diff --git a/.travis.yml b/.travis.yml new file mode 100644 index 0000000..e422c3f --- /dev/null +++ b/.travis.yml @@ -0,0 +1,14 @@ +os: + - linux + - osx + +sudo: false + +language: perl + +# normally cpanm is called for perl, but we do not need it so skip the installation of dependencies +install: true + +script: + - cd t + - prove ./test.sh diff --git a/bin/SeqChunker b/bin/SeqChunker index c936424..af51977 100755 --- a/bin/SeqChunker +++ b/bin/SeqChunker @@ -7,9 +7,42 @@ # # Last Modified: Thomas Hackl, 2014-09-10 -# Version 0.3 -# reliable detect binary folder -Bin="$(dirname "$(readlink -f "$0")")" +# Version 0.4 +# reliable detect binary folder with compability to MacOSX +function expand_link { + FILE="$1" + + TRACKING_FILE=$(mktemp) + + echo "$FILE" >"$TRACKING_FILE" + + NEW_FILE=$(readlink "$FILE"); + + while [ "$?" -eq 0 ] + do + echo "$NEW_FILE" >>"$TRACKING_FILE" + + # check for duplicates + NUM_DUPLICATES=$(cat "$TRACKING_FILE" | sort | uniq -d | wc -l) + + if [ "$NUM_DUPLICATES" -gt 0 ] + then + break + fi + + FILE=$(dirname "$FILE")/"$NEW_FILE" + echo "$FILE" >&2 + NEW_FILE=$(readlink "$FILE") + done + + rm "$TRACKING_FILE" + + echo "FILE should be located at '$FILE'" >&2 + + echo "$FILE" +} + +Bin="$(dirname "$(expand_link "$0")")" # check if perl exists, than use the perl version if [ ! -z $(which perl) ]; then diff --git a/t/reference.md5 b/t/reference.md5 new file mode 100644 index 0000000..70d8662 --- /dev/null +++ b/t/reference.md5 @@ -0,0 +1,4504 @@ +05d16795ddb596ccef09589bccbdde4d ec.fa +55eb992e90d3c659d6b3095412464f99 ec.fq + +05d16795ddb596ccef09589bccbdde4d ./tmp.1.01 +05d16795ddb596ccef09589bccbdde4d ./tmp.15.01 +05d16795ddb596ccef09589bccbdde4d ./tmp.29.01 +05d16795ddb596ccef09589bccbdde4d ./tmp.43.01 + +5b626a6e5a2fded44ce55c1f8a740e07 ./tmp.2.01 +5b626a6e5a2fded44ce55c1f8a740e07 ./tmp.16.01 +5b626a6e5a2fded44ce55c1f8a740e07 ./tmp.30.01 +5b626a6e5a2fded44ce55c1f8a740e07 ./tmp.44.01 +47b487c1d645e7baf0d4955c8699d666 ./tmp.2.02 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./tmp.41.19 +287d0f553aec285754bdb68d3b197642 ./tmp.55.19 +791425936228150be6430453fe9a7d10 ./tmp.13.20 +791425936228150be6430453fe9a7d10 ./tmp.27.20 +791425936228150be6430453fe9a7d10 ./tmp.41.20 +791425936228150be6430453fe9a7d10 ./tmp.55.20 + +287d0f553aec285754bdb68d3b197642 ./tmp.14.19 +287d0f553aec285754bdb68d3b197642 ./tmp.28.19 +287d0f553aec285754bdb68d3b197642 ./tmp.42.19 +287d0f553aec285754bdb68d3b197642 ./tmp.56.19 diff --git a/t/test.sh b/t/test.sh index 682df58..59dbf88 100755 --- a/t/test.sh +++ b/t/test.sh @@ -2,330 +2,257 @@ DIR=$(dirname $0); cd $DIR; -EC="$DIR/ec.fa" SC="$DIR/../bin/SeqChunker" TC=0; rm -f tmp*; +TEMPFILENAME="$DIR/tmp" +# delete all existing tmp files +rm -f "$TEMPFILENAME"*; + +TESTCOUNTER=1; + +TOTAL_NUMBER_OF_TESTS=56 + +echo "$TESTCOUNTER..$TOTAL_NUMBER_OF_TESTS" + +##----------------------------------------------------------------------------## +# +# Define a SeqChunker test script +# ##----------------------------------------------------------------------------## -# FASTA -#1 -DESC="split pipe" -echo "Test #"$((++TC))" $DESC"; -TF="$DIR/tmp" -cmd="$SC -n 10 $EC" -echo "$cmd"; -$cmd > $TF - -DIFF=$(diff $EC $TF) -if [ ! -z "$DIFF" ]; then - echo "..failed" - echo "unexpected difference found:" 1>&2; - echo "$DIFF" 1>&2; - exit 1; -fi; -echo "..ok" - - -#2 split in chunks -DESC="split file" -echo "Test #"$((++TC))" $DESC"; -TF="$DIR/tmp" -cmd="$SC -n 20 $EC -o tmp.