Tool Test Results (powered by Planemo)

# HG changeset patch # User bgruening # Date 1420726051 18000 # Node ID 8928e6d1e7badde6c3b1f9038ebd39ca64bec686 # Parent 3f0e0d4c15a9145b1592ae65c0862d081c072bed Uploaded diff -r 3f0e0d4c15a9 -r 8928e6d1e7ba awk.xml --- a/awk.xml Wed Jan 07 11:15:41 2015 -0500 +++ b/awk.xml Thu Jan 08 09:07:31 2015 -0500 @@ -11,17 +11,17 @@ "$output" + -f "$awk_script" + "$infile" + > "$outfile" ]]> - - + + @@ -30,21 +30,19 @@ - - $url_paste - + $code - + - - - - - + + + + + + - 23** will match lines that after subtracting the value of the fourth column from the value of the fifth column, gives value alrger than 23. - **/AG..AG/** will match lines that contain the regular expression **AG..AG** (meaning the characeters AG followed by any two characeters followed by AG). (This is the way to specify regular expressions on the entire line, similar to GREP.) - **$7 ~ /A{4}U/** will match lines whose seventh column contains 4 consecutive A's followed by a U. (This is the way to specify regular expressions on a specific field.) -- **10000 < $4 && $4 < 20000** will match lines whose fourth column value is larger than 10,000 but smaller than 20,000 +- **10000 < $4 && $4 < 20000** will match lines whose fourth column value is larger than 10,000 but smaller than 20,000 - If no pattern is specified, all lines match (meaning the **action** part will be executed on all lines). - **Action Examples** - **{ print }** or **{ print $0 }** will print the entire input line (the line that matched in **pattern**). **$0** is a special marker meaning 'the entire line'. @@ -98,7 +94,6 @@ - If no action part is specified (not even the curly brackets) - the default action is to print the entire line. - **AWK's Regular Expression Syntax** The select tool searches the data for lines containing or not containing a match to the given pattern. A Regular Expression is a pattern descibing a certain amount of text. diff -r 3f0e0d4c15a9 -r 8928e6d1e7ba cut.xml --- a/cut.xml Wed Jan 07 11:15:41 2015 -0500 +++ b/cut.xml Thu Jan 08 09:07:31 2015 -0500 @@ -43,7 +43,7 @@ - + @@ -185,16 +185,24 @@ - - - - + + + + - - - - + + + + + + + + + + + + diff -r 3f0e0d4c15a9 -r 8928e6d1e7ba easyjoin.xml --- a/easyjoin.xml Wed Jan 07 11:15:41 2015 -0500 +++ b/easyjoin.xml Thu Jan 08 09:07:31 2015 -0500 @@ -55,7 +55,7 @@ - + diff -r 3f0e0d4c15a9 -r 8928e6d1e7ba find_and_replace.xml --- a/find_and_replace.xml Wed Jan 07 11:15:41 2015 -0500 +++ b/find_and_replace.xml Thu Jan 08 09:07:31 2015 -0500 @@ -28,14 +28,14 @@ - + - @@ -60,7 +60,7 @@ - + @@ -116,7 +116,7 @@ **Examples of Replace Patterns** - **WORLD** The word 'WORLD' will be placed whereever the find pattern was found. -- **FOO-$&-BAR** Each time the find pattern is found, it will be surrounded with 'FOO-' at the begining and '-BAR' at the end. **$&** (dollar-ampersand) represents the matched find pattern. +- **FOO-$&-BAR** Each time the find pattern is found, it will be surrounded with 'FOO-' at the begining and '-BAR' at the end. **$&** (dollar-ampersand) represents the matched find pattern. - **$1** The text which matched the first parenthesis in the Find Pattern. diff -r 3f0e0d4c15a9 -r 8928e6d1e7ba grep.xml --- a/grep.xml Wed Jan 07 11:15:41 2015 -0500 +++ b/grep.xml Thu Jan 08 09:07:31 2015 -0500 @@ -66,7 +66,7 @@ - + @@ -75,26 +75,26 @@ - + - + - + - + diff -r 3f0e0d4c15a9 -r 8928e6d1e7ba head.xml --- a/head.xml Wed Jan 07 11:15:41 2015 -0500 +++ b/head.xml Thu Jan 08 09:07:31 2015 -0500 @@ -21,10 +21,10 @@ + label="Number of lines" help="These will be kept/discarded depending on 'operation'. (--lines)" /> - + diff -r 3f0e0d4c15a9 -r 8928e6d1e7ba multijoin.xml --- a/multijoin.xml Wed Jan 07 11:15:41 2015 -0500 +++ b/multijoin.xml Thu Jan 08 09:07:31 2015 -0500 @@ -1,4 +1,4 @@ - + (combine multiple files) macros.xml @@ -45,16 +45,16 @@ - + - - - - - - - + + + + + + + diff -r 3f0e0d4c15a9 -r 8928e6d1e7ba readme.rst --- a/readme.rst Wed Jan 07 11:15:41 2015 -0500 +++ b/readme.rst Thu Jan 08 09:07:31 2015 -0500 @@ -8,12 +8,13 @@ Tools: +------ -* awk - The AWK programmning language ( http://www.gnu.org/software/gawk/ ) -* sed - Stream Editor ( http://sed.sf.net ) -* grep - Search files ( http://www.gnu.org/software/grep/ ) -* sort_columns - Sorting every line according to there columns -* GNU Coreutils programs ( http://www.gnu.org/software/coreutils/ ): + * awk - The AWK programmning language ( http://www.gnu.org/software/gawk/ ) + * sed - Stream Editor ( http://sed.sf.net ) + * grep - Search files ( http://www.gnu.org/software/grep/ ) + * sort_columns - Sorting every line according to there columns + * GNU Coreutils programs ( http://www.gnu.org/software/coreutils/ ): * sort - sort files * join - join two files, based on common key field. @@ -22,8 +23,11 @@ * sorted_uniq - keep unique/duplicated lines in a file * head - keep the first X lines in a file. * tail - keep the last X lines in a file. + * unfold_column - unfold a column with multiple entities into multiple lines + Few improvements over the standard tools: +----------------------------------------- * EasyJoin - A Join tool that does not require pre-sorted the files ( https://github.com/agordon/filo/blob/scripts/src/scripts/easyjoin ) * Multi-Join - Join multiple (>2) files ( https://github.com/agordon/filo/blob/scripts/src/scripts/multijoin ) @@ -32,15 +36,15 @@ * HTML'd Grep - grep text in a file, and produced high-lighted HTML output, for easier viewing ( uses https://github.com/agordon/filo/blob/scripts/src/scripts/sort-header ) -Requirements ------------- +Requirements: +------------- -1. Coreutils vesion 8.22 or later. -2. AWK version 4.0.1 or later. -3. SED version 4.2 *with* a special patch -4. Grep with PCRE support + * Coreutils vesion 8.22 or later. + * AWK version 4.0.1 or later. + * SED version 4.2 *with* a special patch + * Grep with PCRE support -These will be installed automatically with the Galaxy `Tool Shed`_. +All dependencies will be installed automatically with the Galaxy `Tool Shed`_ and the following repository: https://toolshed.g2.bx.psu.edu/view/bgruening/text_processing ------------------- @@ -52,23 +56,22 @@ or reading/writing arbitrary files with awk's redirection and sed's "r/w" commands. These commands