
322 fi 345 fi
323 fi 346 fi
324 # 347 #
325 # Clean up 348 # Clean up
328 /bin/mv Output/microsat_summary.txt $MICROSAT_SUMMARY 351 /bin/mv Output/microsat_summary.txt $MICROSAT_SUMMARY
329 fi 352 fi
330 if [ -f Output/PAL_summary.txt ] ; then 353 if [ -f Output/PAL_summary.txt ] ; then
331 /bin/mv Output/PAL_summary.txt $PAL_SUMMARY 354 /bin/mv Output/PAL_summary.txt $PAL_SUMMARY
332 fi 355 fi
333 if [ ! -z "$FILTERED_MICROSATS" ] && [ -f pal_finder_filter_output.txt ] ; then 356 if [ ! -z "$FILTERED_MICROSATS" ] && [ -f PAL_summary.filtered ] ; then
334 /bin/mv pal_finder_filter_output.txt $FILTERED_MICROSATS 357 /bin/mv PAL_summary.filtered $FILTERED_MICROSATS
358 fi
359 if [ ! -z "$OUTPUT_ASSEMBLY" ] ; then
360 assembly=${fastq_r1%.*}_pal_finder_assembly_output.txt
361 if [ -f "$assembly" ] ; then
362 /bin/mv $assembly "$OUTPUT_ASSEMBLY"
363 fi
335 fi 364 fi
336 if [ ! -z "$OUTPUT_CONFIG_FILE" ] && [ -f config.txt ] ; then 365 if [ ! -z "$OUTPUT_CONFIG_FILE" ] && [ -f config.txt ] ; then
337 /bin/mv config.txt $OUTPUT_CONFIG_FILE 366 /bin/mv config.txt $OUTPUT_CONFIG_FILE
338 fi 367 fi
339 ## 368 ##