$TC.%02d" -echo "$cmd"; -$cmd; -cat tmp.$TC.* > $TF; - -DIFF=$(diff $EC $TF) -if [ ! -z "$DIFF" ]; then - echo "..failed" - echo "unexpected difference found:" 1>&2; - #echo "$DIFF" 1>&2; - exit 1; -fi; -echo "..ok" - - -#3 split steps -DESC="split steps" -echo "Test #"$((++TC))" $DESC"; -TF="$DIR/tmp" -cmd="$SC -n 20 -x 5 $EC -o tmp.$TC.%02d" -echo "$cmd"; -$cmd; - -DIFF=$( diff tmp.$TC.01 tmp.$(($TC-1)).01 ) -if [ ! -z "$DIFF" ]; then - echo "..failed" - echo "unexpected difference found:" 1>&2; - # echo "$DIFF" 1>&2; - exit 1; -fi; -DIFF=$( diff tmp.$TC.06 tmp.$(($TC-1)).06 ) -if [ ! -z "$DIFF" ]; then - echo "..failed" - echo "unexpected difference found:" 1>&2; - # echo "$DIFF" 1>&2; - exit 1; -fi; -DIFF=$( diff tmp.$TC.16 tmp.$(($TC-1)).16 ) -if [ ! -z "$DIFF" ]; then - echo "..failed" - echo "unexpected difference found:" 1>&2; - # echo "$DIFF" 1>&2; - exit 1; -fi; -echo "..ok" - - -#4 split first last step -DESC="split first last step" -echo "Test #"$((++TC))" $DESC"; -TF="$DIR/tmp" -cmd="$SC -n 20 -x 5 -y 2 -f 2 -l 12 $EC -o tmp.$TC.%02d" -echo "$cmd"; -$cmd; -DIFF=$( diff tmp.$TC.02 tmp.$(($TC-2)).02 ) -if [ ! -z "$DIFF" ]; then - echo "..failed" - echo "unexpected difference found:" 1>&2; - echo "$DIFF" 1>&2; - exit 1; -fi; -DIFF=$( diff tmp.$TC.03 tmp.$(($TC-2)).03) -if [ ! -z "$DIFF" ]; then - echo "..failed" - echo "unexpected difference found:" 1>&2; - echo "$DIFF" 1>&2; - exit 1; -fi; - -DIFF=$( diff tmp.$TC.07 tmp.$(($TC-2)).07 ) -if [ ! -z "$DIFF" ]; then - echo "..failed" - echo "unexpected difference found:" 1>&2; - echo "$DIFF" 1>&2; - exit 1; -fi; -DIFF=$( diff tmp.$TC.12 tmp.$(($TC-2)).12 ) -if [ ! -z "$DIFF" ]; then - echo "..failed" - echo "unexpected difference found:" 1>&2; - echo "$DIFF" 1>&2; - exit 1; -fi; -if [ -e "tmp.$TC.13" ]; then - echo "..failed" - echo "last not respected" 1>&2; - echo "$DIFF" 1>&2; - exit 1; -fi; -echo "..ok" - - - - -#5 split in many chunks -DESC="split file many chunks" -echo "Test #"$((++TC))" $DESC"; -TF="$DIR/tmp" -cmd="$SC -n 1000 $EC -o tmp.$TC.%04d" -echo "$cmd"; -$cmd; -cat tmp.$TC.* > $TF; - -DIFF=$(diff $EC $TF) -if [ ! -z "$DIFF" ]; then - echo "..failed" - echo "unexpected difference found:" 1>&2; - #echo "$DIFF" 1>&2; - exit 1; -fi; -echo "..ok" - - -#6 split late first -DESC="split late first" -echo "Test #"$((++TC))" $DESC"; -TF="$DIR/tmp" -cmd="$SC -n 1000 -f 1000 -l 1000 $EC -o tmp.$TC.%04d" -echo "$cmd"; -$cmd; - -DIFF=$( diff tmp.$TC.1000 tmp.$(($TC-1)).1000 2>&1) -if [ ! -z "$DIFF" ]; then - echo "..failed" - echo "unexpected difference found:" 1>&2; - echo "$DIFF" 1>&2; - exit 1; -fi; -echo "..ok" +function test_SeqChunker { + local DESC="$1" + local cmd="$2" + + # assume empty special flag + local SPECIAL_FLAG="" + local TAP_DIRECTIVE="" + local STATUS="ok" + # assume the third parameter set special switches + if [ $# -ge 3 ] + then + SPECIAL_FLAG="$3" + fi + # assume the fourth parameter set TODO/SKIP + if [ $# -ge 4 ] + then + TAP_DIRECTIVE="$4" + fi + if [[ $SPECIAL_FLAG =~ PIPE ]] + then + $cmd 2>/dev/null >"$TEMPFILENAME"."