are DISABLED using the "--sandbox" parameter to awk and sed. -User trying to run an awk program similar to: +User trying to run an awk program similar to:: BEGIN { system("ls") } -Will get an error (in Galaxy) saying: +Will get an error (in Galaxy) saying:: fatal: 'system' function not allowed in sandbox mode. -User trying to run a SED program similar to: +User trying to run a SED program similar to:: 1els -will get an error (in Galaxy) saying: +will get an error (in Galaxy) saying:: sed: -e expression #1, char 2: e/r/w commands disabled in sandbox mode - That being said, if you do find some vulnerability in these tools, please let me know and I'll try fix them. ------------ @@ -76,6 +79,7 @@ ------------ Should be done via the Galaxy `Tool Shed`_. +Install the following repository: https://toolshed.g2.bx.psu.edu/view/bgruening/text_processing .. _`Tool Shed`: http://wiki.galaxyproject.org/Tool%20Shed @@ -84,20 +88,19 @@ TODO ---- -- add shuf - we can remove the random feature from sort and use shuf instead -- move some advanced settings under a conditional, for example the cut tools offers to cut bytes -- cut wrapper has some output conditional magic for interval files, that needs to be checked -- comm wrapper, see the Galaxy default one -- evaluate the join wrappers against the Galaxy ones, maybe we should drop them + * add shuf, we can remove the random feature from sort and use shuf instead + * move some advanced settings under a conditional, for example the cut tools offers to cut bytes + * cut wrapper has some output conditional magic for interval files, that needs to be checked + * comm wrapper, see the Galaxy default one + * evaluate the join wrappers against the Galaxy ones, maybe we should drop them ------- License ------- -* Copyright (c) 2009-2013 A. Gordon (gordon cshl dot edu) -* Copyright (c) 2013-2015 B. Gruening (bjoern dot gruening gmail dot com) + * Copyright (c) 2009-2013 A. Gordon (gordon cshl dot edu) + * Copyright (c) 2013-2015 B. Gruening (bjoern dot gruening gmail dot com) Permission is hereby granted, free of charge, to any person obtaining diff -r 3f0e0d4c15a9 -r 8928e6d1e7ba recurring_lines.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/recurring_lines.xml Thu Jan 08 09:07:31 2015 -0500 @@ -0,0 +1,78 @@ + + with recurring lines + + macros.xml + + + yes --version | head -n 1 + +/dev/null | head -n \$times >> $outfile; + #end for +]]> + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff -r 3f0e0d4c15a9 -r 8928e6d1e7ba replace_text_in_column.xml --- a/replace_text_in_column.xml Wed Jan 07 11:15:41 2015 -0500 +++ b/replace_text_in_column.xml Thu Jan 08 09:07:31 2015 -0500 @@ -7,16 +7,14 @@ gnu_awk awk --version | head -n 1 - + "$output" + > "$outfile" ]]> @@ -39,22 +37,22 @@ - + - + - - + + gnu_sed sed --version | head -n 1 - + "$output" + "$infile" + > "$outfile" ]]> - + @@ -35,21 +35,21 @@ - + - + - + sed --version | head -n 1 - + @@ -36,7 +36,7 @@ - + @@ -45,24 +45,25 @@ - $url_paste + $code - + - - + + - + - - - - + + + + + @@ -95,8 +96,8 @@ - **s/hsa//** will remove the first instance of 'hsa' in every line. - **s/hsa//g** will remove all instances (beacuse of the **g**) of 'hsa' in every line. -- **s/A{4,}/--&--/g** will find sequences of 4 or more consecutive A's, and once found, will surround them with two dashes from each side. The **&** marker is a place holder for 'whatever matched the regular expression'. -- **s/hsa-mir-([^ ]+)/short name: \\1 full name: &/** will find strings such as 'hsa-mir-43a' (the regular expression is 'hsa-mir-' followed by non-space characters) and will replace it will string such as 'short name: 43a full name: hsa-mir-43a'. The **\\1** marker is a place holder for 'whatever matched the first parenthesis' (similar to perl's **$1**) . +- **s/A{4,}/--&--/g** will find sequences of 4 or more consecutive A's, and once found, will surround them with two dashes from each side. The **&** marker is a place holder for 'whatever matched the regular expression'. +- **s/hsa-mir-([^ ]+)/short name: \\1 full name: &/** will find strings such as 'hsa-mir-43a' (the regular expression is 'hsa-mir-' followed by non-space characters) and will replace it will string such as 'short name: 43a full name: hsa-mir-43a'. The **\\1** marker is a place holder for 'whatever matched the first parenthesis' (similar to perl's **$1**) . **sed's Regular Expression Syntax** diff -r 3f0e0d4c15a9 -r 8928e6d1e7ba sort.xml --- a/sort.xml Wed Jan 07 11:15:41 2015 -0500 +++ b/sort.xml Thu Jan 08 09:07:31 2015 -0500 @@ -10,6 +10,7 @@ 0: sed -u '${header}'q && #end if @@ -50,14 +51,13 @@ label="Output unique values" help="Print only unique values, based on sorted key columns. See help section for details. (--unique)" /> - - + - + @@ -72,7 +72,7 @@ - + @@ -87,7 +87,7 @@ - + diff -r 3f0e0d4c15a9 -r 8928e6d1e7ba sort_rows.xml --- a/sort_rows.xml Wed Jan 07 11:15:41 2015 -0500 +++ b/sort_rows.xml Thu Jan 08 09:07:31 2015 -0500 @@ -12,7 +12,7 @@ - + diff -r 3f0e0d4c15a9 -r 8928e6d1e7ba sorted_uniq.xml --- a/sorted_uniq.xml Wed Jan 07 11:15:41 2015 -0500 +++ b/sorted_uniq.xml Thu Jan 08 09:07:31 2015 -0500 @@ -51,7 +51,7 @@ label="Only print unique lines" help="(-u)" /> - @@ -66,10 +66,9 @@ label="Ignore differences in case when comparing" help="(-i)"/> - - + diff -r 3f0e0d4c15a9 -r 8928e6d1e7ba tac.xml --- a/tac.xml Wed Jan 07 11:15:41 2015 -0500 +++ b/tac.xml Thu Jan 08 09:07:31 2015 -0500 @@ -11,18 +11,20 @@ #if str($separator.separator_select) == "yes": $separator.before $separator.regex - $separator.separator_string + #if $separator.separator_string: + "$separator.separator_string" + #end if #end if - "$input" + "$infile" > "$outfile" ]]> - + + - @@ -36,15 +38,19 @@ - + - - - + + + + + + + - + diff -r 3f0e0d4c15a9 -r 8928e6d1e7ba test-data/awk1.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/awk1.txt Thu Jan 08 09:07:31 2015 -0500 @@ -0,0 +1,10 @@ +chr10 0.4 +chr1 1.4 +chrM 3e-1 +chr2 1.1e2 +chr15 3.14e-2 +chr15 0.0314 +chr4 0.1 +chr20 0.9 +chr22 +1.3 +chrX -0.3 diff -r 3f0e0d4c15a9 -r 8928e6d1e7ba test-data/awk_results1.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/awk_results1.txt Thu Jan 08 09:07:31 2015 -0500 @@ -0,0 +1,4 @@ +12.6 chr1 +990 chr2 +8.1 chr20 +11.7 chr22 diff -r 3f0e0d4c15a9 -r 8928e6d1e7ba test-data/cut1.