# HG changeset patch # User pjbriggs # Date 1521121745 14400 # Node ID d26fb5260c678b14e090914a1e4cd0500f13ddc9 # Parent 84613d5f1713b08090a6a85d9476d596eb45bebd 0.02.04.6: update to use conda to resolve dependencies. diff -r 84613d5f1713 -r d26fb5260c67 README.rst --- a/README.rst Mon Jul 24 11:04:27 2017 -0400 +++ b/README.rst Thu Mar 15 09:49:05 2018 -0400 @@ -61,9 +61,10 @@ Version Changes ---------- ---------------------------------------------------------------------- -0.02.04.6 - Trap for errors in ``pal_finder_v0.02.04.pl`` resulting in bad - ranges being supplied to ``primer3_core`` for some reads via - ``PRIMER_PRODUCT_RANGE_SIZE``. +0.02.04.6 - Update to get dependencies using ``conda`` when installed from the + toolshed (this removes the explicit dependency on Perl 5.16 + introduced in 0.02.04.2, as a result the outputs from the tool are + now non-deterministic in some cases). 0.02.04.5 - Update to handle large output files which can sometimes be generated by the ``pal_finder_v0.02.04.pl`` or ``pal_filter.py`` scripts (logs of hundreds of Gb's have been observed in production): log files diff -r 84613d5f1713 -r d26fb5260c67 pal_finder_macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/pal_finder_macros.xml Thu Mar 15 09:49:05 2018 -0400 @@ -0,0 +1,40 @@ + + + if [ -z "\$PALFINDER_SCRIPT_DIR" ]; then export PALFINDER_SCRIPT_DIR=\$(dirname \$(readlink -e \$(which pal_finder))); fi + if [ -z "\$PALFINDER_DATA_DIR" ]; then export PALFINDER_DATA_DIR=\$(dirname \$(readlink -e \$(which pal_finder))); fi + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff -r 84613d5f1713 -r d26fb5260c67 pal_finder_wrapper.sh --- a/pal_finder_wrapper.sh Mon Jul 24 11:04:27 2017 -0400 +++ b/pal_finder_wrapper.sh Thu Mar 15 09:49:05 2018 -0400 @@ -53,9 +53,6 @@ # Maximum size reporting log file contents MAX_LINES=500 # -# Get helper functions -. $(dirname $0)/pal_finder_wrapper_utils.sh -# # Initialise locations of scripts, data and executables # # Set these in the environment to overide at execution time @@ -66,18 +63,31 @@ # Filter script is in the same directory as this script PALFINDER_FILTER=$(dirname $0)/pal_filter.py if [ ! -f $PALFINDER_FILTER ] ; then - fatal No $PALFINDER_FILTER script + echo No $PALFINDER_FILTER script >&2 + exit 1 fi # # Check that we have all the components +function have_program() { + local program=$1 + local got_program=$(which $program 2>&1 | grep "no $(basename $program) in") + if [ -z "$got_program" ] ; then + echo yes + else + echo no + fi +} if [ "$(have_program $PRIMER3_CORE_EXE)" == "no" ] ; then - fatal "primer3_core missing: ${PRIMER3_CORE_EXE} not found" + echo "ERROR primer3_core missing: ${PRIMER3_CORE_EXE} not found" >&2 + exit 1 fi if [ ! -f "${PALFINDER_DATA_DIR}/config.txt" ] ; then - fatal "pal_finder config.txt not found in ${PALFINDER_DATA_DIR}" + echo "ERROR pal_finder config.txt not found in ${PALFINDER_DATA_DIR}" >&2 + exit 1 fi if [ ! -f "${PALFINDER_SCRIPT_DIR}/pal_finder_v0.02.04.pl" ] ; then - fatal "pal_finder_v0.02.04.pl not found in ${PALFINDER_SCRIPT_DIR}" + echo "ERROR pal_finder_v0.02.04.pl not found in ${PALFINDER_SCRIPT_DIR}" >&2 + exit 1 fi # # Initialise parameters used in the config.txt file @@ -108,7 +118,7 @@ if [ $# -lt 2 ] ; then echo "Usage: $0 FASTQ_R1 FASTQ_R2 MICROSAT_SUMMARY PAL_SUMMARY [OPTIONS]" echo " $0 --454 FASTA MICROSAT_SUMMARY PAL_SUMMARY [OPTIONS]" - fatal "Bad command line" + exits fi if [ "$1" == "--454" ] ; then PLATFORM="454" @@ -225,14 +235,16 @@ # Check that primer3_core is available got_primer3=`which $PRIMER3_CORE_EXE 2>&1 | grep -v "no primer3_core in"` if [ -z "$got_primer3" ] ; then - fatal "primer3_core not found" + echo ERROR primer3_core not found >&2 + exit 1 fi # # Set up the working dir if [ "$PLATFORM" == "Illumina" ] ; then # Paired end Illumina data as input if [ $FASTQ_R1 == $FASTQ_R2 ] ; then - fatal ERROR R1 and R2 fastqs are the same file + echo ERROR R1 and R2 fastqs are the same file >&2 + exit 1 fi ln -s $FASTQ_R1 ln -s $FASTQ_R2 @@ -252,6 +264,17 @@ /bin/cp $PALFINDER_DATA_DIR/config.txt . # # Update the config.txt file with new values +function set_config_value() { + local key=$1 + local value=$2 + local config_txt=$3 + if [ -z "$value" ] ; then + echo "No value for $key, left as default" + else + echo Setting "$key" to "$value" + sed -i 's,^'"$key"' .*,'"$key"' '"$value"',' $config_txt + fi +} # Input files set_config_value platform $PLATFORM config.txt if [ "$PLATFORM" == "Illumina" ] ; then @@ -276,7 +299,6 @@ # Primer3 settings set_config_value primer3input Output/pr3in.txt config.txt set_config_value primer3output Output/pr3out.txt config.txt -set_config_value keepPrimer3files 1 config.txt set_config_value primer3executable $PRIMER3_CORE_EXE config.txt set_config_value prNamePrefix ${PRIMER_PREFIX}_ config.txt set_config_value PRIMER_MISPRIMING_LIBRARY "$PRIMER_MISPRIMING_LIBRARY" config.txt @@ -307,32 +329,20 @@ # # Check that log ends with "Done!!" message if [ -z "$(tail -n 1 pal_finder.log | grep Done!!)" ] ; then - fatal ERROR pal_finder failed to complete successfully -fi -echo "### pal_finder finished ###" -# -# Check for errors in pal_finder output -echo "### Checking for errors ###" -if [ ! -z "$(grep 'primer3_core: Illegal element in PRIMER_PRODUCT_SIZE_RANGE' pal_finder.log)" ] ; then - echo ERROR primer3 terminated prematurely due to bad product size ranges - cat >&2 <&2 - cat >&2 <&2 + exit 1 fi # -# Sort outputs into a consistent order regardless of Perl version -echo "### Sorting outputs ###" +# Sort microsat_summary output +echo "### Sorting microsat summary output ###" +head -n 7 Output/microsat_summary.txt | sort >microsat_summary.sorted +grep "^$" Output/microsat_summary.txt>>microsat_summary.sorted +grep "^Microsat Type" Output/microsat_summary.txt >>microsat_summary.sorted +tail -n +11 Output/microsat_summary.txt >>microsat_summary.sorted +mv microsat_summary.sorted Output/microsat_summary.txt +# +# Sort PAL_summary output +echo "### Sorting PAL summary output ###" head -1 Output/PAL_summary.txt > Output/PAL_summary.sorted.txt if [ "$PLATFORM" == "Illumina" ] ; then grep -v "^readPairID" Output/PAL_summary.txt | sort -k 1 >> Output/PAL_summary.sorted.txt @@ -352,9 +362,11 @@ fi tail -$MAX_LINES pal_filter.log if [ $? -ne 0 ] ; then - fatal $PALFINDER_FILTER exited with non-zero status + echo ERROR $PALFINDER_FILTER exited with non-zero status >&2 + exit 1 elif [ ! -f PAL_summary.filtered ] ; then - fatal no output from $PALFINDER_FILTER + echo ERROR no output from $PALFINDER_FILTER >&2 + exit 1 fi fi # @@ -374,7 +386,8 @@ if [ -f "$assembly" ] ; then /bin/mv $assembly "$OUTPUT_ASSEMBLY" else - fatal no assembly output found + echo ERROR no assembly output found >&2 + exit 1 fi fi if [ ! -z "$OUTPUT_CONFIG_FILE" ] && [ -f config.txt ] ; then diff -r 84613d5f1713 -r d26fb5260c67 pal_finder_wrapper.xml --- a/pal_finder_wrapper.xml Mon Jul 24 11:04:27 2017 -0400 +++ b/pal_finder_wrapper.xml Thu Mar 15 09:49:05 2018 -0400 @@ -1,13 +1,18 @@ Find microsatellite repeat elements from sequencing reads and design PCR primers to amplify them + + pal_finder_macros.xml + - perl pal_finder - primer3_core + python biopython pandaseq - pal_finder_wrapper.sh + + ]]> @@ -169,18 +174,18 @@ + - - - - + + + + - @@ -189,64 +194,65 @@ - - - + + + + - - - + + + - - - - + + + + - - - - + + + + - - - - + + + + - - - + + @@ -274,29 +280,6 @@ ------------- -.. class:: warning - -**Known problems** - -.. class:: infomark - -**Bad primer product size ranges** - -For some datasets pal_finder may generate 'bad' product size ranges (where the -lower limit exceeds the upper limit) for one or more reads, for input into -primer3_core. - -If this occurs then the tool will terminate with an error. A list of the reads -for which the bad ranges were generated can be found in the error message -which can be accessed via the 'bug' icon from a failed dataset. - -The conditions which cause this error are unclear. However we believe it to be -associated with short or low quality reads. It is recommended that the input -data are sufficiently trimmed and filtered (using e.g. the Trimmomatic tool) -before rerunning pal_finder. - -------------- - .. class:: infomark **Credits** diff -r 84613d5f1713 -r d26fb5260c67 pal_finder_wrapper_utils.sh --- a/pal_finder_wrapper_utils.sh Mon Jul 24 11:04:27 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,71 +0,0 @@ -#!