Mercurial > repos > pjbriggs > pal_finder

comparison pal_finder_wrapper.sh @ 5:ef95b26a2407 draft

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Uploaded 0.02.04.4.
author pjbriggs
date Wed, 24 Feb 2016 08:09:51 -0500
parents 1cea7b4b838f
children 67ab365c29a7
comparison
equal deleted inserted replaced
4:431849236cb9 5:ef95b26a2407
56 : ${PALFINDER_SCRIPT_DIR:=/usr/bin} 56 : ${PALFINDER_SCRIPT_DIR:=/usr/bin}
57 : ${PALFINDER_DATA_DIR:=/usr/share/pal_finder_v0.02.04} 57 : ${PALFINDER_DATA_DIR:=/usr/share/pal_finder_v0.02.04}
58 : ${PRIMER3_CORE_EXE:=primer3_core} 58 : ${PRIMER3_CORE_EXE:=primer3_core}
59 # 59 #
60 # Filter script is in the same directory as this script 60 # Filter script is in the same directory as this script
61 PALFINDER_FILTER=$(dirname $0)/pal_finder_filter_and_assembly.py 61 PALFINDER_FILTER=$(dirname $0)/pal_filter.py
62 if [ ! -f $PALFINDER_FILTER ] ; then 62 if [ ! -f $PALFINDER_FILTER ] ; then
63 echo No $PALFINDER_FILTER script >&2 63 echo No $PALFINDER_FILTER script >&2
64 exit 1 64 exit 1
65 fi 65 fi
66 # 66 #
113 # 113 #
114 # Collect command line arguments 114 # Collect command line arguments
115 if [ $# -lt 2 ] ; then 115 if [ $# -lt 2 ] ; then
116 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]"
117 echo " $0 --454 FASTA MICROSAT_SUMMARY PAL_SUMMARY [OPTIONS]" 117 echo " $0 --454 FASTA MICROSAT_SUMMARY PAL_SUMMARY [OPTIONS]"
118 exit 118 exits
119 fi 119 fi
120 if [ "$1" == "--454" ] ; then 120 if [ "$1" == "--454" ] ; then
121 PLATFORM="454" 121 PLATFORM="454"
122 FNA=$2 122 FNA=$2
123 else 123 else
355 fi 355 fi
356 if [ ! -z "$FILTERED_MICROSATS" ] && [ -f PAL_summary.filtered ] ; then 356 if [ ! -z "$FILTERED_MICROSATS" ] && [ -f PAL_summary.filtered ] ; then
357 /bin/mv PAL_summary.filtered $FILTERED_MICROSATS 357 /bin/mv PAL_summary.filtered $FILTERED_MICROSATS
358 fi 358 fi
359 if [ ! -z "$OUTPUT_ASSEMBLY" ] ; then 359 if [ ! -z "$OUTPUT_ASSEMBLY" ] ; then
360 assembly=${fastq_r1%.*}_pal_finder_assembly_output.txt 360 assembly=${fastq_r1%.*}_pal_filter_assembly_output.txt
361 if [ -f "$assembly" ] ; then 361 if [ -f "$assembly" ] ; then
362 /bin/mv $assembly "$OUTPUT_ASSEMBLY" 362 /bin/mv $assembly "$OUTPUT_ASSEMBLY"
363 else
364 echo ERROR no assembly output found >&2
365 exit 1
363 fi 366 fi
364 fi 367 fi
365 if [ ! -z "$OUTPUT_CONFIG_FILE" ] && [ -f config.txt ] ; then 368 if [ ! -z "$OUTPUT_CONFIG_FILE" ] && [ -f config.txt ] ; then
366 /bin/mv config.txt $OUTPUT_CONFIG_FILE 369 /bin/mv config.txt $OUTPUT_CONFIG_FILE
367 fi 370 fi