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cut1.txt Thu Jan 08 09:07:31 2015 -0500 @@ -0,0 +1,4 @@ +fruit color weight price +apple red 1.4 0.4 +orange orange 1.1 0.2 +banana yellow 0.9 0.35 diff -r 3f0e0d4c15a9 -r 8928e6d1e7ba test-data/cut_results1.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cut_results1.txt Thu Jan 08 09:07:31 2015 -0500 @@ -0,0 +1,4 @@ +fruit weight price +apple 1.4 0.4 +orange 1.1 0.2 +banana 0.9 0.35 diff -r 3f0e0d4c15a9 -r 8928e6d1e7ba test-data/cut_results2.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cut_results2.txt Thu Jan 08 09:07:31 2015 -0500 @@ -0,0 +1,4 @@ +fruit weight price +apple 1.4 0.4 +orange 1.1 0.2 +banana 0.9 0.35 diff -r 3f0e0d4c15a9 -r 8928e6d1e7ba test-data/cut_results3.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cut_results3.txt Thu Jan 08 09:07:31 2015 -0500 @@ -0,0 +1,4 @@ +fru +app +ora +ban diff -r 3f0e0d4c15a9 -r 8928e6d1e7ba test-data/eq-cut.dat --- a/test-data/eq-cut.dat Wed Jan 07 11:15:41 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,65 +0,0 @@ -chr1 CCDS989.1_cds_0_0_chr1_147962193_r 147962192 147962580 -chr1 CCDS990.1_cds_0_0_chr1_147984546_f 147984545 147984630 -chr1 CCDS993.1_cds_0_0_chr1_148078401_r 148078400 148078582 -chr1 CCDS996.1_cds_0_0_chr1_148185137_f 148185136 148185276 -chr10 CCDS7248.1_cds_0_0_chr10_55251624_r 55251623 55253124 -chr11 CCDS8374.1_cds_0_0_chr11_116124408_r 116124407 116124501 -chr11 CCDS8377.1_cds_0_0_chr11_116206509_f 116206508 116206563 -chr11 CCDS8378.1_cds_0_0_chr11_116211734_r 116211733 116212337 -chr11 CCDS7726.1_cds_0_0_chr11_1812378_f 1812377 1812407 -chr12 CCDS8736.1_cds_0_0_chr12_38440095_r 38440094 38440321 -chr13 CCDS9526.1_cds_0_0_chr13_112381695_f 112381694 112381953 -chr14 CCDS9949.1_cds_0_0_chr14_98710241_r 98710240 98712285 -chr15 CCDS10096.1_cds_0_0_chr15_41486873_r 41486872 41487060 -chr15 CCDS10097.1_cds_0_0_chr15_41673709_f 41673708 41673857 -chr15 CCDS10098.1_cds_0_0_chr15_41679162_r 41679161 41679250 -chr15 CCDS10101.1_cds_0_0_chr15_41826030_f 41826029 41826196 -chr16 CCDS10397.1_cds_0_0_chr16_142909_f 142908 143003 -chr16 CCDS10401.1_cds_0_0_chr16_179964_r 179963 180135 -chr16 CCDS10402.1_cds_0_0_chr16_244414_f 244413 244681 -chr16 CCDS10403.1_cds_0_0_chr16_259269_r 259268 259383 -chr18 CCDS11891.1_cds_0_0_chr18_23786115_r 23786114 23786321 -chr18 CCDS11985.1_cds_0_0_chr18_59406882_f 59406881 59407046 -chr18 CCDS11986.1_cds_0_0_chr18_59455933_r 59455932 59456337 -chr18 CCDS11988.1_cds_0_0_chr18_59600587_f 59600586 59600754 -chr19 CCDS12866.1_cds_0_0_chr19_59068596_f 59068595 59069564 -chr19 CCDS12872.1_cds_0_0_chr19_59236027_r 59236026 59236146 -chr19 CCDS12877.1_cds_0_0_chr19_59297999_f 59297998 59298008 -chr19 CCDS12878.1_cds_0_0_chr19_59302169_r 59302168 59302288 -chr2 CCDS2120.1_cds_0_0_chr2_118288584_f 118288583 118288668 -chr2 CCDS2121.1_cds_0_0_chr2_118394149_r 118394148 118394202 -chr2 CCDS2441.1_cds_0_0_chr2_220190203_f 220190202 220190242 -chr2 CCDS2443.1_cds_0_0_chr2_220229610_r 220229609 220230869 -chr20 CCDS13249.1_cds_0_0_chr20_33330414_r 33330413 33330423 -chr20 CCDS13255.1_cds_0_0_chr20_33513607_f 33513606 33513792 -chr20 CCDS13256.1_cds_0_0_chr20_33579501_r 33579500 33579527 -chr20 CCDS13257.1_cds_0_0_chr20_33593261_f 33593260 33593348 -chr21 CCDS13614.1_cds_0_0_chr21_32707033_f 32707032 32707192 -chr21 CCDS13615.1_cds_0_0_chr21_32869642_r 32869641 32870022 -chr21 CCDS13620.1_cds_0_0_chr21_33321041_f 33321040 33322012 -chr21 CCDS13625.1_cds_0_0_chr21_33744995_r 33744994 33745040 -chr22 CCDS13897.1_cds_0_0_chr22_30120224_f 30120223 30120265 -chr22 CCDS13898.1_cds_0_0_chr22_30160420_r 30160419 30160661 -chr22 CCDS13901.1_cds_0_0_chr22_30665274_f 30665273 30665360 -chr22 CCDS13903.1_cds_0_0_chr22_30939055_r 30939054 30939266 -chr5 CCDS4149.1_cds_0_0_chr5_131424299_f 131424298 131424460 -chr5 CCDS4151.1_cds_0_0_chr5_131556602_r 131556601 131556672 -chr5 CCDS4152.1_cds_0_0_chr5_131621327_f 131621326 131621419 -chr5 CCDS4155.1_cds_0_0_chr5_131847542_r 131847541 131847666 -chr6 CCDS5061.1_cds_0_0_chr6_108299601_r 108299600 108299744 -chr6 CCDS5063.1_cds_0_0_chr6_108594663_f 108594662 108594687 -chr6 CCDS5064.1_cds_0_0_chr6_108640046_r 108640045 108640151 -chr6 CCDS5067.1_cds_0_0_chr6_108722977_f 108722976 108723115 -chr7 CCDS5760.1_cds_0_0_chr7_113660518_f 113660517 113660685 -chr7 CCDS5771.1_cds_0_0_chr7_116512160_r 116512159 116512389 -chr7 CCDS5773.1_cds_0_0_chr7_116714100_f 116714099 116714152 -chr7 CCDS5774.1_cds_0_0_chr7_116945542_r 116945541 116945787 -chr8 CCDS6324.1_cds_0_0_chr8_118881132_r 118881131 118881317 -chr9 CCDS6914.1_cds_0_0_chr9_128764157_f 128764156 128764189 -chr9 CCDS6915.1_cds_0_0_chr9_128787520_r 128787519 128789136 -chr9 CCDS6917.1_cds_0_0_chr9_128882428_f 128882427 128882523 -chr9 CCDS6919.1_cds_0_0_chr9_128937230_r 128937229 128937445 -chrX CCDS14606.1_cds_0_0_chrX_122745048_f 122745047 122745924 -chrX CCDS14733.1_cds_0_0_chrX_152648965_r 152648964 152649196 -chrX CCDS14735.1_cds_0_0_chrX_152691447_f 152691446 152691471 -chrX CCDS14736.1_cds_0_0_chrX_152694030_r 152694029 152694263 diff -r 3f0e0d4c15a9 -r 8928e6d1e7ba test-data/grep1.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/grep1.txt Thu Jan 08 09:07:31 2015 -0500 @@ -0,0 +1,152 @@ +>FC0000042:5:1:220:1502 +AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +>FC0000042:5:1:34:1398 +GATCTCAGTCCACCGCTGGGATTAACCTTGCCCCCC +>FC0000042:5:1:164:1396 +TATCTTATAGATATTTCCCTCTATACTAGTGACCCC +>FC0000042:5:1:333:925 +GAGCTTATAGCTTGTTATATACGTCAACCCCCCCCC +>FC0000042:5:1:204:1476 +GTACTTATATAGATACAAAATATGTATAGGATTGTC +>FC0000042:5:1:119:1511 +GATCTGCATGACCTGGGATTTGTTGGACCCCCCCCC +>FC0000042:5:1:202:1487 +CATGTATAGTCTCCAGTCTATACAACAACCCCCCCC +>FC0000042:5:1:182:1434 +GCTATAGAAATGTTAACATCGAATGTACATTATAAC +>FC0000042:5:1:627:866 +AATATAGATATGGGACAAAACACATTTAGACCCCCC +>FC0000042:5:1:24:1357 +GATATAATATCAATATCAATCCACGCTTGTTCCCCC +>FC0000042:5:1:187:1492 +TATAGAAGCAGAAGAAACAACCTACTTTCACATGTT +>FC0000042:5:1:45:1344 +CAGCTAACAATCAAGCGTTACAGATTAGCCCCCCCC +>FC0000042:5:1:87:1299 +AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +>FC0000042:5:1:206:1341 +GATATATAGCAGTGACCACCTCTAAGCCCCCCCCCC +>FC0000042:5:1:144:929 +GCCCTGGCATATTGTCAATATCTTTAAACCCCCCCC +>FC0000042:5:1:662:820 +TGTCTTTTCGATTTTTTTCTTTGCGTCACCCCCCCC +>FC0000042:5:1:53:1507 +GACCTCACTGTGGCATGAATCATACATTCCCCCCCC +>FC0000042:5:1:182:1502 +AATGCTTGGCAAAGCTCAACTTCGTTGCCCCCCCCC +>FC0000042:5:1:194:1423 +GATCCTATAGGTCTCGATTGGTCTTTTATTCTTTTT +>FC0000042:5:1:35:1444 +GCTATAGCACGGCATAGTGCGATACTAGTACCCCCC +>FC0000042:5:1:667:872 +GACTATAGGCGGAATGATAATGTCAAATAAGTAGTT +>FC0000042:5:1:147:1438 +GATCAAGGAGACTAGGGAGGTAGGAGTTACTCCCCC +>FC0000042:5:1:467:510 +GAACCACTATAGTGACATGGAACACGCGTGAACCCC +>FC0000042:5:1:1553:1707 +TATAGTTACCCTACTGGGCCGACGATTCCCTTACGA +>FC0000042:5:1:207:964 +AATCTATAGATTTTTCTATTATTGTGTCCTCACCCC +>FC0000042:5:1:169:1468 +GCTCTATAGTTCGAGTTACCAAACTCTTCCCCCCCC +>FC0000042:5:1:42:1465 +GCTCTTTAGGTTTGAACCTGTAGACTTGAGGGGCAT +>FC0000042:5:1:55:1331 +GAACTTGCGTAACGTACAAAAATGCAAGCAAAAAGT +>FC0000042:5:1:175:1501 +GCTCTGTTAATCTAGAAAATGTGTCTCCCCCCCCCC +>FC0000042:5:1:221:1465 +TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT +>FC0000042:5:1:196:1450 +AATATAGTCTATCCAACAAGATGTAACCCCCCCCCC +>FC0000042:5:1:86:1413 +TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT +>FC0000042:5:1:453:514 +GATATCTTCGTTTTATATTGAAACTGGCCCCCCCCC +>FC0000042:5:1:150:1415 +TATAGGGCCCTGTATGGTTGCTTGACTAGGGGCTGC +>FC0000042:5:1:191:1475 +GATCCATCCCAATCTCTACGATTGAAAGCATCGGGA +>FC0000042:5:1:26:1407 +GTTATAGAGGCGGGAAGGTGAGAATGCCCCCCCCCC +>FC0000042:5:1:107:1407 +AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +>FC0000042:5:1:388:780 +GATCTATAGCTTCTTTAGCTTGGAAACTGGTCAGCC +>FC0000042:5:1:223:1535 +AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +>FC0000042:5:1:145:783 +AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +>FC0000042:5:1:449:876 +GACCATCAATCAGGTGGAAAGCAGGGCCCCCCCCCC +>FC0000042:5:1:212:1325 +TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT +>FC0000042:5:1:194:1485 +GAACCGAATCCAACCTGTTTCATTCCTCAGATCCCC +>FC0000042:5:1:507:494 +GATCTTATAGAATTTTTGACAACATAAGTTACCCCC +>FC0000042:5:1:416:938 +AATCGTATAGCTCGGGCCGGATACTAGTACACCCCC +>FC0000042:5:1:633:480 +GAGCTGTGTGCATCTGTCCTGAGAGAGGCAAGATTT +>FC0000042:5:1:53:1443 +GTAATGTTATAGCTAGGATTTTGGAGTTTGGTCCTC +>FC0000042:5:1:45:915 +GTATAGCAGCCTAATAAGGAGCTGGGGACCCCCCCC +>FC0000042:5:1:39:1343 +GTTCTATTTTCGATAAAACTGAACCACCCCCCCCCC +>FC0000042:5:1:46:1501 +GATATAGTGGATAACTAATGCTCCCCCAGAACTGTT +>FC0000042:5:1:187:1507 +GAACTAATCCTGATTTATACAACGGCTCCCCCCCCC +>FC0000042:5:1:91:1364 +AATTTATAGCCACTCTAATTCCGTTTGGTTCCCCCC +>FC0000042:5:1:1542:1751 +AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +>FC0000042:5:1:146:886 +GATCTACGATGTACCTTACGCCTCCGAGCATCCCCC +>FC0000042:5:1:615:861 +GATCTACATTATAGATAATGAAGTTCCATTTCCCCC +>FC0000042:5:1:52:792 +GATGTGGTATAGAGAGCAATTCGTTGGTTTTGCCCC +>FC0000042:5:1:153:1433 +GGTCTTTCTATAGAACGGAACGATATATTTTTCCCC +>FC0000042:5:1:540:800 +GAGCGAAAGTGATAGATGGAGGACTATATCTGCCCC +>FC0000042:5:1:160:1344 +GGTGTACTATAGCTATTAAGTCCAATCATGATAATA +>FC0000042:5:1:544:413 +GATCTCTGGAAAATATAAACCGGTGACCCCCCCCCC +>FC0000042:5:1:579:895 +AGTCTCGAATCAATGTATTTCATCGTGGTAATCCCC +>FC0000042:5:1:468:495 +TATTGATGCTCCCTGCCTGAAAGATACCCCCCCCCC +>FC0000042:5:1:383:831 +CTTCATGAATCTACTGTTGGCGTTTATTTTATCTGG +>FC0000042:5:1:112:1416 +TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT +>FC0000042:5:1:37:1299 +GATCGTGAGCTCTGTACCGGAAGTTCGTGGCTGCCA +>FC0000042:5:1:205:780 +TATAGTGTTCCACAAAGACTAGGTAACGCTTCATTT +>FC0000042:5:1:33:702 +GAACGGACTATAGCCGGTATCCAAACATAAATGTTC +>FC0000042:5:1:54:1019 +AATCGCAGCATTCTGACACACAGGTTTCGGATGTAC +>FC0000042:5:1:587:867 +TATCTAATGTCATATTTTCAGACAAATTACTAGAAA +>FC0000042:5:1:319:990 +GATTTGTAAATTACTTCGAACATAGAAGTTCCCCCC +>FC0000042:5:1:453:829 +GAACTTACGGCATTAAGTTTAATCTTCAGCCACCCC +>FC0000042:5:1:159:1470 +GATCTGATAGTGTTGCGACGTAAATAAGTCCCCCCC +>FC0000042:5:1:487:820 +GATCTCGCAGGGATCAGTTATCCAGGTATTCCCCCC +>FC0000042:5:1:48:371 +AATCTATAATCTTTACCCGAGTTTAAGTCCCCCCCC +>FC0000042:5:1:1346:1739 +GATATAGGTTATACGTTTTTAGTCTTAGAGAAGTTT +>FC0000042:5:1:661:459 +GATCTGCTTTAACGATTGAGGACGATGCCCCCCCCC diff -r 3f0e0d4c15a9 -r 8928e6d1e7ba test-data/grep_results1.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/grep_results1.txt Thu Jan 08 09:07:31 2015 -0500 @@ -0,0 +1,14 @@ +>FC0000042:5:1:182:1434 +GCTATAGAAATGTTAACATCGAATGTACATTATAAC +>FC0000042:5:1:45:1344 +CAGCTAACAATCAAGCGTTACAGATTAGCCCCCCCC +>FC0000042:5:1:55:1331 +GAACTTGCGTAACGTACAAAAATGCAAGCAAAAAGT +>FC0000042:5:1:175:1501 +GCTCTGTTAATCTAGAAAATGTGTCTCCCCCCCCCC +>FC0000042:5:1:416:938 +AATCGTATAGCTCGGGCCGGATACTAGTACACCCCC +>FC0000042:5:1:46:1501 +GATATAGTGGATAACTAATGCTCCCCCAGAACTGTT +>FC0000042:5:1:33:702 +GAACGGACTATAGCCGGTATCCAAACATAAATGTTC diff -r 3f0e0d4c15a9 -r 8928e6d1e7ba test-data/grep_results2.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/grep_results2.html Thu Jan 08 09:07:31 2015 -0500 @@ -0,0 +1,307 @@ + + + + + + + +

+GCTATAGAAATGTTAACATCGAATGTACATTATAAC
+--
+CAGCTAACAATCAAGCGTTACAGATTAGCCCCCCCC
+--
+GAACTTGCGTAACGTACAAAAATGCAAGCAAAAAGT
+--
+GCTCTGTTAATCTAGAAAATGTGTCTCCCCCCCCCC
+--
+AATCGTATAGCTCGGGCCGGATACTAGTACACCCCC
+--
+GATATAGTGGATAACTAATGCTCCCCCAGAACTGTT
+--
+GAACGGACTATAGCCGGTATCCAAACATAAATGTTC
+

+ + diff -r 3f0e0d4c15a9 -r 8928e6d1e7ba test-data/multijoin_result1.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/multijoin_result1.txt Thu Jan 08 09:07:31 2015 -0500 @@ -0,0 +1,19 @@ +key dataset_1_V7 dataset_1_V8 dataset_1_V9 dataset_2_V7 dataset_2_V8 dataset_2_V9 dataset_3_V7 dataset_3_V8 dataset_3_V9 +FBtr0089116 0 0 0 56 1296 15144 0 0 0 +FBtr0089223 5293 13394 13690 0 0 0 17646 13536 13690 +FBtr0089229 3944 6428 6831 0 0 0 9927 6738 6831 +FBtr0089231 3944 6428 6831 0 0 0 9927 6738 6831 +FBtr0089233 3944 6428 6831 0 0 0 9927 6738 6831 +FBtr0111044 28 683 2138 0 0 0 17 714 2138 +FBtr0111045 28 683 2138 0 0 0 17 714 2138 +FBtr0111046 7 166 642 0 0 0 5 304 642 +FBtr0300796 0 0 0 56 1296 14475 0 0 0 +FBtr0300797 0 0 0 56 1296 13987 0 0 0 +FBtr0300798 0 0 0 56 1296 14473 0 0 0 +FBtr0300799 0 0 0 56 1296 14473 0 0 0 +FBtr0300800 0 0 0 56 1296 14475 0 0 0 +FBtr0308086 0 0 0 56 1296 14456 0 0 0 +FBtr0308087 0 0 0 56 1296 14456 0 0 0 +FBtr0308778 266 1527 1722 0 0 0 0 0 0 +FBtr0309803 0 0 0 657 29084 44167 0 0 0 +FBtr0310651 3944 6428 6850 0 0 0 9927 6738 6850 diff -r 3f0e0d4c15a9 -r 8928e6d1e7ba test-data/recurring_result1.