/bin/bash -# -# Helper functions for the pal_finder_wrapper.sh script -# -# Utility function for terminating on fatal error -function fatal() { - echo "FATAL $@" >&2 - exit 1 -} -# -# Check that specified program is available -function have_program() { - local program=$1 - local got_program=$(which $program 2>&1 | grep "no $(basename $program) in") - if [ -z "$got_program" ] ; then - echo yes - else - echo no - fi -} -# -# Set the value for a parameter in the pal_finder config file -function set_config_value() { - local key=$1 - local value=$2 - local config_txt=$3 - if [ -z "$value" ] ; then - echo "No value for $key, left as default" - else - echo Setting "$key" to "$value" - sed -i 's,^'"$key"' .*,'"$key"' '"$value"',' $config_txt - fi -} -# -# Identify 'bad' PRIMER_PRODUCT_SIZE_RANGE from pr3in.txt file -function find_bad_primer_ranges() { - # Parses a pr3in.txt file from pal_finder and reports - # sequence ids where the PRIMER_PRODUCT_SIZE_RANGE has - # upper limit which is smaller than lower limit - local pr3in=$1 - local pattern="^(SEQUENCE_ID|PRIMER_PRODUCT_SIZE_RANGE)" - for line in $(grep -E "$pattern" $pr3in | sed 's/ /^/' | sed 'N;s/\n/*/') - do - # Loop over pairs of SEQUENCE_ID and PRIMER_PRODUCT_SIZE_RANGE - # keywords in the primer3 input - if [ ! -z "$(echo $line | grep ^SEQUENCE_ID)" ] ; then - # Extract the values - local size_range=$(echo $line | cut -d'*' -f2 | cut -d'=' -f2 | tr '^' ' ') - local seq_id=$(echo $line | cut -d'*' -f1 | cut -d'=' -f2) - else - local size_range=$(echo $line | cut -d'*' -f1 | cut -d'=' -f2) - local seq_id=$(echo $line | cut -d'*' -f2 | cut -d'=' -f2) - fi - seq_id=$(echo $seq_id | cut -d')' -f3) - # Check the upper and lower limits in each range - # to see if it's okay - local bad_range= - for range in $(echo $size_range) ; do - local lower=$(echo $range | cut -d'-' -f1) - local upper=$(echo $range | cut -d'-' -f2) - if [ $lower -gt $upper ] ; then - bad_range=yes - break - fi - done - # Report if the range is wrong - if [ ! -z "$bad_range" ] ; then - echo "$seq_id ($size_range)" - fi - done -} diff -r 84613d5f1713 -r d26fb5260c67 test-data/454_microsat_types.out --- a/test-data/454_microsat_types.out Mon Jul 24 11:04:27 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,13 +0,0 @@ -totalBases: 8639 -readsWithPrimers: 0 -totalReads: 38 -compound: 0 -broken: 1 -readsWithMicrosat: 1 - - -Microsat Type monomer length reads with loci total loci loci amplified total loci bases loci bases amplified -TC 2 0 0 0 0 0 -AC 2 1 2 0 48 0 -CG 2 0 0 0 0 0 -AT 2 0 0 0 0 0 diff -r 84613d5f1713 -r d26fb5260c67 test-data/454_microsat_types.out.re_match --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/454_microsat_types.out.re_match Thu Mar 15 09:49:05 2018 -0400 @@ -0,0 +1,14 @@ + +broken\:\ 1 +compound\:\ 0 +readsWithMicrosat\:\ 1 +readsWithPrimers\:\ 0 +totalBases\:\ 8639 +totalReads\:\ 38 + + +Microsat\ Type\ monomer\ length\ reads\ with\ loci\ total\ loci\ loci\ amplified\ total\ loci\ bases\ loci\ bases\ amplified +AC\ 2\ 1\ 2\ \ 48\ +AT\ 2\ 0\ 0\ 0\ 0\ 0 +CG\ 2\ 0\ 0\ 0\ 0\ 0 +TG\ 2\ 0\ 0\ 0\ 0\ 0 diff -r 84613d5f1713 -r d26fb5260c67 test-data/454_microsats.out --- a/test-data/454_microsats.out Mon Jul 24 11:04:27 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,2 +0,0 @@ -SequenceID Repeat Motif Size Repeat Motif Number Tandem Repeats Primer Designed (1=y,0=n) F Primer Name Forward Primer R Primer Name Reverse Primer Total Repeats In Amplicon Occurances of Forward Primer in Reads Occurances of Reverse Primer in Reads Occurances of Amplifiable Primer Pair in Reads Occurances of Amplifiable Primer Pair in PALs -FW1N29Q04EP35X 2 AC 18 0 diff -r 84613d5f1713 -r d26fb5260c67 test-data/454_microsats.out.re_match --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/454_microsats.out.re_match Thu Mar 15 09:49:05 2018 -0400 @@ -0,0 +1,2 @@ +SequenceID\ Repeat\ Motif\ Size\ Repeat\ Motif\ Number\ Tandem\ Repeats\ Primer\ Designed\ $1\=y\,0\=n$\ F\ Primer\ Name\ Forward\ Primer\ R\ Primer\ Name\ Reverse\ Primer\ Total\ Repeats\ In\ Amplicon\ Occurances\ of\ Forward\ Primer\ in\ Reads\ Occurances\ of\ Reverse\ Primer\ in\ Reads\ Occurances\ of\ Amplifiable\ Primer\ Pair\ in\ Reads\ Occurances\ of\ Amplifiable\ Primer\ Pair\ in\ PALs +FW1N29Q04EP35X\ 2\ (AC|TG)\ 18\ 0\ \ \ \ \ \ \ \ \ diff -r 84613d5f1713 -r d26fb5260c67 test-data/454_microsats.out.re_match~ --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/454_microsats.out.re_match~ Thu Mar 15 09:49:05 2018 -0400 @@ -0,0 +1,2 @@ +SequenceID\ Repeat\ Motif\ Size\ Repeat\ Motif\ Number\ Tandem\ Repeats\ Primer\ Designed\ $1\=y\,0\=n$\ F\ Primer\ Name\ Forward\ Primer\ R\ Primer\ Name\ Reverse\ Primer\ Total\ Repeats\ In\ Amplicon\ Occurances\ of\ Forward\ Primer\ in\ Reads\ Occurances\ of\ Reverse\ Primer\ in\ Reads\ Occurances\ of\ Amplifiable\ Primer\ Pair\ in\ Reads\ Occurances\ of\ Amplifiable\ Primer\ Pair\ in\ PALs +FW1N29Q04EP35X\ 2\ AC\ 18\ 0\ \ \ \ \ \ \ \ \ diff -r 84613d5f1713 -r d26fb5260c67 test-data/illuminaPE_filtered_microsats.out --- a/test-data/illuminaPE_filtered_microsats.out Mon Jul 24 11:04:27 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -readPairID Motifs(bases) Bases in all Motifs Possible Extended Possible Spanning Primers found (1=y,0=n) F Primer Name Forward Primer R Primer Name Reverse Primer Amplicon Motifs Number motif bases in amplicon Primers on sep reads Extend with primers Spand with primers Occurances of Forward Primer in Reads Occurances of Reverse Primer in Reads Occurances of Amplifiable Primer Pair in Reads Occurances of Amplifiable Primer Pair in PALs R1_Sequence_ID R1_Sequence R2_Sequence_ID R2_Sequence -ILLUMINA-545855:49:FC61RLR:2:1:8157:1636 AC(12) 12 1 test_5 AAGTACAGTGGGGAGGCTGG test_6 TTTTCTACACAGCTCAAGTAGCCC AC(12) 12 1 1 1 1 1 >ILLUMINA-545855:49:FC61RLR:2:1:8157:1636 1:N:0:TCCTGA TACTAGTCTAATAATTGCAGGCAGCTGAACTAGATAGGTCCTAAAGTACAGTGGGGAGGCTGGTGTGTGTGTGTGCATGGGATTGTCAGCCTTACCATCAGTCCTGATTTGTAGGT >ILLUMINA-545855:49:FC61RLR:2:1:8157:1636 2:N:0:TCCTGA TAAACAACCAAATGAAACCATCTTTTCTACACAGCTCAAGTAGCCCTACATACAACACAAGCCACCTACAAATCAGGACTGATGGTAAGGCTGACAATCCAATCCACCACAACAAC -ILLUMINA-545855:49:FC61RLR:2:1:1978:1220 AC(12) 12 1 test_3 GCAGTAAACAAAGGCAAAGGG test_4 CCTGGGCAGAGGTGTTCC AC(12) 12 1 1 1 1 1 >ILLUMINA-545855:49:FC61RLR:2:1:1978:1220 1:N:0:TCCTGA TCATAAGAATGAGCAGTAAACAAAGGCAAAGGGGAGATAACACACACACACAAAATAAAAAAACATCAATTTCTAATACACGCCTTTATTATAAAGAAATAAATCACTGAAAAACA >ILLUMINA-545855:49:FC61RLR:2:1:1978:1220 2:N:0:TCCTGA TCCTCTGACTAGGCAACAACAGCTTTTTTGCTCCTGGGCAGAGGTGTTCCGAGTGTATATTTTTTATAATTACGGCGCGCATTGGAAATTGATGTTATTTTATTTTGCGTGTGTGT -ILLUMINA-545855:49:FC61RLR:2:1:10979:1695 TC(14) 14 1 test_7 TTCTCCCACTATATTTTGCATTGG test_8 TCCAGACTGAAGCTACCCTGG TC(14) 14 1 1 1 1 1 >ILLUMINA-545855:49:FC61RLR:2:1:10979:1695 1:N:0:TCCTGA TACTGTTTAGAATAGACTGTTCTCCCACTATATTTTGCATTGGTGCATACTCAGCTTTAGTAATAAGTGTGATTCTGGTAGAGAGAGAGAGAGATACCAACCTCTTCTTCCCACTA >ILLUMINA-545855:49:FC61RLR:2:1:10979:1695 2:N:0:TCCTGA TACTGTTTAGAAAGCCTGTTCCAGAACTTGATCACTGTCACAGAAAATCTTTCTTACTATCCAGACTGAAGCTACCCTGGTGCAGCTTTGTGCTGTTACCTTGAGTCATGTCATCA diff -r 84613d5f1713 -r d26fb5260c67 test-data/illuminaPE_filtered_microsats.out.re_match --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/illuminaPE_filtered_microsats.out.re_match Thu Mar 15 09:49:05 2018 -0400 @@ -0,0 +1,4 @@ +readPairID\ Motifs$bases$\ Bases\ in\ all\ Motifs\ Possible\ Extended\ Possible\ Spanning\ Primers\ found\ $1\=y\,0\=n$\ F\ Primer\ Name\ Forward\ Primer\ R\ Primer\ Name\ Reverse\ Primer\ Amplicon\ Motifs\ Number\ motif\ bases\ in\ amplicon\ Primers\ on\ sep\ reads\ Extend\ with\ primers\ Spand\ with\ primers\ Occurances\ of\ Forward\ Primer\ in\ Reads\ Occurances\ of\ Reverse\ Primer\ in\ Reads\ Occurances\ of\ Amplifiable\ Primer\ Pair\ in\ Reads\ Occurances\ of\ Amplifiable\ Primer\ Pair\ in\ PALs\ R1\_Sequence\_ID\ R1\_Sequence\ R2\_Sequence\_ID\ R2\_Sequence +ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8157\:1636\ (AC|TG)$12$\ \ 12\ \ \ 1\ test\_.*\ AAGTACAGTGGGGAGGCTGG\ test\_.*\ TTTTCTACACAGCTCAAGTAGCCC\ (AC|TG)$12$\ \ 12\ 1\ \ \ 1\ 1\ 1\ 1\ \>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8157\:1636\ 1\:N\:0\:TCCTGA\ TACTAGTCTAATAATTGCAGGCAGCTGAACTAGATAGGTCCTAAAGTACAGTGGGGAGGCTGGTGTGTGTGTGTGCATGGGATTGTCAGCCTTACCATCAGTCCTGATTTGTAGGT\ \>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8157\:1636\ 2\:N\:0\:TCCTGA\ TAAACAACCAAATGAAACCATCTTTTCTACACAGCTCAAGTAGCCCTACATACAACACAAGCCACCTACAAATCAGGACTGATGGTAAGGCTGACAATCCAATCCACCACAACAAC +ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:1978\:1220\ (AC|TG)$12$\ \ 12\ \ \ 1\ test\_.*\ GCAGTAAACAAAGGCAAAGGG\ test\_.*\ CCTGGGCAGAGGTGTTCC\ (AC|TG)$12$\ \ 12\ 1\ \ \ 1\ 1\ 1\ 1\ \>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:1978\:1220\ 1\:N\:0\:TCCTGA\ TCATAAGAATGAGCAGTAAACAAAGGCAAAGGGGAGATAACACACACACACAAAATAAAAAAACATCAATTTCTAATACACGCCTTTATTATAAAGAAATAAATCACTGAAAAACA\ \>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:1978\:1220\ 2\:N\:0\:TCCTGA\ TCCTCTGACTAGGCAACAACAGCTTTTTTGCTCCTGGGCAGAGGTGTTCCGAGTGTATATTTTTTATAATTACGGCGCGCATTGGAAATTGATGTTATTTTATTTTGCGTGTGTGT +ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:10979\:1695\ (AG|TC)$14$\ \ 14\ \ \ 1\ test\_.*\ TTCTCCCACTATATTTTGCATTGG\ test\_.*\ TCCAGACTGAAGCTACCCTGG\ (AG|TC)$14$\ \ 14\ 1\ \ \ 1\ 1\ 1\ 1\ \>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:10979\:1695\ 1\:N\:0\:TCCTGA\ TACTGTTTAGAATAGACTGTTCTCCCACTATATTTTGCATTGGTGCATACTCAGCTTTAGTAATAAGTGTGATTCTGGTAGAGAGAGAGAGAGATACCAACCTCTTCTTCCCACTA\ \>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:10979\:1695\ 2\:N\:0\:TCCTGA\ TACTGTTTAGAAAGCCTGTTCCAGAACTTGATCACTGTCACAGAAAATCTTTCTTACTATCCAGACTGAAGCTACCCTGGTGCAGCTTTGTGCTGTTACCTTGAGTCATGTCATCA diff -r 84613d5f1713 -r d26fb5260c67 test-data/illuminaPE_filtered_microsats.out.re_match~ --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/illuminaPE_filtered_microsats.out.re_match~ Thu Mar 15 09:49:05 2018 -0400 @@ -0,0 +1,4 @@ +readPairID\ Motifs$bases$\ Bases\ in\ all\ Motifs\ Possible\ Extended\ Possible\ Spanning\ Primers\ found\ $1\=y\,0\=n$\ F\ Primer\ Name\ Forward\ Primer\ R\ Primer\ Name\ Reverse\ Primer\ Amplicon\ Motifs\ Number\ motif\ bases\ in\ amplicon\ Primers\ on\ sep\ reads\ Extend\ with\ primers\ Spand\ with\ primers\ Occurances\ of\ Forward\ Primer\ in\ Reads\ Occurances\ of\ Reverse\ Primer\ in\ Reads\ Occurances\ of\ Amplifiable\ Primer\ Pair\ in\ Reads\ Occurances\ of\ Amplifiable\ Primer\ Pair\ in\ PALs\ R1\_Sequence\_ID\ R1\_Sequence\ R2\_Sequence\_ID\ R2\_Sequence +ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8157\:1636\ AC$12$\ \ 12\ \ \ 1\ test\_3\ AAGTACAGTGGGGAGGCTGG\ test\_6\ TTTTCTACACAGCTCAAGTAGCCC\ AC$12$\ \ 12\ 1\ \ \ 1\ 1\ 1\ 1\ \>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8157\:1636\ 1\:N\:0\:TCCTGA\ TACTAGTCTAATAATTGCAGGCAGCTGAACTAGATAGGTCCTAAAGTACAGTGGGGAGGCTGGTGTGTGTGTGTGCATGGGATTGTCAGCCTTACCATCAGTCCTGATTTGTAGGT\ \>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8157\:1636\ 2\:N\:0\:TCCTGA\ TAAACAACCAAATGAAACCATCTTTTCTACACAGCTCAAGTAGCCCTACATACAACACAAGCCACCTACAAATCAGGACTGATGGTAAGGCTGACAATCCAATCCACCACAACAAC +ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:1978\:1220\ AC$12$\ \ 12\ \ \ 1\ test\_7\ GCAGTAAACAAAGGCAAAGGG\ test\_4\ CCTGGGCAGAGGTGTTCC\ AC$12$\ \ 12\ 1\ \ \ 1\ 1\ 1\ 1\ \>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:1978\:1220\ 1\:N\:0\:TCCTGA\ TCATAAGAATGAGCAGTAAACAAAGGCAAAGGGGAGATAACACACACACACAAAATAAAAAAACATCAATTTCTAATACACGCCTTTATTATAAAGAAATAAATCACTGAAAAACA\ \>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:1978\:1220\ 2\:N\:0\:TCCTGA\ TCCTCTGACTAGGCAACAACAGCTTTTTTGCTCCTGGGCAGAGGTGTTCCGAGTGTATATTTTTTATAATTACGGCGCGCATTGGAAATTGATGTTATTTTATTTTGCGTGTGTGT +ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:10979\:1695\ AG$14$\ \ 14\ \ \ 1\ test\_5\ TTCTCCCACTATATTTTGCATTGG\ test\_1\ TCCAGACTGAAGCTACCCTGG\ AG$14$\ \ 14\ 1\ \ \ 1\ 1\ 1\ 1\ \>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:10979\:1695\ 1\:N\:0\:TCCTGA\ TACTGTTTAGAATAGACTGTTCTCCCACTATATTTTGCATTGGTGCATACTCAGCTTTAGTAATAAGTGTGATTCTGGTAGAGAGAGAGAGAGATACCAACCTCTTCTTCCCACTA\ \>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:10979\:1695\ 2\:N\:0\:TCCTGA\ TACTGTTTAGAAAGCCTGTTCCAGAACTTGATCACTGTCACAGAAAATCTTTCTTACTATCCAGACTGAAGCTACCCTGGTGCAGCTTTGTGCTGTTACCTTGAGTCATGTCATCA diff -r 84613d5f1713 -r d26fb5260c67 test-data/illuminaPE_filtered_microsats_occurrences.out --- a/test-data/illuminaPE_filtered_microsats_occurrences.out Mon Jul 24 11:04:27 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -readPairID Motifs(bases) Bases in all Motifs Possible Extended Possible Spanning Primers found (1=y,0=n) F Primer Name Forward Primer R Primer Name Reverse Primer Amplicon Motifs Number motif bases in amplicon Primers on sep reads Extend with primers Spand with primers Occurances of Forward Primer in Reads Occurances of Reverse Primer in Reads Occurances of Amplifiable Primer Pair in Reads Occurances of Amplifiable Primer Pair in PALs R1_Sequence_ID R1_Sequence R2_Sequence_ID R2_Sequence -ILLUMINA-545855:49:FC61RLR:2:1:10979:1695 TC(14) 14 1 test_7 TTCTCCCACTATATTTTGCATTGG test_8 TCCAGACTGAAGCTACCCTGG TC(14) 14 1 1 1 1 1 >ILLUMINA-545855:49:FC61RLR:2:1:10979:1695 1:N:0:TCCTGA TACTGTTTAGAATAGACTGTTCTCCCACTATATTTTGCATTGGTGCATACTCAGCTTTAGTAATAAGTGTGATTCTGGTAGAGAGAGAGAGAGATACCAACCTCTTCTTCCCACTA >ILLUMINA-545855:49:FC61RLR:2:1:10979:1695 2:N:0:TCCTGA TACTGTTTAGAAAGCCTGTTCCAGAACTTGATCACTGTCACAGAAAATCTTTCTTACTATCCAGACTGAAGCTACCCTGGTGCAGCTTTGTGCTGTTACCTTGAGTCATGTCATCA -ILLUMINA-545855:49:FC61RLR:2:1:1978:1220 AC(12) 12 1 test_3 GCAGTAAACAAAGGCAAAGGG test_4 CCTGGGCAGAGGTGTTCC AC(12) 12 1 1 1 1 1 >ILLUMINA-545855:49:FC61RLR:2:1:1978:1220 1:N:0:TCCTGA TCATAAGAATGAGCAGTAAACAAAGGCAAAGGGGAGATAACACACACACACAAAATAAAAAAACATCAATTTCTAATACACGCCTTTATTATAAAGAAATAAATCACTGAAAAACA >ILLUMINA-545855:49:FC61RLR:2:1:1978:1220 2:N:0:TCCTGA TCCTCTGACTAGGCAACAACAGCTTTTTTGCTCCTGGGCAGAGGTGTTCCGAGTGTATATTTTTTATAATTACGGCGCGCATTGGAAATTGATGTTATTTTATTTTGCGTGTGTGT -ILLUMINA-545855:49:FC61RLR:2:1:8157:1636 AC(12) 12 1 test_5 AAGTACAGTGGGGAGGCTGG test_6 TTTTCTACACAGCTCAAGTAGCCC AC(12) 12 1 1 1 1 1 >ILLUMINA-545855:49:FC61RLR:2:1:8157:1636 