$TESTCOUNTER".01 + else + $cmd 2>/dev/null >/dev/null + fi + # perform test of required output files based on md5 checksums + test_for_expected_md5_sums "$TEMPFILENAME"'\.'"$TESTCOUNTER"'\.' reference.md5 + RESULT=$? + if [ $RESULT -eq 0 ] + then + STATUS="ok" + else + STATUS="not ok" + fi + echo "$STATUS $TESTCOUNTER - $DESC (command was '$cmd') $TAP_DIRECTIVE" + # finally increment the test counter + TESTCOUNTER=$((TESTCOUNTER+1)) +} +##----------------------------------------------------------------------------## +# +# Define a md5 sum compare script to assess the correct splitting +# +##----------------------------------------------------------------------------## +function test_for_expected_md5_sums { + local FILEPATTERN=$1 + local REFERENCE_FILE=$2 + local md5_temp_file="tmp.md5" + local output=0 # assuming no error + # extract the reference md5 sums + grep "$FILEPATTERN" "$REFERENCE_FILE" >"$md5_temp_file" + # test if tmp.md5 has a length of more than 0 + if [ ! -s "$md5_temp_file" ] + then + echo "No expected MD5 sums for the given pattern '$FILEPATTERN' defined" >&2 + return 10 + fi -##----------------------------------------------------------------------------## + # under MacOSX we need to use another approach than on Linux, + # therefore we need to decide which OS is running: + local MD5="" + case "$OSTYPE" in + darwin*) + MD5="md5 -r" + ;; + linux-gnu) + MD5="md5sum" + ;; + esac + + # test if all expected files are correct + while read -r line || [[ -n "$line" ]] + do + local exp_checksum=${line% *}; file=${line#* }; + local cmd="$MD5 $file | awk '{print \$1}'"; + + local got_checksum="" + + if [ -e "$file" ] + then + got_checksum=$(bash -c "$cmd"); + else + got_checksum="-1" + echo "Missing file '$file' for MD5 comparison" >&2 + fi -# FASTQ -EC="$DIR/ec.fq" -DESC="split pipe" -echo "Test #"$((++TC))" $DESC"; -TF="$DIR/tmp" -cmd="$SC -n 10 $EC" -echo "$cmd"; -$cmd > $TF - -DIFF=$(diff $EC $TF) -if [ ! -z "$DIFF" ]; then - echo "..failed" - echo "unexpected difference found:" 1>&2; - echo "$DIFF" 1>&2; - exit 1; -fi; -echo "..ok" - - -# split in chunks -DESC="split file" -echo "Test #"$((++TC))" $DESC"; -TF="$DIR/tmp" -cmd="$SC -n 20 $EC -o tmp.$TC.%02d" -echo "$cmd"; -$cmd; -cat tmp.$TC.* > $TF; - -DIFF=$(diff $EC $TF) -if [ ! -z "$DIFF" ]; then - echo "..failed" - echo "unexpected difference found:" 1>&2; - #echo "$DIFF" 1>&2; - exit 1; -fi; -echo "..ok" - - -# split steps -DESC="split steps" -echo "Test #"$((++TC))" $DESC"; -TF="$DIR/tmp" -cmd="$SC -n 20 -x 5 $EC -o tmp.$TC.%02d" -echo "$cmd"; -$cmd; - -DIFF=$( diff tmp.$TC.01 tmp.$(($TC-1)).01 ) -if [ ! -z "$DIFF" ]; then - echo "..failed" - echo "unexpected difference found:" 1>&2; - # echo "$DIFF" 1>&2; - exit 1; -fi; -DIFF=$( diff tmp.$TC.06 tmp.$(($TC-1)).06 ) -if [ ! -z "$DIFF" ]; then - echo "..failed" - echo "unexpected difference found:" 1>&2; - # echo "$DIFF" 1>&2; - exit 1; -fi; -DIFF=$( diff tmp.$TC.16 tmp.$(($TC-1)).16 ) -if [ ! -z "$DIFF" ]; then - echo "..failed" - echo "unexpected difference found:" 1>&2; - # echo "$DIFF" 1>&2; - exit 1; -fi; -echo "..ok" - - -# split first last step -DESC="split first last step" -echo "Test #"$((++TC))" $DESC"; -TF="$DIR/tmp" -cmd="$SC -n 20 -x 5 -y 2 -f 2 -l 12 $EC -o tmp.$TC.%02d" -echo "$cmd"; -$cmd; - -DIFF=$( diff tmp.$TC.02 tmp.