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/recurring_result1.txt Thu Jan 08 09:07:31 2015 -0500 @@ -0,0 +1,10 @@ +freedom +freedom +freedom +freedom +freedom +freedom +freedom +freedom +freedom +freedom diff -r 3f0e0d4c15a9 -r 8928e6d1e7ba test-data/recurring_result2.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/recurring_result2.txt Thu Jan 08 09:07:31 2015 -0500 @@ -0,0 +1,20 @@ +freedom +freedom +freedom +freedom +freedom +freedom +freedom +freedom +freedom +freedom +war is over +war is over +war is over +war is over +war is over +war is over +war is over +war is over +war is over +war is over diff -r 3f0e0d4c15a9 -r 8928e6d1e7ba test-data/replace_text_in_column1.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/replace_text_in_column1.txt Thu Jan 08 09:07:31 2015 -0500 @@ -0,0 +1,3 @@ +chr7 56632 56652 D17003_CTCF_R6 310 + +chr7 56736 56756 D17003_CTCF_R7 354 + +chr7 56761 56781 D17003_CTCF_R4 220 + diff -r 3f0e0d4c15a9 -r 8928e6d1e7ba test-data/replace_text_in_column_in1.txt --- a/test-data/replace_text_in_column_in1.txt Wed Jan 07 11:15:41 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,3 +0,0 @@ -chr7 56632 56652 D17003_CTCF_R6 310 + -chr7 56736 56756 D17003_CTCF_R7 354 + -chr7 56761 56781 D17003_CTCF_R4 220 + diff -r 3f0e0d4c15a9 -r 8928e6d1e7ba test-data/replace_text_in_column_output1.txt --- a/test-data/replace_text_in_column_output1.txt Wed Jan 07 11:15:41 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,3 +0,0 @@ -chr7 56632 56652 R6 310 + -chr7 56736 56756 R7 354 + -chr7 56761 56781 R4 220 + diff -r 3f0e0d4c15a9 -r 8928e6d1e7ba test-data/replace_text_in_column_results1.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/replace_text_in_column_results1.txt Thu Jan 08 09:07:31 2015 -0500 @@ -0,0 +1,3 @@ +chr7 56632 56652 R6 310 + +chr7 56736 56756 R7 354 + +chr7 56761 56781 R4 220 + diff -r 3f0e0d4c15a9 -r 8928e6d1e7ba test-data/replace_text_in_line1.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/replace_text_in_line1.txt Thu Jan 08 09:07:31 2015 -0500 @@ -0,0 +1,3 @@ +chr7 56632 56652 D17003_CTCF_R6 310 + +chr7 56736 56756 D17003_CTCF_R7 354 + +chr7 56761 56781 D17003_CTCF_R4 220 + diff -r 3f0e0d4c15a9 -r 8928e6d1e7ba test-data/replace_text_in_line_in1.txt --- a/test-data/replace_text_in_line_in1.txt Wed Jan 07 11:15:41 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,3 +0,0 @@ -chr7 56632 56652 D17003_CTCF_R6 310 + -chr7 56736 56756 D17003_CTCF_R7 354 + -chr7 56761 56781 D17003_CTCF_R4 220 + diff -r 3f0e0d4c15a9 -r 8928e6d1e7ba test-data/replace_text_in_line_output1.txt --- a/test-data/replace_text_in_line_output1.txt Wed Jan 07 11:15:41 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,3 +0,0 @@ -chr7 56632 56652 D17003_FOOBAR_R6 310 + -chr7 56736 56756 D17003_FOOBAR_R7 354 + -chr7 56761 56781 D17003_FOOBAR_R4 220 + diff -r 3f0e0d4c15a9 -r 8928e6d1e7ba test-data/replace_text_in_line_results1.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/replace_text_in_line_results1.txt Thu Jan 08 09:07:31 2015 -0500 @@ -0,0 +1,3 @@ +chr7 56632 56652 D17003_FOOBAR_R6 310 + +chr7 56736 56756 D17003_FOOBAR_R7 354 + +chr7 56761 56781 D17003_FOOBAR_R4 220 + diff -r 3f0e0d4c15a9 -r 8928e6d1e7ba test-data/sed1.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sed1.txt Thu Jan 08 09:07:31 2015 -0500 @@ -0,0 +1,4 @@ +This is a header line +Lorem ipsum dolor foo sit amet foo, +consectetur adipiscing elit. +Nam foo ut nulla non neque faucibus commodo diff -r 3f0e0d4c15a9 -r 8928e6d1e7ba test-data/sed_results1.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sed_results1.txt Thu Jan 08 09:07:31 2015 -0500 @@ -0,0 +1,3 @@ +Lorem ipsum dolor bar sit amet foo, +consectetur adipiscing elit. +Nam bar ut nulla non neque faucibus commodo diff -r 3f0e0d4c15a9 -r 8928e6d1e7ba test-data/sed_results2.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sed_results2.txt Thu Jan 08 09:07:31 2015 -0500 @@ -0,0 +1,2 @@ +Lorem ipsum dolor baz sit amet baz, +Nam baz ut nulla non neque faucibus commodo diff -r 3f0e0d4c15a9 -r 8928e6d1e7ba test-data/sort1.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sort1.bed Thu Jan 08 09:07:31 2015 -0500 @@ -0,0 +1,32 @@ +# comment 1 \n\n''" again +# comment 2 **}"''' special +# comment 3 @n/n""" characters +chr6 108298214 108386086 NM_007214 0 - 108299600 108385906 0 21 1530,105,99,102,159,174,60,83,148,155,93,133,95,109,51,59,62,113,115,100,304, 0,2490,6246,10831,12670,23164,23520,27331,31052,32526,34311,36130,36365,38609,41028,42398,43048,51479,54500,59097,87568, +chr6 108593954 108616704 NM_003269 0 + 108594662 108615360 0 9 733,146,88,236,147,97,150,106,1507, 0,5400,8778,10445,12037,14265,14749,15488,21243, +chr6 108639410 108689143 NM_152827 0 - 108640045 108688818 0 3 741,125,487, 0,2984,49246, +chr6 108722790 108950942 NM_145315 0 + 108722976 108950321 0 13 325,224,52,102,131,100,59,83,71,101,141,114,750, 0,28931,52094,60760,61796,71339,107102,152319,181970,182297,215317,224802,227402, +chr7 113320332 113924911 AK131266 0 + 113862563 113893433 0 20 285,91,178,90,58,75,138,51,201,178,214,105,88,84,77,102,122,70,164,1124, 0,201692,340175,448290,451999,484480,542213,543265,543478,545201,556083,558358,565876,567599,573029,573245,575738,577123,577946,603455, +chr7 116511232 116557294 NM_003391 0 - 116512159 116556994 0 5 1157,265,278,227,383, 0,20384,37843,43339,45679, +chr7 116713967 116902666 NM_000492 0 + 116714099 116901113 0 27 185,111,109,216,90,164,126,247,93,183,192,95,87,724,129,38,251,80,151,228,101,249,156,90,173,106,1754, 0,24290,29071,50936,54313,55285,56585,60137,62053,68678,79501,107776,110390,111971,114967,122863,123569,126711,130556,131618,134650,147559,162475,172879,184725,185496,186945, +chr7 116944658 117107512 AF377960 0 - 116945541 116979926 0 23 1129,102,133,64,186,206,179,188,153,100,87,80,96,276,118,255,151,100,204,1654,225,108,173, 0,7364,8850,10413,13893,14398,17435,24259,24615,35177,35359,45901,47221,49781,56405,66857,69787,72208,73597,80474,100111,150555,162681, +chr2 118288484 118306183 NM_006773 0 + 118288583 118304530 0 14 184,285,144,136,101,200,115,140,162,153,114,57,178,1796, 0,2765,4970,6482,6971,7183,7468,9890,10261,10768,11590,14270,14610,15903, +chr2 118389378 118390700 BC005078 0 - 118390395 118390500 0 1 1322, 0, +chr8 118880786 