1:N:0:TCCTGA TACTAGTCTAATAATTGCAGGCAGCTGAACTAGATAGGTCCTAAAGTACAGTGGGGAGGCTGGTGTGTGTGTGTGCATGGGATTGTCAGCCTTACCATCAGTCCTGATTTGTAGGT >ILLUMINA-545855:49:FC61RLR:2:1:8157:1636 2:N:0:TCCTGA TAAACAACCAAATGAAACCATCTTTTCTACACAGCTCAAGTAGCCCTACATACAACACAAGCCACCTACAAATCAGGACTGATGGTAAGGCTGACAATCCAATCCACCACAACAAC diff -r 84613d5f1713 -r d26fb5260c67 test-data/illuminaPE_filtered_microsats_occurrences.out.re_match --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/illuminaPE_filtered_microsats_occurrences.out.re_match Thu Mar 15 09:49:05 2018 -0400 @@ -0,0 +1,4 @@ +readPairID\ Motifs$bases$\ Bases\ in\ all\ Motifs\ Possible\ Extended\ Possible\ Spanning\ Primers\ found\ $1\=y\,0\=n$\ F\ Primer\ Name\ Forward\ Primer\ R\ Primer\ Name\ Reverse\ Primer\ Amplicon\ Motifs\ Number\ motif\ bases\ in\ amplicon\ Primers\ on\ sep\ reads\ Extend\ with\ primers\ Spand\ with\ primers\ Occurances\ of\ Forward\ Primer\ in\ Reads\ Occurances\ of\ Reverse\ Primer\ in\ Reads\ Occurances\ of\ Amplifiable\ Primer\ Pair\ in\ Reads\ Occurances\ of\ Amplifiable\ Primer\ Pair\ in\ PALs\ R1\_Sequence\_ID\ R1\_Sequence\ R2\_Sequence\_ID\ R2\_Sequence +ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:10979\:1695\ (AG|TC)$14$\ \ 14\ \ \ 1\ test\_.*\ TTCTCCCACTATATTTTGCATTGG\ test\_.*\ TCCAGACTGAAGCTACCCTGG\ (AG|TC)$14$\ \ 14\ 1\ \ \ 1\ 1\ 1\ 1\ \>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:10979\:1695\ 1\:N\:0\:TCCTGA\ TACTGTTTAGAATAGACTGTTCTCCCACTATATTTTGCATTGGTGCATACTCAGCTTTAGTAATAAGTGTGATTCTGGTAGAGAGAGAGAGAGATACCAACCTCTTCTTCCCACTA\ \>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:10979\:1695\ 2\:N\:0\:TCCTGA\ TACTGTTTAGAAAGCCTGTTCCAGAACTTGATCACTGTCACAGAAAATCTTTCTTACTATCCAGACTGAAGCTACCCTGGTGCAGCTTTGTGCTGTTACCTTGAGTCATGTCATCA +ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:1978\:1220\ (AC|TG)$12$\ \ 12\ \ \ 1\ test\_.*\ GCAGTAAACAAAGGCAAAGGG\ test\_.*\ CCTGGGCAGAGGTGTTCC\ (AC|TG)$12$\ \ 12\ 1\ \ \ 1\ 1\ 1\ 1\ \>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:1978\:1220\ 1\:N\:0\:TCCTGA\ TCATAAGAATGAGCAGTAAACAAAGGCAAAGGGGAGATAACACACACACACAAAATAAAAAAACATCAATTTCTAATACACGCCTTTATTATAAAGAAATAAATCACTGAAAAACA\ \>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:1978\:1220\ 2\:N\:0\:TCCTGA\ TCCTCTGACTAGGCAACAACAGCTTTTTTGCTCCTGGGCAGAGGTGTTCCGAGTGTATATTTTTTATAATTACGGCGCGCATTGGAAATTGATGTTATTTTATTTTGCGTGTGTGT +ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8157\:1636\ (AC|TG)$12$\ \ 12\ \ \ 1\ test\_.*\ AAGTACAGTGGGGAGGCTGG\ test\_.*\ TTTTCTACACAGCTCAAGTAGCCC\ (AC|TG)$12$\ \ 12\ 1\ \ \ 1\ 1\ 1\ 1\ \>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8157\:1636\ 1\:N\:0\:TCCTGA\ TACTAGTCTAATAATTGCAGGCAGCTGAACTAGATAGGTCCTAAAGTACAGTGGGGAGGCTGGTGTGTGTGTGTGCATGGGATTGTCAGCCTTACCATCAGTCCTGATTTGTAGGT\ \>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8157\:1636\ 2\:N\:0\:TCCTGA\ TAAACAACCAAATGAAACCATCTTTTCTACACAGCTCAAGTAGCCCTACATACAACACAAGCCACCTACAAATCAGGACTGATGGTAAGGCTGACAATCCAATCCACCACAACAAC diff -r 84613d5f1713 -r d26fb5260c67 test-data/illuminaPE_filtered_microsats_occurrences.out.re_match~ --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/illuminaPE_filtered_microsats_occurrences.out.re_match~ Thu Mar 15 09:49:05 2018 -0400 @@ -0,0 +1,4 @@ +readPairID\ Motifs$bases$\ Bases\ in\ all\ Motifs\ Possible\ Extended\ Possible\ Spanning\ Primers\ found\ $1\=y\,0\=n$\ F\ Primer\ Name\ Forward\ Primer\ R\ Primer\ Name\ Reverse\ Primer\ Amplicon\ Motifs\ Number\ motif\ bases\ in\ amplicon\ Primers\ on\ sep\ reads\ Extend\ with\ primers\ Spand\ with\ primers\ Occurances\ of\ Forward\ Primer\ in\ Reads\ Occurances\ of\ Reverse\ Primer\ in\ Reads\ Occurances\ of\ Amplifiable\ Primer\ Pair\ in\ Reads\ Occurances\ of\ Amplifiable\ Primer\ Pair\ in\ PALs\ R1\_Sequence\_ID\ R1\_Sequence\ R2\_Sequence\_ID\ R2\_Sequence +ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:10979\:1695\ AG$14$\ \ 14\ \ \ 1\ test\_7\ TTCTCCCACTATATTTTGCATTGG\ test\_6\ TCCAGACTGAAGCTACCCTGG\ AG$14$\ \ 14\ 1\ \ \ 1\ 1\ 1\ 1\ \>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:10979\:1695\ 1\:N\:0\:TCCTGA\ TACTGTTTAGAATAGACTGTTCTCCCACTATATTTTGCATTGGTGCATACTCAGCTTTAGTAATAAGTGTGATTCTGGTAGAGAGAGAGAGAGATACCAACCTCTTCTTCCCACTA\ \>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:10979\:1695\ 2\:N\:0\:TCCTGA\ TACTGTTTAGAAAGCCTGTTCCAGAACTTGATCACTGTCACAGAAAATCTTTCTTACTATCCAGACTGAAGCTACCCTGGTGCAGCTTTGTGCTGTTACCTTGAGTCATGTCATCA +ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:1978\:1220\ AC$12$\ \ 12\ \ \ 1\ test\_5\ GCAGTAAACAAAGGCAAAGGG\ test\_2\ CCTGGGCAGAGGTGTTCC\ AC$12$\ \ 12\ 1\ \ \ 1\ 1\ 1\ 1\ \>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:1978\:1220\ 1\:N\:0\:TCCTGA\ TCATAAGAATGAGCAGTAAACAAAGGCAAAGGGGAGATAACACACACACACAAAATAAAAAAACATCAATTTCTAATACACGCCTTTATTATAAAGAAATAAATCACTGAAAAACA\ \>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:1978\:1220\ 2\:N\:0\:TCCTGA\ TCCTCTGACTAGGCAACAACAGCTTTTTTGCTCCTGGGCAGAGGTGTTCCGAGTGTATATTTTTTATAATTACGGCGCGCATTGGAAATTGATGTTATTTTATTTTGCGTGTGTGT +ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8157\:1636\ AC$12$\ \ 12\ \ \ 1\ test\_8\ AAGTACAGTGGGGAGGCTGG\ test\_4\ TTTTCTACACAGCTCAAGTAGCCC\ AC$12$\ \ 12\ 1\ \ \ 1\ 1\ 1\ 1\ \>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8157\:1636\ 1\:N\:0\:TCCTGA\ TACTAGTCTAATAATTGCAGGCAGCTGAACTAGATAGGTCCTAAAGTACAGTGGGGAGGCTGGTGTGTGTGTGTGCATGGGATTGTCAGCCTTACCATCAGTCCTGATTTGTAGGT\ \>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8157\:1636\ 2\:N\:0\:TCCTGA\ TAAACAACCAAATGAAACCATCTTTTCTACACAGCTCAAGTAGCCCTACATACAACACAAGCCACCTACAAATCAGGACTGATGGTAAGGCTGACAATCCAATCCACCACAACAAC diff -r 84613d5f1713 -r d26fb5260c67 test-data/illuminaPE_filtered_microsats_primers.out --- a/test-data/illuminaPE_filtered_microsats_primers.out Mon Jul 24 11:04:27 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,5 +0,0 @@ -readPairID Motifs(bases) Bases in all Motifs Possible Extended Possible Spanning Primers found (1=y,0=n) F Primer Name Forward Primer R Primer Name Reverse Primer Amplicon Motifs Number motif bases in amplicon Primers on sep reads Extend with primers Spand with primers Occurances of Forward Primer in Reads Occurances of Reverse Primer in Reads Occurances of Amplifiable Primer Pair in Reads Occurances of Amplifiable Primer Pair in PALs R1_Sequence_ID R1_Sequence R2_Sequence_ID R2_Sequence -ILLUMINA-545855:49:FC61RLR:2:1:10979:1695 TC(14) 14 1 test_7 TTCTCCCACTATATTTTGCATTGG test_8 TCCAGACTGAAGCTACCCTGG TC(14) 14 1 1 1 1 1 >ILLUMINA-545855:49:FC61RLR:2:1:10979:1695 1:N:0:TCCTGA TACTGTTTAGAATAGACTGTTCTCCCACTATATTTTGCATTGGTGCATACTCAGCTTTAGTAATAAGTGTGATTCTGGTAGAGAGAGAGAGAGATACCAACCTCTTCTTCCCACTA >ILLUMINA-545855:49:FC61RLR:2:1:10979:1695 2:N:0:TCCTGA TACTGTTTAGAAAGCCTGTTCCAGAACTTGATCACTGTCACAGAAAATCTTTCTTACTATCCAGACTGAAGCTACCCTGGTGCAGCTTTGTGCTGTTACCTTGAGTCATGTCATCA -ILLUMINA-545855:49:FC61RLR:2:1:1978:1220 AC(12) 12 1 test_3 GCAGTAAACAAAGGCAAAGGG test_4 CCTGGGCAGAGGTGTTCC AC(12) 12 1 1 1 1 1 >ILLUMINA-545855:49:FC61RLR:2:1:1978:1220 1:N:0:TCCTGA TCATAAGAATGAGCAGTAAACAAAGGCAAAGGGGAGATAACACACACACACAAAATAAAAAAACATCAATTTCTAATACACGCCTTTATTATAAAGAAATAAATCACTGAAAAACA >ILLUMINA-545855:49:FC61RLR:2:1:1978:1220 2:N:0:TCCTGA TCCTCTGACTAGGCAACAACAGCTTTTTTGCTCCTGGGCAGAGGTGTTCCGAGTGTATATTTTTTATAATTACGGCGCGCATTGGAAATTGATGTTATTTTATTTTGCGTGTGTGT -ILLUMINA-545855:49:FC61RLR:2:1:8157:1636 AC(12) 12 1 test_5 AAGTACAGTGGGGAGGCTGG test_6 TTTTCTACACAGCTCAAGTAGCCC AC(12) 12 1 1 1 1 1 >ILLUMINA-545855:49:FC61RLR:2:1:8157:1636 1:N:0:TCCTGA TACTAGTCTAATAATTGCAGGCAGCTGAACTAGATAGGTCCTAAAGTACAGTGGGGAGGCTGGTGTGTGTGTGTGCATGGGATTGTCAGCCTTACCATCAGTCCTGATTTGTAGGT >ILLUMINA-545855:49:FC61RLR:2:1:8157:1636 2:N:0:TCCTGA TAAACAACCAAATGAAACCATCTTTTCTACACAGCTCAAGTAGCCCTACATACAACACAAGCCACCTACAAATCAGGACTGATGGTAAGGCTGACAATCCAATCCACCACAACAAC -ILLUMINA-545855:49:FC61RLR:2:1:8899:1514 AC(12) AC(12) 24 1 test_2 TCTTTATCTAAACACATCCTGAAATACC test_1 AAACGCAATTATTTTGAGATGTCC AC(12) AC(12) 24 1 1 2 1 1 >ILLUMINA-545855:49:FC61RLR:2:1:8899:1514 1:N:0:TCCTGA TCTTTATCTAAACACATCCTGAAATACCATCTGTTACACACACACACAGCAGTGGAAGTATAAAAAAAAATCTGGACATCTCAAAATAATTGCGTTTCTGAAGTGTTACATTTTTC >ILLUMINA-545855:49:FC61RLR:2:1:8899:1514 2:N:0:TCCTGA TATCATTGAAATTTTTATAAAAACTGTGAAGAGAAAAATGTAACACTTCAGAAACGCAATTATTTTGAGATGTCCAGATTTTTTTTTATACTTCCACTGCTGTGTGTGTGTGTAAC diff -r 84613d5f1713 -r d26fb5260c67 test-data/illuminaPE_filtered_microsats_primers.out.re_match --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/illuminaPE_filtered_microsats_primers.out.re_match Thu Mar 15 09:49:05 2018 -0400 @@ -0,0 +1,5 @@ +readPairID\ Motifs$bases$\ Bases\ in\ all\ Motifs\ Possible\ Extended\ Possible\ Spanning\ Primers\ found\ $1\=y\,0\=n$\ F\ Primer\ Name\ Forward\ Primer\ R\ Primer\ Name\ Reverse\ Primer\ Amplicon\ Motifs\ Number\ motif\ bases\ in\ amplicon\ Primers\ on\ sep\ reads\ Extend\ with\ primers\ Spand\ with\ primers\ Occurances\ of\ Forward\ Primer\ in\ Reads\ Occurances\ of\ Reverse\ Primer\ in\ Reads\ Occurances\ of\ Amplifiable\ Primer\ Pair\ in\ Reads\ Occurances\ of\ Amplifiable\ Primer\ Pair\ in\ PALs\ R1\_Sequence\_ID\ R1\_Sequence\ R2\_Sequence\_ID\ R2\_Sequence +ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:10979\:1695\ (AG|TC)$14$\ \ 14\ \ \ 1\ test\_.*\ TTCTCCCACTATATTTTGCATTGG\ test\_.*\ TCCAGACTGAAGCTACCCTGG\ (AG|TC)$14$\ \ 14\ 1\ \ \ 1\ 1\ 1\ 1\ \>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:10979\:1695\ 1\:N\:0\:TCCTGA\ TACTGTTTAGAATAGACTGTTCTCCCACTATATTTTGCATTGGTGCATACTCAGCTTTAGTAATAAGTGTGATTCTGGTAGAGAGAGAGAGAGATACCAACCTCTTCTTCCCACTA\ \>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:10979\:1695\ 2\:N\:0\:TCCTGA\ TACTGTTTAGAAAGCCTGTTCCAGAACTTGATCACTGTCACAGAAAATCTTTCTTACTATCCAGACTGAAGCTACCCTGGTGCAGCTTTGTGCTGTTACCTTGAGTCATGTCATCA +ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:1978\:1220\ (AC|TG)$12$\ \ 12\ \ \ 1\ test\_.*\ GCAGTAAACAAAGGCAAAGGG\ test\_.*\ CCTGGGCAGAGGTGTTCC\ (AC|TG)$12$\ \ 12\ 1\ \ \ 1\ 1\ 1\ 1\ \>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:1978\:1220\ 1\:N\:0\:TCCTGA\ TCATAAGAATGAGCAGTAAACAAAGGCAAAGGGGAGATAACACACACACACAAAATAAAAAAACATCAATTTCTAATACACGCCTTTATTATAAAGAAATAAATCACTGAAAAACA\ \>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:1978\:1220\ 2\:N\:0\:TCCTGA\ TCCTCTGACTAGGCAACAACAGCTTTTTTGCTCCTGGGCAGAGGTGTTCCGAGTGTATATTTTTTATAATTACGGCGCGCATTGGAAATTGATGTTATTTTATTTTGCGTGTGTGT +ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8157\:1636\ (AC|TG)$12$\ \ 12\ \ \ 1\ test\_.*\ AAGTACAGTGGGGAGGCTGG\ test\_.*\ TTTTCTACACAGCTCAAGTAGCCC\ (AC|TG)$12$\ \ 12\ 1\ \ \ 1\ 1\ 1\ 1\ \>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8157\:1636\ 1\:N\:0\:TCCTGA\ TACTAGTCTAATAATTGCAGGCAGCTGAACTAGATAGGTCCTAAAGTACAGTGGGGAGGCTGGTGTGTGTGTGTGCATGGGATTGTCAGCCTTACCATCAGTCCTGATTTGTAGGT\ \>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8157\:1636\ 2\:N\:0\:TCCTGA\ TAAACAACCAAATGAAACCATCTTTTCTACACAGCTCAAGTAGCCCTACATACAACACAAGCCACCTACAAATCAGGACTGATGGTAAGGCTGACAATCCAATCCACCACAACAAC +ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8899\:1514\ (AC|TG)$12$\ (AC|TG)$12$\ \ 24\ \ \ 1\ test\_.*\ TCTTTATCTAAACACATCCTGAAATACC\ test\_.*\ AAACGCAATTATTTTGAGATGTCC\ (AC|TG)$12$\ (AC|TG)$12$\ \ 24\ 1\ \ \ 1\ 2\ 1\ 1\ \>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8899\:1514\ 1\:N\:0\:TCCTGA\ TCTTTATCTAAACACATCCTGAAATACCATCTGTTACACACACACACAGCAGTGGAAGTATAAAAAAAAATCTGGACATCTCAAAATAATTGCGTTTCTGAAGTGTTACATTTTTC\ \>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8899\:1514\ 2\:N\:0\:TCCTGA\ TATCATTGAAATTTTTATAAAAACTGTGAAGAGAAAAATGTAACACTTCAGAAACGCAATTATTTTGAGATGTCCAGATTTTTTTTTATACTTCCACTGCTGTGTGTGTGTGTAAC diff -r 84613d5f1713 -r d26fb5260c67 test-data/illuminaPE_filtered_microsats_primers.out.re_match~ --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/illuminaPE_filtered_microsats_primers.out.re_match~ Thu Mar 15 09:49:05 2018 -0400 @@ -0,0 +1,5 @@ +readPairID\ Motifs$bases$\ Bases\ in\ all\ Motifs\ Possible\ Extended\ Possible\ Spanning\ Primers\ found\ $1\=y\,0\=n$\ F\ Primer\ Name\ Forward\ Primer\ R\ Primer\ Name\ Reverse\ Primer\ Amplicon\ Motifs\ Number\ motif\ bases\ in\ amplicon\ Primers\ on\ sep\ reads\ Extend\ with\ primers\ Spand\ with\ primers\ Occurances\ of\ Forward\ Primer\ in\ Reads\ Occurances\ of\ Reverse\ Primer\ in\ Reads\ Occurances\ of\ Amplifiable\ Primer\ Pair\ in\ Reads\ Occurances\ of\ Amplifiable\ Primer\ Pair\ in\ PALs\ R1\_Sequence\_ID\ R1\_Sequence\ R2\_Sequence\_ID\ R2\_Sequence +ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:10979\:1695\ AG$14$\ \ 14\ \ \ 1\ test\_7\ TTCTCCCACTATATTTTGCATTGG\ test\_2\ TCCAGACTGAAGCTACCCTGG\ AG$14$\ \ 14\ 1\ \ \ 1\ 1\ 1\ 1\ \>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:10979\:1695\ 1\:N\:0\:TCCTGA\ TACTGTTTAGAATAGACTGTTCTCCCACTATATTTTGCATTGGTGCATACTCAGCTTTAGTAATAAGTGTGATTCTGGTAGAGAGAGAGAGAGATACCAACCTCTTCTTCCCACTA\ \>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:10979\:1695\ 2\:N\:0\:TCCTGA\ TACTGTTTAGAAAGCCTGTTCCAGAACTTGATCACTGTCACAGAAAATCTTTCTTACTATCCAGACTGAAGCTACCCTGGTGCAGCTTTGTGCTGTTACCTTGAGTCATGTCATCA +ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:1978\:1220\ TG$12$\ \ 12\ \ \ 1\ test\_5\ GCAGTAAACAAAGGCAAAGGG\ test\_3\ CCTGGGCAGAGGTGTTCC\ TG$12$\ \ 12\ 1\ \ \ 1\ 1\ 1\ 1\ \>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:1978\:1220\ 1\:N\:0\:TCCTGA\ TCATAAGAATGAGCAGTAAACAAAGGCAAAGGGGAGATAACACACACACACAAAATAAAAAAACATCAATTTCTAATACACGCCTTTATTATAAAGAAATAAATCACTGAAAAACA\ \>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:1978\:1220\ 2\:N\:0\:TCCTGA\ TCCTCTGACTAGGCAACAACAGCTTTTTTGCTCCTGGGCAGAGGTGTTCCGAGTGTATATTTTTTATAATTACGGCGCGCATTGGAAATTGATGTTATTTTATTTTGCGTGTGTGT +ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8157\:1636\ TG$12$\ \ 12\ \ \ 1\ test\_4\ AAGTACAGTGGGGAGGCTGG\ test\_6\ TTTTCTACACAGCTCAAGTAGCCC\ TG$12$\ \ 12\ 1\ \ \ 1\ 1\ 1\ 1\ \>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8157\:1636\ 1\:N\:0\:TCCTGA\ TACTAGTCTAATAATTGCAGGCAGCTGAACTAGATAGGTCCTAAAGTACAGTGGGGAGGCTGGTGTGTGTGTGTGCATGGGATTGTCAGCCTTACCATCAGTCCTGATTTGTAGGT\ \>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8157\:1636\ 2\:N\:0\:TCCTGA\ TAAACAACCAAATGAAACCATCTTTTCTACACAGCTCAAGTAGCCCTACATACAACACAAGCCACCTACAAATCAGGACTGATGGTAAGGCTGACAATCCAATCCACCACAACAAC +ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8899\:1514\ TG$12$\ TG$12$\ \ 24\ \ \ 1\ test\_8\ TCTTTATCTAAACACATCCTGAAATACC\ test\_1\ AAACGCAATTATTTTGAGATGTCC\ TG$12$\ TG$12$\ \ 24\ 1\ \ \ 1\ 2\ 1\ 1\ \>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8899\:1514\ 1\:N\:0\:TCCTGA\ TCTTTATCTAAACACATCCTGAAATACCATCTGTTACACACACACACAGCAGTGGAAGTATAAAAAAAAATCTGGACATCTCAAAATAATTGCGTTTCTGAAGTGTTACATTTTTC\ \>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8899\:1514\ 2\:N\:0\:TCCTGA\ TATCATTGAAATTTTTATAAAAACTGTGAAGAGAAAAATGTAACACTTCAGAAACGCAATTATTTTGAGATGTCCAGATTTTTTTTTATACTTCCACTGCTGTGTGTGTGTGTAAC diff -r 84613d5f1713 -r d26fb5260c67 test-data/illuminaPE_filtered_microsats_rankmotifs.out --- a/test-data/illuminaPE_filtered_microsats_rankmotifs.out Mon Jul 24 11:04:27 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,8 +0,0 @@ -readPairID Motifs(bases) Bases in all Motifs Possible Extended Possible Spanning Primers found (1=y,0=n) F Primer Name Forward Primer R Primer Name Reverse Primer Amplicon Motifs Number motif bases in amplicon Primers on sep reads Extend with primers Spand with primers Occurances of Forward Primer in Reads Occurances of Reverse Primer in Reads Occurances of Amplifiable Primer Pair in Reads Occurances of Amplifiable Primer Pair in PALs R1_Sequence_ID R1_Sequence R2_Sequence_ID R2_Sequence -ILLUMINA-545855:49:FC61RLR:2:1:8157:1636 AC(12) 12 1 test_5 AAGTACAGTGGGGAGGCTGG test_6 TTTTCTACACAGCTCAAGTAGCCC AC(12) 12 1 1 1 1 1 >ILLUMINA-545855:49:FC61RLR:2:1:8157:1636 1:N:0:TCCTGA TACTAGTCTAATAATTGCAGGCAGCTGAACTAGATAGGTCCTAAAGTACAGTGGGGAGGCTGGTGTGTGTGTGTGCATGGGATTGTCAGCCTTACCATCAGTCCTGATTTGTAGGT >ILLUMINA-545855:49:FC61RLR:2:1:8157:1636 2:N:0:TCCTGA TAAACAACCAAATGAAACCATCTTTTCTACACAGCTCAAGTAGCCCTACATACAACACAAGCCACCTACAAATCAGGACTGATGGTAAGGCTGACAATCCAATCCACCACAACAAC -ILLUMINA-545855:49:FC61RLR:2:1:8044:1926 AT(12) 12 0 >ILLUMINA-545855:49:FC61RLR:2:1:8044:1926 1:N:0:TCCTGA TAGATTTTTTTTTTTATATATATATAAATATAGATGTACATATATTTATATAAATATAAAAGCACAGCATCCTCCTGTCTCTCCTCCTGATTTATTATGGTTAAAGCTTGTGACAG >ILLUMINA-545855:49:FC61RLR:2:1:8044:1926 2:N:0:TCCTGA TCAGGCAAGGTCACTGCCACCACTGGGGAGTGCCTGTTTCTGAAGGGCCCAGCCAACTCTGTCACAAGCTTTAACCATAATAAATCAGGAGGAGAGACAGGAGGATGCTGTGCTTT -ILLUMINA-545855:49:FC61RLR:2:1:6204:1090 TC(12) 12 0 >ILLUMINA-545855:49:FC61RLR:2:1:6204:1090 1:N:0:TCCTGA TGCTTTGGTTCTAAGAGAAAAACAATTATTATAAATGTTTATAATTGATGATAAGCATTTTTGTACAAAGCCAAGACCATTCTGAATGAAGCACCCAAAAAGCCCGGAGGCAACAA >ILLUMINA-545855:49:FC61RLR:2:1:6204:1090 2:N:0:TCCTGA TGCTTTGGTTCTAAGAGAAAAACAAGTGATGCACAAGCAATTCCTCGCCACCACCCAACTGATGCCCAGCCACCCCCCCAAGCAGTGAAAGAGAGAGAGAGATGAACCCCCTTCAA -ILLUMINA-545855:49:FC61RLR:2:1:5879:1238 AT(12) 12 0 >ILLUMINA-545855:49:FC61RLR:2:1:5879:1238 1:N:0:TCCTGA TCCCCACCCTGTCATGGTTCTATGTTTTTGTTTTTGTTTTTGTTTTTATGGTTTCCGTATTCCACATTAAAACCTTATGTAACGTACGGGCCAATAAATAGTTACTCGCCATATCC >ILLUMINA-545855:49:FC61RLR:2:1:5879:1238 2:N:0:TCCTGA TCCCCACCCTGTCATGGTTCTATGTATATATATATAGCCATGTGTGTGGTACCAGGGATAGGTACCTGGGATTGGGGCAGTGACACTTTAGTGCCCCGTACACTACATGATGTTTT -ILLUMINA-545855:49:FC61RLR:2:1:1978:1220 AC(12) 12 1 test_3 GCAGTAAACAAAGGCAAAGGG test_4 CCTGGGCAGAGGTGTTCC AC(12) 12 1 1 1 1 1 >ILLUMINA-545855:49:FC61RLR:2:1:1978:1220 1:N:0:TCCTGA TCATAAGAATGAGCAGTAAACAAAGGCAAAGGGGAGATAACACACACACACAAAATAAAAAAACATCAATTTCTAATACACGCCTTTATTATAAAGAAATAAATCACTGAAAAACA >ILLUMINA-545855:49:FC61RLR:2:1:1978:1220 2:N:0:TCCTGA TCCTCTGACTAGGCAACAACAGCTTTTTTGCTCCTGGGCAGAGGTGTTCCGAGTGTATATTTTTTATAATTACGGCGCGCATTGGAAATTGATGTTATTTTATTTTGCGTGTGTGT -ILLUMINA-545855:49:FC61RLR:2:1:17449:1584 AC(36) 36 0 >ILLUMINA-545855:49:FC61RLR:2:1:17449:1584 1:N:0:TCCTGA TCGTAGCATGTGTATGCTTTGGGGTTTCATGCTGTTGATTCATAACTGCTGCTGGCTGTAGACTGAACCTTCTGGGTAGGAGGAATATGCTTAGACAAGCACACCAGTCAGCCCGA >ILLUMINA-545855:49:FC61RLR:2:1:17449:1584 2:N:0:TCCTGA TCTGTGTGTGAGCACACACACACACACACACACACACACACACACACATGCAGGTACTTGCTCTGCCACCCCTGGCGGGCTGCGTGGTGTGCCTGACGACGTATTCTAATCCTACA -ILLUMINA-545855:49:FC61RLR:2:1:10979:1695 TC(14) 14 1 test_7 TTCTCCCACTATATTTTGCATTGG test_8 TCCAGACTGAAGCTACCCTGG TC(14) 14 1 1 1 1 1 >ILLUMINA-545855:49:FC61RLR:2:1:10979:1695 1:N:0:TCCTGA TACTGTTTAGAATAGACTGTTCTCCCACTATATTTTGCATTGGTGCATACTCAGCTTTAGTAATAAGTGTGATTCTGGTAGAGAGAGAGAGAGATACCAACCTCTTCTTCCCACTA >ILLUMINA-545855:49:FC61RLR:2:1:10979:1695 2:N:0:TCCTGA TACTGTTTAGAAAGCCTGTTCCAGAACTTGATCACTGTCACAGAAAATCTTTCTTACTATCCAGACTGAAGCTACCCTGGTGCAGCTTTGTGCTGTTACCTTGAGTCATGTCATCA diff -r 84613d5f1713 -r d26fb5260c67 test-data/illuminaPE_filtered_microsats_rankmotifs.out.re_match --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/illuminaPE_filtered_microsats_rankmotifs.out.re_match Thu Mar 15 09:49:05 2018 -0400 @@ -0,0 +1,8 @@ +readPairID\ Motifs$bases$\ Bases\ in\ all\ Motifs\ Possible\ Extended\ Possible\ Spanning\ Primers\ found\ $1\=y\,0\=n$\ F\ Primer\ Name\ Forward\ Primer\ R\ Primer\ Name\ Reverse\ Primer\ Amplicon\ Motifs\ Number\ motif\ bases\ in\ amplicon\ Primers\ on\ sep\ reads\ Extend\ with\ primers\ Spand\ with\ primers\ Occurances\ of\ Forward\ Primer\ in\ Reads\ Occurances\ of\ Reverse\ Primer\ in\ Reads\ Occurances\ of\ Amplifiable\ Primer\ Pair\ in\ Reads\ Occurances\ of\ Amplifiable\ Primer\ Pair\ in\ PALs\ R1\_Sequence\_ID\ R1\_Sequence\ R2\_Sequence\_ID\ R2\_Sequence +ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8157\:1636\ (AC|TG)$12$\ \ 12\ \ \ 1\ test\_.*\ AAGTACAGTGGGGAGGCTGG\ test\_.*\ TTTTCTACACAGCTCAAGTAGCCC\ (AC|TG)$12$\ \ 12\ 1\ \ \ 1\ 1\ 1\ 1\ \>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8157\:1636\ 1\:N\:0\:TCCTGA\ TACTAGTCTAATAATTGCAGGCAGCTGAACTAGATAGGTCCTAAAGTACAGTGGGGAGGCTGGTGTGTGTGTGTGCATGGGATTGTCAGCCTTACCATCAGTCCTGATTTGTAGGT\ \>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8157\:1636\ 2\:N\:0\:TCCTGA\ TAAACAACCAAATGAAACCATCTTTTCTACACAGCTCAAGTAGCCCTACATACAACACAAGCCACCTACAAATCAGGACTGATGGTAAGGCTGACAATCCAATCCACCACAACAAC +ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8044\:1926\ AT$12$\ \ 12\ \ \ 0\ \ \ \ \ \ \ \ \ \ \ \ \ \ \>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8044\:1926\ 1\:N\:0\:TCCTGA\ TAGATTTTTTTTTTTATATATATATAAATATAGATGTACATATATTTATATAAATATAAAAGCACAGCATCCTCCTGTCTCTCCTCCTGATTTATTATGGTTAAAGCTTGTGACAG\ \>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8044\:1926\ 2\:N\:0\:TCCTGA\ TCAGGCAAGGTCACTGCCACCACTGGGGAGTGCCTGTTTCTGAAGGGCCCAGCCAACTCTGTCACAAGCTTTAACCATAATAAATCAGGAGGAGAGACAGGAGGATGCTGTGCTTT +ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:6204\:1090\ (AG|TC)$12$\ \ 12\ \ \ 0\ \ \ \ \ \ \ \ \ \ \ \ \ \ \>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:6204\:1090\ 1\:N\:0\:TCCTGA\ TGCTTTGGTTCTAAGAGAAAAACAATTATTATAAATGTTTATAATTGATGATAAGCATTTTTGTACAAAGCCAAGACCATTCTGAATGAAGCACCCAAAAAGCCCGGAGGCAACAA\ \>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:6204\:1090\ 2\:N\:0\:TCCTGA\ TGCTTTGGTTCTAAGAGAAAAACAAGTGATGCACAAGCAATTCCTCGCCACCACCCAACTGATGCCCAGCCACCCCCCCAAGCAGTGAAAGAGAGAGAGAGATGAACCCCCTTCAA +ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:5879\:1238\ AT$12$\ \ 12\ \ \ 0\ \ \ \ \ \ \ \ \ \ \ \ \ \ \>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:5879\:1238\ 1\:N\:0\:TCCTGA\ TCCCCACCCTGTCATGGTTCTATGTTTTTGTTTTTGTTTTTGTTTTTATGGTTTCCGTATTCCACATTAAAACCTTATGTAACGTACGGGCCAATAAATAGTTACTCGCCATATCC\ \>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:5879\:1238\ 2\:N\:0\:TCCTGA\ TCCCCACCCTGTCATGGTTCTATGTATATATATATAGCCATGTGTGTGGTACCAGGGATAGGTACCTGGGATTGGGGCAGTGACACTTTAGTGCCCCGTACACTACATGATGTTTT +ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:1978\:1220\ (AC|TG)$12$\ \ 12\ \ \ 1\ test\_.*\ GCAGTAAACAAAGGCAAAGGG\ test\_.*\ CCTGGGCAGAGGTGTTCC\ (AC|TG)$12$\ \ 12\ 1\ \ \ 1\ 1\ 1\ 1\ \>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:1978\:1220\ 1\:N\:0\:TCCTGA\ TCATAAGAATGAGCAGTAAACAAAGGCAAAGGGGAGATAACACACACACACAAAATAAAAAAACATCAATTTCTAATACACGCCTTTATTATAAAGAAATAAATCACTGAAAAACA\ \>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:1978\:1220\ 2\:N\:0\:TCCTGA\ TCCTCTGACTAGGCAACAACAGCTTTTTTGCTCCTGGGCAGAGGTGTTCCGAGTGTATATTTTTTATAATTACGGCGCGCATTGGAAATTGATGTTATTTTATTTTGCGTGTGTGT +ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:17449\:1584\ (AC|TG)$36$\ \ 36\ \ \ 0\ \ \ \ \ \ \ \ \ \ \ \ \ \ \>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:17449\:1584\ 1\:N\:0\:TCCTGA\ TCGTAGCATGTGTATGCTTTGGGGTTTCATGCTGTTGATTCATAACTGCTGCTGGCTGTAGACTGAACCTTCTGGGTAGGAGGAATATGCTTAGACAAGCACACCAGTCAGCCCGA\ \>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:17449\:1584\ 2\:N\:0\:TCCTGA\ TCTGTGTGTGAGCACACACACACACACACACACACACACACACACACATGCAGGTACTTGCTCTGCCACCCCTGGCGGGCTGCGTGGTGTGCCTGACGACGTATTCTAATCCTACA +ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:10979\:1695\ (AG|TC)$14$\ \ 14\ \ \ 1\ test\_.