$(($TC-2)).02 ) -if [ ! -z "$DIFF" ]; then - echo "..failed" - echo "unexpected difference found:" 1>&2; - # echo "$DIFF" 1>&2; - exit 1; -fi; -DIFF=$( diff tmp.$TC.03 tmp.$(($TC-2)).03) -if [ ! -z "$DIFF" ]; then - echo "..failed" - echo "unexpected difference found:" 1>&2; - # echo "$DIFF" 1>&2; - exit 1; -fi; -DIFF=$( diff tmp.$TC.07 tmp.$(($TC-2)).07 ) -if [ ! -z "$DIFF" ]; then - echo "..failed" - echo "unexpected difference found:" 1>&2; - # echo "$DIFF" 1>&2; - exit 1; -fi; -DIFF=$( diff tmp.$TC.12 tmp.$(($TC-2)).12 ) -if [ ! -z "$DIFF" ]; then - echo "..failed" - echo "unexpected difference found:" 1>&2; - # echo "$DIFF" 1>&2; - exit 1; -fi; -if [ -e "tmp.$TC.13" ]; then - echo "..failed" - echo "last not respected" 1>&2; - # echo "$DIFF" 1>&2; - exit 1; -fi; -echo "..ok" - - -# split first last step -DESC="split late first" -echo "Test #"$((++TC))" $DESC"; -TF="$DIR/tmp" -cmd="$SC -n 20 -f 19 -l 19 $EC -o tmp.$TC.%02d" -echo "$cmd"; -$cmd; - -DIFF=$( diff tmp.$TC.19 tmp.$(($TC-3)).19 ) -if [ ! -z "$DIFF" ]; then - echo "..failed" - echo "unexpected difference found:" 1>&2; - # echo "$DIFF" 1>&2; - exit 1; -fi; -echo "..ok" - -# check against the dd-based estimated checksums -DESC="Checksum test" -echo "Test #"$((++TC))" $DESC"; -cmd="md5sum -c MD5SUM.dd --quiet" -echo "$cmd"; -$cmd; -if [ $? -ne 0 ]; then - echo "..failed" - echo "Different checksums found:" 1>&2; - exit 1; -fi; -echo "..ok" - -rm tmp* + if [[ $exp_checksum != $got_checksum ]] + then + output=1 # indicating an error + echo "MD5 mismatch for '$file' expected MD5: exp:$exp_checksum but found $got_checksum" >&2 + fi + done <"$md5_temp_file" + # test if no other files were created, so each file following the + # pattern need to be represented in the expected file + for got_file in $(find . | grep "$FILEPATTERN") + do + # check if the file exists + if [ ! -e "$got_file" ] + then + output=1 # indicating an error + echo "File '$got_file' does not exist" >&2 + fi + + local cmd="$MD5 $got_file | awk '{print \$1}'"; + + local got_checksum="" + + got_checksum=$(bash -c "$cmd"); + + # build a grep expression + local need_to_be_defined='^'"$got_checksum"'[[:space:]]*.*'"$got_file"'$' + + # test via grep if that line exists + grep "$need_to_be_defined" "$md5_temp_file" 2>/dev/null >/dev/null + + if [ $? -ne 0 ] + then + output=1 # indicating an error + echo "MD5 entry not found via grep pattern '$need_to_be_defined' for file '$got_file'" >&2 + fi + done + + return "$output" +} + + +##----------------------------------------------------------------------------## +# +# Cycle through all SeqChunker implementations +# +##----------------------------------------------------------------------------## +for SC in "$DIR"/../bin/SeqChunker "$DIR"/../bin/SeqChunker-perl "$DIR"/../bin/SeqChunker-dd "$DIR"/../bin/SeqChunker-sed +do + TAP_DIRECTIVE="" + ##----------------------------------------------------------------------------## + # Set TAP directive to TODO if SeqChunker-sed is called + ##----------------------------------------------------------------------------## + if [[ "$SC" =~ -sed ]] + then + TAP_DIRECTIVE="# TODO SeqChunker-sed seems to be broken" + fi + + ##----------------------------------------------------------------------------## + # Set TAP directive to TODO if SeqChunker-dd is called and bash version <4 + ##----------------------------------------------------------------------------## + if [[ "$SC" =~ -dd ]] + then + BASH_MAJOR_VER=$(bash --version | grep -Eo [0-9][.][0-9] | cut -d. -f1) + if [ $BASH_MAJOR_VER -lt 4 ] + then + TAP_DIRECTIVE="# TODO SeqChunker-dd requires bash version >= 4" + fi + fi + + + ##----------------------------------------------------------------------------## + # + # Run FASTA test scripts + # + ##----------------------------------------------------------------------------## + + # define input file + EC="$DIR/ec.fa" + + test_SeqChunker "FASTA: split pipe" "$SC -n 10 $EC" "PIPE" "$TAP_DIRECTIVE" + test_SeqChunker "FASTA: split file" "$SC -n 20 $EC -o $TEMPFILENAME.$TESTCOUNTER.%02d" "" "$TAP_DIRECTIVE" + test_SeqChunker "FASTA: split steps" "$SC -n 20 -x 5 $EC -o $TEMPFILENAME.$TESTCOUNTER.%02d" "AGAINST_LAST_RUN" "$TAP_DIRECTIVE" + test_SeqChunker "FASTA: split file many chunks" "$SC -n 1000 $EC -o $TEMPFILENAME.$TESTCOUNTER.%04d" "" "$TAP_DIRECTIVE" + test_SeqChunker "FASTA: split last first" "$SC -n 1000 -f 1000 -l 1000 $EC -o $TEMPFILENAME.$TESTCOUNTER.%04d" "AGAINST_LAST_RUN" "$TAP_DIRECTIVE" + test_SeqChunker "FASTA: split file as preparation (same as split file test)" "$SC -n 20 $EC -o $TEMPFILENAME.$TESTCOUNTER.%02d" "" "$TAP_DIRECTIVE" + test_SeqChunker "FASTA: split first last step" "$SC -n 20 -x 5 -y 2 -f 2 -l 12 $EC -o tmp.$TESTCOUNTER.%02d" "AGAINST_LAST_RUN" "$TAP_DIRECTIVE" + + ##----------------------------------------------------------------------------## + # + # Run FASTQ test scripts + # + ##----------------------------------------------------------------------------## + + # define input file + EC="$DIR/ec.fq" + + test_SeqChunker "FASTQ: split pipe" "$SC -n 10 $EC" "PIPE" "$TAP_DIRECTIVE" + test_SeqChunker "FASTQ: split file" "$SC -n 20 $EC -o $TEMPFILENAME.$TESTCOUNTER.%02d" "" "$TAP_DIRECTIVE" + test_SeqChunker "FASTQ: split steps" "$SC -n 20 -x 5 $EC -o $TEMPFILENAME.$TESTCOUNTER.%02d" "AGAINST_LAST_RUN" "$TAP_DIRECTIVE" + test_SeqChunker "FASTQ: split file as preparation (same as split file test)" "$SC -n 20 $EC -o $TEMPFILENAME.$TESTCOUNTER.%02d" "" "$TAP_DIRECTIVE" + test_SeqChunker "FASTQ: split first last step" "$SC -n 20 -x 5 -y 2 -f 2 -l 12 $EC -o $TEMPFILENAME.$TESTCOUNTER.%02d" "AGAINST_LAST_RUN" "$TAP_DIRECTIVE" + test_SeqChunker "FASTQ: split file as preparation (same as split file test)" "$SC -n 20 $EC -o $TEMPFILENAME.$TESTCOUNTER.%02d" "" "$TAP_DIRECTIVE" + test_SeqChunker "FASTQ: split first last step" "$SC -n 20 -f 19 -l 19 $EC -o $TEMPFILENAME.$TESTCOUNTER.%02d" "AGAINST_LAST_RUN" "$TAP_DIRECTIVE" + + ##----------------------------------------------------------------------------## + # + # Clean up + # + ##----------------------------------------------------------------------------## + rm tmp* + + ##----------------------------------------------------------------------------## + # + # And skip md5 based tests for now + # + ##----------------------------------------------------------------------------## + continue + + # check against the dd-based estimated checksums + DESC="Checksum test" + echo "Test #"$((++TC))" $DESC"; + cmd="md5sum -c MD5SUM.dd --quiet" + echo "$cmd"; + $cmd; + if [ $? -ne 0 ]; then + echo "..failed" + echo "Different checksums found:" 1>&2; + exit 1; + fi; + echo "..ok" + +done