119193239 NM_000127 0 - 118881131 119192466 0 11 531,172,161,90,96,119,133,120,108,94,1735, 0,5355,7850,13505,19068,20309,23098,30863,36077,37741,310718, +chrX 122719582 122773357 NM_001167 0 + 122745047 122766566 0 7 96,909,100,79,43,201,6985, 0,25433,28421,31040,32533,40295,46790, +chr9 128763240 128783870 NM_174933 0 + 128764156 128783586 0 12 261,118,74,159,76,48,56,63,129,117,127,370, 0,522,875,5630,12374,12603,15040,15175,18961,19191,20037,20260, +chr9 128787362 128789566 NM_014908 0 - 128787519 128789136 0 1 2204, 0, +chr9 128789530 128848928 NM_015354 0 + 128789552 128848511 0 44 54,55,74,85,81,45,93,120,212,115,201,90,66,120,127,153,127,88,77,115,121,67,129,140,107,207,170,70,68,196,78,86,146,182,201,93,159,138,75,228,132,74,130,594, 0,1491,5075,8652,9254,10312,11104,11317,20808,21702,23060,25462,31564,32908,33566,34851,35204,35595,35776,37202,38860,39111,39891,40349,42422,45499,45827,46675,47158,47621,50453,50840,51474,51926,53831,54186,55119,55619,57449,57605,57947,58352,58541,58804, +chr9 128849867 128870133 NM_020145 0 - 128850516 128869987 0 11 757,241,101,90,24,63,93,134,129,142,209, 0,1071,1736,2085,2635,4201,6376,6736,13056,14247,20057, +chr5 131170738 131357870 AF099740 0 - 131311206 131357817 0 31 112,124,120,81,65,40,120,129,61,88,94,79,72,102,144,117,89,73,96,135,135,78,74,52,33,179,100,102,65,115,248, 0,11593,44117,47607,104668,109739,114675,126366,135488,137518,138009,140437,152389,153373,155388,159269,160793,162981,164403,165577,166119,167611,169501,178260,179675,180901,181658,182260,182953,183706,186884, +chr5 131424245 131426795 NM_000588 0 + 131424298 131426383 0 5 215,42,90,42,535, 0,313,1658,1872,2015, +chr5 131556201 131590458 NM_004199 0 - 131556601 131582218 0 15 471,97,69,66,54,100,71,177,194,240,138,152,97,100,170, 0,2316,2802,5596,6269,11138,11472,15098,16528,17674,21306,24587,25142,25935,34087, +chr5 131621285 131637046 NM_003687 0 + 131621326 131635821 0 7 134,152,82,179,164,118,1430, 0,4915,8770,13221,13609,14097,14331, +chr1 147962006 147975713 NM_005997 0 - 147962192 147975670 0 6 574,145,177,115,153,160, 0,1543,7859,9048,9340,13547, +chr1 147984101 148035079 BC007833 0 + 147984545 148033414 0 14 529,32,81,131,118,153,300,206,84,49,85,130,46,1668, 0,25695,28767,33118,33695,33998,35644,38005,39629,40577,41402,43885,48367,49310, +chr1 148077485 148111797 NM_002651 0 - 148078400 148111728 0 12 1097,121,133,266,124,105,110,228,228,45,937,77, 0,2081,2472,6871,9907,10257,11604,14199,15637,18274,23636,34235, +chr1 148185113 148187485 NM_002796 0 + 148185136 148187378 0 7 163,207,147,82,117,89,120, 0,416,877,1199,1674,1977,2252, +chrX 152648233 152662158 NM_000425 0 - 152648964 152662138 0 28 963,12,73,135,156,120,174,123,202,116,223,71,198,111,125,157,167,112,144,132,185,112,171,123,203,106,11,100, 0,1436,1545,1951,2390,2653,2889,3156,3367,3772,4717,5122,5424,5868,6066,6370,6629,6909,7588,7871,8124,8456,8858,9125,10220,10660,11296,13825, +chrX 152691216 152693487 NM_000054 0 + 152691446 152693029 0 3 255,885,664, 0,616,1607, +chrX 152693677 152712545 NM_001666 0 - 152694029 152712503 0 22 586,100,93,184,74,234,106,135,78,61,103,28,85,192,102,222,129,183,63,163,205,109, 0,1693,2066,2364,2635,2794,3129,3323,3545,3752,5323,5647,5841,6032,6401,11455,11778,13249,13719,13987,14227,18759, +chr2 220108603 220116964 NM_001927 0 + 220108689 220116217 0 9 664,61,96,162,126,221,44,83,789, 0,1718,1874,2118,2451,2963,5400,7286,7572, +chr2 220229182 220233943 NM_024536 0 - 220229609 220233765 0 4 1687,180,574,492, 0,1990,2660,4269, diff -r 3f0e0d4c15a9 -r 8928e6d1e7ba test-data/sort2.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sort2.bed Thu Jan 08 09:07:31 2015 -0500 @@ -0,0 +1,6 @@ +chr10 100 200 feature1 100.01 + +chr20 800 900 feature2 1.1 + +chr2 500 600 feature3 1000.1 + +chr1 300 400 feature4 1.1e-05 + +chr21 300 500 feature5 1.1e2 + +chr15 700 800 feature6 1.1e4 + diff -r 3f0e0d4c15a9 -r 8928e6d1e7ba test-data/sort_in1.bed --- a/test-data/sort_in1.bed Wed Jan 07 11:15:41 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,32 +0,0 @@ -# comment 1 \n\n''" again -# comment 2 **}"''' special -# comment 3 @n/n""" characters -chr6 108298214 108386086 NM_007214 0 - 108299600 108385906 0 21 1530,105,99,102,159,174,60,83,148,155,93,133,95,109,51,59,62,113,115,100,304, 0,2490,6246,10831,12670,23164,23520,27331,31052,32526,34311,36130,36365,38609,41028,42398,43048,51479,54500,59097,87568, -chr6 108593954 108616704 NM_003269 0 + 108594662 108615360 0 9 733,146,88,236,147,97,150,106,1507, 0,5400,8778,10445,12037,14265,14749,15488,21243, -chr6 108639410 108689143 NM_152827 0 - 108640045 108688818 0 3 741,125,487, 0,2984,49246, -chr6 108722790 108950942 NM_145315 0 + 108722976 108950321 0 13 325,224,52,102,131,100,59,83,71,101,141,114,750, 0,28931,52094,60760,61796,71339,107102,152319,181970,182297,215317,224802,227402, -chr7 113320332 113924911 AK131266 0 + 113862563 113893433 0 20 285,91,178,90,58,75,138,51,201,178,214,105,88,84,77,102,122,70,164,1124, 0,201692,340175,448290,451999,484480,542213,543265,543478,545201,556083,558358,565876,567599,573029,573245,575738,577123,577946,603455, -chr7 116511232 116557294 NM_003391 0 - 116512159 116556994 0 5 1157,265,278,227,383, 0,20384,37843,43339,45679, -chr7 116713967 116902666 NM_000492 0 + 116714099 116901113 0 27 185,111,109,216,90,164,126,247,93,183,192,95,87,724,129,38,251,80,151,228,101,249,156,90,173,106,1754, 0,24290,29071,50936,54313,55285,56585,60137,62053,68678,79501,107776,110390,111971,114967,122863,123569,126711,130556,131618,134650,147559,162475,172879,184725,185496,186945, -chr7 116944658 117107512 AF377960 0 - 116945541 116979926 0 23 1129,102,133,64,186,206,179,188,153,100,87,80,96,276,118,255,151,100,204,1654,225,108,173, 0,7364,8850,10413,13893,14398,17435,24259,24615,35177,35359,45901,47221,49781,56405,66857,69787,72208,73597,80474,100111,150555,162681, -chr2 118288484 118306183 NM_006773 0 + 118288583 118304530 0 14 184,285,144,136,101,200,115,140,162,153,114,57,178,1796, 0,2765,4970,6482,6971,7183,7468,9890,10261,10768,11590,14270,14610,15903, -chr2 118389378 118390700 BC005078 0 - 118390395 118390500 0 1 1322, 0, -chr8 118880786 119193239 NM_000127 0 - 118881131 119192466 0 11 531,172,161,90,96,119,133,120,108,94,1735, 