*\ TTCTCCCACTATATTTTGCATTGG\ test\_.*\ TCCAGACTGAAGCTACCCTGG\ (AG|TC)$14$\ \ 14\ 1\ \ \ 1\ 1\ 1\ 1\ \>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:10979\:1695\ 1\:N\:0\:TCCTGA\ TACTGTTTAGAATAGACTGTTCTCCCACTATATTTTGCATTGGTGCATACTCAGCTTTAGTAATAAGTGTGATTCTGGTAGAGAGAGAGAGAGATACCAACCTCTTCTTCCCACTA\ \>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:10979\:1695\ 2\:N\:0\:TCCTGA\ TACTGTTTAGAAAGCCTGTTCCAGAACTTGATCACTGTCACAGAAAATCTTTCTTACTATCCAGACTGAAGCTACCCTGGTGCAGCTTTGTGCTGTTACCTTGAGTCATGTCATCA diff -r 84613d5f1713 -r d26fb5260c67 test-data/illuminaPE_filtered_microsats_rankmotifs.out.re_match~ --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/illuminaPE_filtered_microsats_rankmotifs.out.re_match~ Thu Mar 15 09:49:05 2018 -0400 @@ -0,0 +1,8 @@ +readPairID\ Motifs$bases$\ Bases\ in\ all\ Motifs\ Possible\ Extended\ Possible\ Spanning\ Primers\ found\ $1\=y\,0\=n$\ F\ Primer\ Name\ Forward\ Primer\ R\ Primer\ Name\ Reverse\ Primer\ Amplicon\ Motifs\ Number\ motif\ bases\ in\ amplicon\ Primers\ on\ sep\ reads\ Extend\ with\ primers\ Spand\ with\ primers\ Occurances\ of\ Forward\ Primer\ in\ Reads\ Occurances\ of\ Reverse\ Primer\ in\ Reads\ Occurances\ of\ Amplifiable\ Primer\ Pair\ in\ Reads\ Occurances\ of\ Amplifiable\ Primer\ Pair\ in\ PALs\ R1\_Sequence\_ID\ R1\_Sequence\ R2\_Sequence\_ID\ R2\_Sequence +ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8157\:1636\ AC$12$\ \ 12\ \ \ 1\ test\_3\ AAGTACAGTGGGGAGGCTGG\ test\_4\ TTTTCTACACAGCTCAAGTAGCCC\ AC$12$\ \ 12\ 1\ \ \ 1\ 1\ 1\ 1\ \>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8157\:1636\ 1\:N\:0\:TCCTGA\ TACTAGTCTAATAATTGCAGGCAGCTGAACTAGATAGGTCCTAAAGTACAGTGGGGAGGCTGGTGTGTGTGTGTGCATGGGATTGTCAGCCTTACCATCAGTCCTGATTTGTAGGT\ \>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8157\:1636\ 2\:N\:0\:TCCTGA\ TAAACAACCAAATGAAACCATCTTTTCTACACAGCTCAAGTAGCCCTACATACAACACAAGCCACCTACAAATCAGGACTGATGGTAAGGCTGACAATCCAATCCACCACAACAAC +ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8044\:1926\ AT$12$\ \ 12\ \ \ 0\ \ \ \ \ \ \ \ \ \ \ \ \ \ \>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8044\:1926\ 1\:N\:0\:TCCTGA\ TAGATTTTTTTTTTTATATATATATAAATATAGATGTACATATATTTATATAAATATAAAAGCACAGCATCCTCCTGTCTCTCCTCCTGATTTATTATGGTTAAAGCTTGTGACAG\ \>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8044\:1926\ 2\:N\:0\:TCCTGA\ TCAGGCAAGGTCACTGCCACCACTGGGGAGTGCCTGTTTCTGAAGGGCCCAGCCAACTCTGTCACAAGCTTTAACCATAATAAATCAGGAGGAGAGACAGGAGGATGCTGTGCTTT +ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:6204\:1090\ TC$12$\ \ 12\ \ \ 0\ \ \ \ \ \ \ \ \ \ \ \ \ \ \>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:6204\:1090\ 1\:N\:0\:TCCTGA\ TGCTTTGGTTCTAAGAGAAAAACAATTATTATAAATGTTTATAATTGATGATAAGCATTTTTGTACAAAGCCAAGACCATTCTGAATGAAGCACCCAAAAAGCCCGGAGGCAACAA\ \>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:6204\:1090\ 2\:N\:0\:TCCTGA\ TGCTTTGGTTCTAAGAGAAAAACAAGTGATGCACAAGCAATTCCTCGCCACCACCCAACTGATGCCCAGCCACCCCCCCAAGCAGTGAAAGAGAGAGAGAGATGAACCCCCTTCAA +ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:5879\:1238\ AT$12$\ \ 12\ \ \ 0\ \ \ \ \ \ \ \ \ \ \ \ \ \ \>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:5879\:1238\ 1\:N\:0\:TCCTGA\ TCCCCACCCTGTCATGGTTCTATGTTTTTGTTTTTGTTTTTGTTTTTATGGTTTCCGTATTCCACATTAAAACCTTATGTAACGTACGGGCCAATAAATAGTTACTCGCCATATCC\ \>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:5879\:1238\ 2\:N\:0\:TCCTGA\ TCCCCACCCTGTCATGGTTCTATGTATATATATATAGCCATGTGTGTGGTACCAGGGATAGGTACCTGGGATTGGGGCAGTGACACTTTAGTGCCCCGTACACTACATGATGTTTT +ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:1978\:1220\ AC$12$\ \ 12\ \ \ 1\ test\_6\ GCAGTAAACAAAGGCAAAGGG\ test\_1\ CCTGGGCAGAGGTGTTCC\ AC$12$\ \ 12\ 1\ \ \ 1\ 1\ 1\ 1\ \>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:1978\:1220\ 1\:N\:0\:TCCTGA\ TCATAAGAATGAGCAGTAAACAAAGGCAAAGGGGAGATAACACACACACACAAAATAAAAAAACATCAATTTCTAATACACGCCTTTATTATAAAGAAATAAATCACTGAAAAACA\ \>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:1978\:1220\ 2\:N\:0\:TCCTGA\ TCCTCTGACTAGGCAACAACAGCTTTTTTGCTCCTGGGCAGAGGTGTTCCGAGTGTATATTTTTTATAATTACGGCGCGCATTGGAAATTGATGTTATTTTATTTTGCGTGTGTGT +ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:17449\:1584\ AC$36$\ \ 36\ \ \ 0\ \ \ \ \ \ \ \ \ \ \ \ \ \ \>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:17449\:1584\ 1\:N\:0\:TCCTGA\ TCGTAGCATGTGTATGCTTTGGGGTTTCATGCTGTTGATTCATAACTGCTGCTGGCTGTAGACTGAACCTTCTGGGTAGGAGGAATATGCTTAGACAAGCACACCAGTCAGCCCGA\ \>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:17449\:1584\ 2\:N\:0\:TCCTGA\ TCTGTGTGTGAGCACACACACACACACACACACACACACACACACACATGCAGGTACTTGCTCTGCCACCCCTGGCGGGCTGCGTGGTGTGCCTGACGACGTATTCTAATCCTACA +ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:10979\:1695\ TC$14$\ \ 14\ \ \ 1\ test\_7\ TTCTCCCACTATATTTTGCATTGG\ test\_2\ TCCAGACTGAAGCTACCCTGG\ TC$14$\ \ 14\ 1\ \ \ 1\ 1\ 1\ 1\ \>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:10979\:1695\ 1\:N\:0\:TCCTGA\ TACTGTTTAGAATAGACTGTTCTCCCACTATATTTTGCATTGGTGCATACTCAGCTTTAGTAATAAGTGTGATTCTGGTAGAGAGAGAGAGAGATACCAACCTCTTCTTCCCACTA\ \>ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:10979\:1695\ 2\:N\:0\:TCCTGA\ TACTGTTTAGAAAGCCTGTTCCAGAACTTGATCACTGTCACAGAAAATCTTTCTTACTATCCAGACTGAAGCTACCCTGGTGCAGCTTTGTGCTGTTACCTTGAGTCATGTCATCA diff -r 84613d5f1713 -r d26fb5260c67 test-data/illuminaPE_microsat_types.out --- a/test-data/illuminaPE_microsat_types.out Mon Jul 24 11:04:27 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,14 +0,0 @@ -totalBases: 2320 -allSpan: 0 -totalReads: 20 (2 x 10) -compound: 2 -broken: 2 -allExtended: 0 -readsWithMicrosat: 13 - - -Microsat Type monomer length total loci loci w/ primers reads with loci total bases extended extended w/ primers spanning spanning w/ primers -TC 2 2 1 2 26 0 0 0 0 -AC 2 7 4 7 116 0 0 0 0 -CG 2 0 0 0 0 0 0 0 0 -AT 2 8 0 6 106 0 0 0 0 diff -r 84613d5f1713 -r d26fb5260c67 test-data/illuminaPE_microsat_types.out.re_match --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/illuminaPE_microsat_types.out.re_match Thu Mar 15 09:49:05 2018 -0400 @@ -0,0 +1,16 @@ +allExtended\:\ 0 +allSpan\:\ 0 +broken\:\ 2 +compound\:\ 2 +readsWithMicrosat\:\ 13 +totalBases\:\ 2320 +totalReads\:\ 20\ $2\ x\ 10$ + + +Microsat\ Type\ monomer\ length\ total\ loci\ loci\ w\/\ primers\ reads\ with\ loci\ total\ bases\ extended\ extended\ w\/\ primers\ spanning\ spanning\ w\/\ primers +(AC\ 2\ 7\ 4\ 7\ 116\ 0\ 0\ 0\ 0)? +(AG\ 2\ 0\ 0\ 0\ 0\ 0\ 0\ 0\ 0)? +(AT\ 2\ 8\ 0\ 6\ 106\ 0\ 0\ 0\ 0)? +CG\ 2\ 0\ 0\ 0\ 0\ 0\ 0\ 0\ 0 +TC\ 2\ 2\ 1\ 2\ 26\ \ \ \ +(TG\ 2\ 7\ 4\ 7\ 116\ \ \ \ )? \ No newline at end of file diff -r 84613d5f1713 -r d26fb5260c67 test-data/illuminaPE_microsat_types.out.re_match~ --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/illuminaPE_microsat_types.out.re_match~ Thu Mar 15 09:49:05 2018 -0400 @@ -0,0 +1,15 @@ +allExtended\:\ 0 +allSpan\:\ 0 +broken\:\ 2 +compound\:\ 2 +readsWithMicrosat\:\ 13 +totalBases\:\ 2320 +totalReads\:\ 20\ $2\ x\ 10$ + + +Microsat\ Type\ monomer\ length\ total\ loci\ loci\ w\/\ primers\ reads\ with\ loci\ total\ bases\ extended\ extended\ w\/\ primers\ spanning\ spanning\ w\/\ primers +AC\ 2\ 7\ 4\ 7\ 116\ 0\ 0\ 0\ 0 +AG\ 2\ 0\ 0\ 0\ 0\ 0\ 0\ 0\ 0 +AT\ 2\ 8\ 0\ 6\ 106\ 0\ 0\ 0\ 0 +CG\ 2\ 0\ 0\ 0\ 0\ 0\ 0\ 0\ 0 +TC\ 2\ 2\ 1\ 2\ 26\ \ \ \ diff -r 84613d5f1713 -r d26fb5260c67 test-data/illuminaPE_microsats.out --- a/test-data/illuminaPE_microsats.out Mon Jul 24 11:04:27 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,11 +0,0 @@ -readPairID Motifs(bases) Bases in all Motifs Possible Extended Possible Spanning Primers found (1=y,0=n) F Primer Name Forward Primer R Primer Name Reverse Primer Amplicon Motifs Number motif bases in amplicon Primers on sep reads Extend with primers Spand with primers Occurances of Forward Primer in Reads Occurances of Reverse Primer in Reads Occurances of Amplifiable Primer Pair in Reads Occurances of Amplifiable Primer Pair in PALs -ILLUMINA-545855:49:FC61RLR:2:1:10979:1695 TC(14) 14 1 test_7 TTCTCCCACTATATTTTGCATTGG test_8 TCCAGACTGAAGCTACCCTGG TC(14) 14 1 1 1 1 1 -ILLUMINA-545855:49:FC61RLR:2:1:17449:1584 AC(36) 36 0 -ILLUMINA-545855:49:FC61RLR:2:1:19063:1614 AT(14) AT(14) AT(14) AT(14) 56 0 -ILLUMINA-545855:49:FC61RLR:2:1:1978:1220 AC(12) 12 1 test_3 GCAGTAAACAAAGGCAAAGGG test_4 CCTGGGCAGAGGTGTTCC AC(12) 12 1 1 1 1 1 -ILLUMINA-545855:49:FC61RLR:2:1:5626:1554 AT(14) AC(16) AC(16) AT(12) 58 0 -ILLUMINA-545855:49:FC61RLR:2:1:5879:1238 AT(12) 12 0 -ILLUMINA-545855:49:FC61RLR:2:1:6204:1090 TC(12) 12 0 -ILLUMINA-545855:49:FC61RLR:2:1:8044:1926 AT(12) 12 0 -ILLUMINA-545855:49:FC61RLR:2:1:8157:1636 AC(12) 12 1 test_5 AAGTACAGTGGGGAGGCTGG test_6 TTTTCTACACAGCTCAAGTAGCCC AC(12) 12 1 1 1 1 1 -ILLUMINA-545855:49:FC61RLR:2:1:8899:1514 AC(12) AC(12) 24 1 test_2 TCTTTATCTAAACACATCCTGAAATACC test_1 AAACGCAATTATTTTGAGATGTCC AC(12) AC(12) 24 1 1 2 1 1 diff -r 84613d5f1713 -r d26fb5260c67 test-data/illuminaPE_microsats.out.re_match --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/illuminaPE_microsats.out.re_match Thu Mar 15 09:49:05 2018 -0400 @@ -0,0 +1,11 @@ +readPairID\ Motifs$bases$\ Bases\ in\ all\ Motifs\ Possible\ Extended\ Possible\ Spanning\ Primers\ found\ $1\=y\,0\=n$\ F\ Primer\ Name\ Forward\ Primer\ R\ Primer\ Name\ Reverse\ Primer\ Amplicon\ Motifs\ Number\ motif\ bases\ in\ amplicon\ Primers\ on\ sep\ reads\ Extend\ with\ primers\ Spand\ with\ primers\ Occurances\ of\ Forward\ Primer\ in\ Reads\ Occurances\ of\ Reverse\ Primer\ in\ Reads\ Occurances\ of\ Amplifiable\ Primer\ Pair\ in\ Reads\ Occurances\ of\ Amplifiable\ Primer\ Pair\ in\ PALs +ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:10979\:1695\ (AG|TC)$14$\ \ 14\ \ \ 1\ test\_.*\ TTCTCCCACTATATTTTGCATTGG\ test\_.*\ TCCAGACTGAAGCTACCCTGG\ (AG|TC)$14$\ \ 14\ 1\ \ \ 1\ 1\ 1\ 1 +ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:17449\:1584\ (AC|TG)$36$\ \ 36\ \ \ 0\ \ \ \ \ \ \ \ \ \ \ \ \ +ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:19063\:1614\ AT$14$\ AT$14$\ AT$14$\ AT$14$\ \ 56\ \ \ 0\ \ \ \ \ \ \ \ \ \ \ \ \ +ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:1978\:1220\ (AC|TG)$12$\ \ 12\ \ \ 1\ test\_.*\ GCAGTAAACAAAGGCAAAGGG\ test\_.*\ CCTGGGCAGAGGTGTTCC\ (AC|TG)$12$\ \ 12\ 1\ \ \ 1\ 1\ 1\ 1 +ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:5626\:1554\ AT$14$\ (AC|TG)$16$\ (AC|TG)$16$\ AT$12$\ \ 58\ \ \ 0\ \ \ \ \ \ \ \ \ \ \ \ \ +ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:5879\:1238\ AT$12$\ \ 12\ \ \ 0\ \ \ \ \ \ \ \ \ \ \ \ \ +ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:6204\:1090\ (AG|TC)$12$\ \ 12\ \ \ 0\ \ \ \ \ \ \ \ \ \ \ \ \ +ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8044\:1926\ AT$12$\ \ 12\ \ \ 0\ \ \ \ \ \ \ \ \ \ \ \ \ +ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8157\:1636\ (AC|TG)$12$\ \ 12\ \ \ 1\ test\_.*\ AAGTACAGTGGGGAGGCTGG\ test\_.*\ TTTTCTACACAGCTCAAGTAGCCC\ (AC|TG)$12$\ \ 12\ 1\ \ \ 1\ 1\ 1\ 1 +ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8899\:1514\ (AC|TG)$12$\ (AC|TG)$12$\ \ 24\ \ \ 1\ test\_.*\ TCTTTATCTAAACACATCCTGAAATACC\ test\_.*\ AAACGCAATTATTTTGAGATGTCC\ (AC|TG)$12$\ (AC|TG)$12$\ \ 24\ 1\ \ \ 1\ 2\ 1\ 1 diff -r 84613d5f1713 -r d26fb5260c67 test-data/illuminaPE_microsats.out.re_match~ --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/illuminaPE_microsats.out.re_match~ Thu Mar 15 09:49:05 2018 -0400 @@ -0,0 +1,11 @@ +readPairID\ Motifs$bases$\ Bases\ in\ all\ Motifs\ Possible\ Extended\ Possible\ Spanning\ Primers\ found\ $1\=y\,0\=n$\ F\ Primer\ Name\ Forward\ Primer\ R\ Primer\ Name\ Reverse\ Primer\ Amplicon\ Motifs\ Number\ motif\ bases\ in\ amplicon\ Primers\ on\ sep\ reads\ Extend\ with\ primers\ Spand\ with\ primers\ Occurances\ of\ Forward\ Primer\ in\ Reads\ Occurances\ of\ Reverse\ Primer\ in\ Reads\ Occurances\ of\ Amplifiable\ Primer\ Pair\ in\ Reads\ Occurances\ of\ Amplifiable\ Primer\ Pair\ in\ PALs +ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:10979\:1695\ TC$14$\ \ 14\ \ \ 1\ test\_7\ TTCTCCCACTATATTTTGCATTGG\ test\_2\ TCCAGACTGAAGCTACCCTGG\ TC$14$\ \ 14\ 1\ \ \ 1\ 1\ 1\ 1 +ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:17449\:1584\ AC$36$\ \ 36\ \ \ 0\ \ \ \ \ \ \ \ \ \ \ \ \ +ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:19063\:1614\ AT$14$\ AT$14$\ AT$14$\ AT$14$\ \ 56\ \ \ 0\ \ \ \ \ \ \ \ \ \ \ \ \ +ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:1978\:1220\ AC$12$\ \ 12\ \ \ 1\ test\_6\ GCAGTAAACAAAGGCAAAGGG\ test\_1\ CCTGGGCAGAGGTGTTCC\ AC$12$\ \ 12\ 1\ \ \ 1\ 1\ 1\ 1 +ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:5626\:1554\ AT$14$\ AC$16$\ AC$16$\ AT$12$\ \ 58\ \ \ 0\ \ \ \ \ \ \ \ \ \ \ \ \ +ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:5879\:1238\ AT$12$\ \ 12\ \ \ 0\ \ \ \ \ \ \ \ \ \ \ \ \ +ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:6204\:1090\ TC$12$\ \ 12\ \ \ 0\ \ \ \ \ \ \ \ \ \ \ \ \ +ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8044\:1926\ AT$12$\ \ 12\ \ \ 0\ \ \ \ \ \ \ \ \ \ \ \ \ +ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8157\:1636\ AC$12$\ \ 12\ \ \ 1\ test\_3\ AAGTACAGTGGGGAGGCTGG\ test\_4\ TTTTCTACACAGCTCAAGTAGCCC\ AC$12$\ \ 12\ 1\ \ \ 1\ 1\ 1\ 1 +ILLUMINA\-545855\:49\:FC61RLR\:2\:1\:8899\:1514\ AC$12$\ AC$12$\ \ 24\ \ \ 1\ test\_8\ TCTTTATCTAAACACATCCTGAAATACC\ test\_5\ AAACGCAATTATTTTGAGATGTCC\ AC$12$\ AC$12$\ \ 24\ 1\ \ \ 1\ 2\ 1\ 1 diff -r 84613d5f1713 -r d26fb5260c67 tool_dependencies.xml --- a/tool_dependencies.xml Mon Jul 24 11:04:27 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,102 +0,0 @@ - - - - - - http://sourceforge.net/projects/palfinder/files/pal_finder_v0.02.04.tar.gz - - pal_finder_v0.02.04.pl - $INSTALL_DIR/bin - - - config.txt - $INSTALL_DIR/data - - - simple.ref - $INSTALL_DIR/data - - - $INSTALL_DIR/bin - - - $INSTALL_DIR/bin - - - $INSTALL_DIR/data - - - - pal_finder also needs Perl - - - - - - http://www.cpan.org/src/5.0/perl-5.16.3.tar.gz - ./Configure -des -Dprefix=$INSTALL_DIR -Dstartperl='#!/usr/bin/env perl' - - - $INSTALL_DIR/bin - - - - - Perl 5 is a highly capable, feature-rich programming language with over 25 years of - development: - - http://www.perl.org/ - - - - - - https://sourceforge.net/projects/primer3/files/primer3/2.0.0-alpha/primer3-2.0.0-alpha.tar.gz - make -C src -f Makefile - - src/primer3_core - $INSTALL_DIR/bin - - - $INSTALL_DIR/bin - - - - primer3_core - - - - - pip install --install-option "--prefix=$INSTALL_DIR" https://pypi.python.org/packages/source/b/biopython/biopython-1.65.tar.gz - - $INSTALL_DIR/lib/python2.7/site-packages - $INSTALL_DIR/lib64/python2.7/site-packages - - - - BioPython 1.65 - - - - - https://github.com/neufeld/pandaseq/archive/v2.8.1.tar.gz - ./autogen.sh - ./configure --prefix=$INSTALL_DIR - make - make install - - $INSTALL_DIR/bin - $INSTALL_DIR/lib - - - - PANDASeq 2.8.1 - - PANDASEQ is a program to align Illumina reads, optionally - with PCR primers embedded in the sequence, and reconstruct - an overlapping sequence. - - https://github.com/neufeld/pandaseq - - -