0,5355,7850,13505,19068,20309,23098,30863,36077,37741,310718, -chrX 122719582 122773357 NM_001167 0 + 122745047 122766566 0 7 96,909,100,79,43,201,6985, 0,25433,28421,31040,32533,40295,46790, -chr9 128763240 128783870 NM_174933 0 + 128764156 128783586 0 12 261,118,74,159,76,48,56,63,129,117,127,370, 0,522,875,5630,12374,12603,15040,15175,18961,19191,20037,20260, -chr9 128787362 128789566 NM_014908 0 - 128787519 128789136 0 1 2204, 0, -chr9 128789530 128848928 NM_015354 0 + 128789552 128848511 0 44 54,55,74,85,81,45,93,120,212,115,201,90,66,120,127,153,127,88,77,115,121,67,129,140,107,207,170,70,68,196,78,86,146,182,201,93,159,138,75,228,132,74,130,594, 0,1491,5075,8652,9254,10312,11104,11317,20808,21702,23060,25462,31564,32908,33566,34851,35204,35595,35776,37202,38860,39111,39891,40349,42422,45499,45827,46675,47158,47621,50453,50840,51474,51926,53831,54186,55119,55619,57449,57605,57947,58352,58541,58804, -chr9 128849867 128870133 NM_020145 0 - 128850516 128869987 0 11 757,241,101,90,24,63,93,134,129,142,209, 0,1071,1736,2085,2635,4201,6376,6736,13056,14247,20057, -chr5 131170738 131357870 AF099740 0 - 131311206 131357817 0 31 112,124,120,81,65,40,120,129,61,88,94,79,72,102,144,117,89,73,96,135,135,78,74,52,33,179,100,102,65,115,248, 0,11593,44117,47607,104668,109739,114675,126366,135488,137518,138009,140437,152389,153373,155388,159269,160793,162981,164403,165577,166119,167611,169501,178260,179675,180901,181658,182260,182953,183706,186884, -chr5 131424245 131426795 NM_000588 0 + 131424298 131426383 0 5 215,42,90,42,535, 0,313,1658,1872,2015, -chr5 131556201 131590458 NM_004199 0 - 131556601 131582218 0 15 471,97,69,66,54,100,71,177,194,240,138,152,97,100,170, 0,2316,2802,5596,6269,11138,11472,15098,16528,17674,21306,24587,25142,25935,34087, -chr5 131621285 131637046 NM_003687 0 + 131621326 131635821 0 7 134,152,82,179,164,118,1430, 0,4915,8770,13221,13609,14097,14331, -chr1 147962006 147975713 NM_005997 0 - 147962192 147975670 0 6 574,145,177,115,153,160, 0,1543,7859,9048,9340,13547, -chr1 147984101 148035079 BC007833 0 + 147984545 148033414 0 14 529,32,81,131,118,153,300,206,84,49,85,130,46,1668, 0,25695,28767,33118,33695,33998,35644,38005,39629,40577,41402,43885,48367,49310, -chr1 148077485 148111797 NM_002651 0 - 148078400 148111728 0 12 1097,121,133,266,124,105,110,228,228,45,937,77, 0,2081,2472,6871,9907,10257,11604,14199,15637,18274,23636,34235, -chr1 148185113 148187485 NM_002796 0 + 148185136 148187378 0 7 163,207,147,82,117,89,120, 0,416,877,1199,1674,1977,2252, -chrX 152648233 152662158 NM_000425 0 - 152648964 152662138 0 28 963,12,73,135,156,120,174,123,202,116,223,71,198,111,125,157,167,112,144,132,185,112,171,123,203,106,11,100, 0,1436,1545,1951,2390,2653,2889,3156,3367,3772,4717,5122,5424,5868,6066,6370,6629,6909,7588,7871,8124,8456,8858,9125,10220,10660,11296,13825, -chrX 152691216 152693487 NM_000054 0 + 152691446 152693029 0 3 255,885,664, 0,616,1607, -chrX 152693677 152712545 NM_001666 0 - 152694029 152712503 0 22 586,100,93,184,74,234,106,135,78,61,103,28,85,192,102,222,129,183,63,163,205,109, 0,1693,2066,2364,2635,2794,3129,3323,3545,3752,5323,5647,5841,6032,6401,11455,11778,13249,13719,13987,14227,18759, -chr2 220108603 220116964 NM_001927 0 + 220108689 220116217 0 9 664,61,96,162,126,221,44,83,789, 0,1718,1874,2118,2451,2963,5400,7286,7572, -chr2 220229182 220233943 NM_024536 0 - 220229609 220233765 0 4 1687,180,574,492, 0,1990,2660,4269, diff -r 3f0e0d4c15a9 -r 8928e6d1e7ba test-data/sort_in2.bed --- a/test-data/sort_in2.bed Wed Jan 07 11:15:41 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,6 +0,0 @@ -chr10 100 200 feature1 100.01 + -chr20 800 900 feature2 1.1 + -chr2 500 600 feature3 1000.1 + -chr1 300 400 feature4 1.1e-05 + -chr21 300 500 feature5 1.1e2 + -chr15 700 800 feature6 1.1e4 + diff -r 3f0e0d4c15a9 -r 8928e6d1e7ba test-data/sort_result3.bed --- a/test-data/sort_result3.bed Wed Jan 07 11:15:41 2015 -0500 +++ b/test-data/sort_result3.bed Thu Jan 08 09:07:31 2015 -0500 @@ -1,6 +1,6 @@ +chr1 300 400 feature4 1.1e-05 + chr20 800 900 feature2 1.1 + -chr1 300 400 feature4 1.1e-05 + +chr10 100 200 feature1 100.01 + chr21 300 500 feature5 1.1e2 + +chr2 500 600 feature3 1000.1 + chr15 700 800 feature6 1.1e4 + -chr10 100 200 feature1 100.01 + -chr2 500 600 feature3 1000.1 + diff -r 3f0e0d4c15a9 -r 8928e6d1e7ba test-data/tac_result1.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tac_result1.txt Thu Jan 08 09:07:31 2015 -0500 @@ -0,0 +1,65 @@ +chrX 152694029 152694263 CCDS14736.1_cds_0_0_chrX_152694030_r 0 - +chrX 152691446 152691471 CCDS14735.1_cds_0_0_chrX_152691447_f 0 + +chrX 152648964 152649196 CCDS14733.1_cds_0_0_chrX_152648965_r 0 - +chrX 122745047 122745924 CCDS14606.1_cds_0_0_chrX_122745048_f 0 + +chr9 128937229 128937445 CCDS6919.1_cds_0_0_chr9_128937230_r 0 - +chr9 128882427 128882523 CCDS6917.1_cds_0_0_chr9_128882428_f 0 + +chr9 128787519 128789136 CCDS6915.1_cds_0_0_chr9_128787520_r 0 - +chr9 128764156 128764189 CCDS6914.1_cds_0_0_chr9_128764157_f 0 + +chr8 118881131 118881317 CCDS6324.1_cds_0_0_chr8_118881132_r 0 - +chr7 116945541 116945787 CCDS5774.1_cds_0_0_chr7_116945542_r 0 - +chr7 116714099 116714152 CCDS5773.1_cds_0_0_chr7_116714100_f 0 + +chr7 116512159 116512389 CCDS5771.1_cds_0_0_chr7_116512160_r 0 - +chr7 113660517 113660685 CCDS5760.1_cds_0_0_chr7_113660518_f 0 + +chr6 108722976 108723115 CCDS5067.1_cds_0_0_chr6_108722977_f 0 + +chr6 108640045 108640151 CCDS5064.1_cds_0_0_chr6_108640046_r 0 - +chr6 108594662 108594687 CCDS5063.1_cds_0_0_chr6_108594663_f 0 + +chr6 108299600 108299744 CCDS5061.1_cds_0_0_chr6_108299601_r 0 - +chr5 131847541 131847666 CCDS4155.1_cds_0_0_chr5_131847542_r 0 - +chr5 131621326 131621419 CCDS4152.1_cds_0_0_chr5_131621327_f 0 + +chr5 131556601 131556672 CCDS4151.1_cds_0_0_chr5_131556602_r 0 - +chr5 131424298 131424460 CCDS4149.1_cds_0_0_chr5_131424299_f 0 + +chr22 30939054 30939266 CCDS13903.1_cds_0_0_chr22_30939055_r 0 - +chr22 30665273 30665360 CCDS13901.1_cds_0_0_chr22_30665274_f 0 + +chr22 30160419 30160661 CCDS13898.1_cds_0_0_chr22_30160420_r 0 - +chr22 30120223 30120265 CCDS13897.1_cds_0_0_chr22_30120224_f 0 + +chr21 33744994 33745040 CCDS13625.1_cds_0_0_chr21_33744995_r 0 - +chr21 33321040 33322012 CCDS13620.1_cds_0_0_chr21_33321041_f 0 + +chr21 32869641 32870022 CCDS13615.1_cds_0_0_chr21_32869642_r 0 - +chr21 32707032 32707192 CCDS13614.1_cds_0_0_chr21_32707033_f 0 + +chr20 33593260 33593348 CCDS13257.1_cds_0_0_chr20_33593261_f 0 + +chr20 33579500 33579527 CCDS13256.1_cds_0_0_chr20_33579501_r 0 - +chr20 33513606 33513792 CCDS13255.1_cds_0_0_chr20_33513607_f 0 + +chr20 33330413 33330423 CCDS13249.1_cds_0_0_chr20_33330414_r 0 - +chr2 220229609 220230869 CCDS2443.1_cds_0_0_chr2_220229610_r 0 - +chr2 220190202 220190242 CCDS2441.1_cds_0_0_chr2_220190203_f 0 + +chr2 118394148 118394202 CCDS2121.1_cds_0_0_chr2_118394149_r 0 - +chr2 118288583 118288668 CCDS2120.1_cds_0_0_chr2_118288584_f 0 + +chr19 59302168 59302288 CCDS12878.1_cds_0_0_chr19_59302169_r 0 - +chr19 59297998 59298008 CCDS12877.1_cds_0_0_chr19_59297999_f 0 + +chr19 59236026 59236146 CCDS12872.1_cds_0_0_chr19_59236027_r 0 - +chr19 59068595 59069564 CCDS12866.1_cds_0_0_chr19_59068596_f 0 + +chr18 59600586 59600754 CCDS11988.1_cds_0_0_chr18_59600587_f 0 + +chr18 59455932 59456337 CCDS11986.1_cds_0_0_chr18_59455933_r 0 - +chr18 59406881 59407046 CCDS11985.1_cds_0_0_chr18_59406882_f 0 + +chr18 23786114 23786321 CCDS11891.1_cds_0_0_chr18_23786115_r 0 - +chr16 259268 259383 CCDS10403.1_cds_0_0_chr16_259269_r 0 - +chr16 244413 244681 CCDS10402.1_cds_0_0_chr16_244414_f 0 + +chr16 179963 180135 CCDS10401.1_cds_0_0_chr16_179964_r 0 - +chr16 142908 143003 CCDS10397.1_cds_0_0_chr16_142909_f 0 + +chr15 41826029 41826196 CCDS10101.1_cds_0_0_chr15_41826030_f 0 + +chr15 41679161 41679250 CCDS10098.1_cds_0_0_chr15_41679162_r 0 - +chr15 41673708 41673857 CCDS10097.1_cds_0_0_chr15_41673709_f 0 + +chr15 41486872 41487060 CCDS10096.1_cds_0_0_chr15_41486873_r 0 - +chr14 98710240 98712285 CCDS9949.1_cds_0_0_chr14_98710241_r 0 - +chr13 112381694 112381953 CCDS9526.1_cds_0_0_chr13_112381695_f 0 + +chr12 38440094 38440321 CCDS8736.1_cds_0_0_chr12_38440095_r 0 - +chr11 1812377 1812407 CCDS7726.1_cds_0_0_chr11_1812378_f 0 + +chr11 116211733 116212337 CCDS8378.1_cds_0_0_chr11_116211734_r 0 - +chr11 116206508 116206563 CCDS8377.1_cds_0_0_chr11_116206509_f 0 + +chr11 116124407 116124501 CCDS8374.1_cds_0_0_chr11_116124408_r 0 - +chr10 55251623 55253124 CCDS7248.1_cds_0_0_chr10_55251624_r 0 - +chr1 148185136 148185276 CCDS996.1_cds_0_0_chr1_148185137_f 0 + +chr1 148078400 148078582 CCDS993.1_cds_0_0_chr1_148078401_r 0 - +chr1 147984545 147984630 CCDS990.1_cds_0_0_chr1_147984546_f 0 + +chr1 147962192 147962580 CCDS989.1_cds_0_0_chr1_147962193_r 0 - diff -r 3f0e0d4c15a9 -r 8928e6d1e7ba test-data/tac_result2.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tac_result2.txt Thu Jan 08 09:07:31 2015 -0500 @@ -0,0 +1,66 @@ + + +chrX 152694029 152694263 CCDS14736.1_cds_0_0_chrX_152694030_r 0 - +chrX 152691446 152691471 CCDS14735.1_cds_0_0_chrX_152691447_f 0 + +chrX 152648964 152649196 CCDS14733.1_cds_0_0_chrX_152648965_r 0 - +chrX 122745047 122745924 CCDS14606.1_cds_0_0_chrX_122745048_f 0 + +chr9 128937229 128937445 CCDS6919.1_cds_0_0_chr9_128937230_r 0 - +chr9 128882427 128882523 CCDS6917.1_cds_0_0_chr9_128882428_f 0 + +chr9 128787519 128789136 CCDS6915.1_cds_0_0_chr9_128787520_r 0 - +chr9 128764156 128764189 CCDS6914.1_cds_0_0_chr9_128764157_f 0 + +chr8 118881131 118881317 CCDS6324.1_cds_0_0_chr8_118881132_r 0 - +chr7 116945541 116945787 CCDS5774.1_cds_0_0_chr7_116945542_r 0 - +chr7 116714099 116714152 CCDS5773.1_cds_0_0_chr7_116714100_f 0 + +chr7 116512159 116512389 CCDS5771.1_cds_0_0_chr7_116512160_r 0 - +chr7 113660517 113660685 CCDS5760.1_cds_0_0_chr7_113660518_f 0 + +chr6 108722976 108723115 CCDS5067.1_cds_0_0_chr6_108722977_f 0 + +chr6 108640045 108640151 CCDS5064.1_cds_0_0_chr6_108640046_r 0 - +chr6 108594662 108594687 CCDS5063.1_cds_0_0_chr6_108594663_f 0 + +chr6 108299600 108299744 CCDS5061.1_cds_0_0_chr6_108299601_r 0 - +chr5 131847541 131847666 CCDS4155.1_cds_0_0_chr5_131847542_r 0 - +chr5 131621326 131621419 CCDS4152.1_cds_0_0_chr5_131621327_f 0 + +chr5 131556601 131556672 CCDS4151.1_cds_0_0_chr5_131556602_r 0 - +chr5 131424298 131424460 CCDS4149.1_cds_0_0_chr5_131424299_f 0 + +chr22 30939054 30939266 CCDS13903.1_cds_0_0_chr22_30939055_r 0 - +chr22 30665273 30665360 CCDS13901.1_cds_0_0_chr22_30665274_f 0 + +chr22 30160419 30160661 CCDS13898.1_cds_0_0_chr22_30160420_r 0 - +chr22 30120223 30120265 CCDS13897.1_cds_0_0_chr22_30120224_f 0 + +chr21 33744994 33745040 CCDS13625.1_cds_0_0_chr21_33744995_r 0 - +chr21 33321040 33322012 CCDS13620.1_cds_0_0_chr21_33321041_f 0 + +chr21 32869641 32870022 CCDS13615.1_cds_0_0_chr21_32869642_r 0 - +chr21 32707032 32707192 CCDS13614.1_cds_0_0_chr21_32707033_f 0 + +chr20 33593260 33593348 CCDS13257.1_cds_0_0_chr20_33593261_f 0 + +chr20 33579500 33579527 CCDS13256.1_cds_0_0_chr20_33579501_r 0 - +chr20 33513606 33513792 CCDS13255.1_cds_0_0_chr20_33513607_f 0 + +chr20 33330413 33330423 CCDS13249.1_cds_0_0_chr20_33330414_r 0 - +chr2 220229609 220230869 CCDS2443.1_cds_0_0_chr2_220229610_r 0 - +chr2 220190202 220190242 CCDS2441.1_cds_0_0_chr2_220190203_f 0 + +chr2 118394148 118394202 CCDS2121.1_cds_0_0_chr2_118394149_r 0 - +chr2 118288583 118288668 CCDS2120.1_cds_0_0_chr2_118288584_f 0 + +chr19 59302168 59302288 CCDS12878.1_cds_0_0_chr19_59302169_r 0 - +chr19 59297998 59298008 CCDS12877.1_cds_0_0_chr19_59297999_f 0 + +chr19 59236026 59236146 CCDS12872.1_cds_0_0_chr19_59236027_r 0 - +chr19 59068595 59069564 CCDS12866.1_cds_0_0_chr19_59068596_f 0 + +chr18 59600586 59600754 CCDS11988.1_cds_0_0_chr18_59600587_f 0 + +chr18 59455932 59456337 CCDS11986.1_cds_0_0_chr18_59455933_r 0 - +chr18 59406881 59407046 CCDS11985.1_cds_0_0_chr18_59406882_f 0 + +chr18 23786114 23786321 CCDS11891.1_cds_0_0_chr18_23786115_r 0 - +chr16 259268 259383 CCDS10403.1_cds_0_0_chr16_259269_r 0 - +chr16 244413 244681 CCDS10402.1_cds_0_0_chr16_244414_f 0 + +chr16 179963 180135 CCDS10401.1_cds_0_0_chr16_179964_r 0 - +chr16 142908 143003 CCDS10397.1_cds_0_0_chr16_142909_f 0 + +chr15 41826029 41826196 CCDS10101.1_cds_0_0_chr15_41826030_f 0 + +chr15 41679161 41679250 CCDS10098.1_cds_0_0_chr15_41679162_r 0 - +chr15 41673708 41673857 CCDS10097.1_cds_0_0_chr15_41673709_f 0 + +chr15 41486872 41487060 CCDS10096.1_cds_0_0_chr15_41486873_r 0 - +chr14 98710240 98712285 CCDS9949.1_cds_0_0_chr14_98710241_r 0 - +chr13 112381694 112381953 CCDS9526.1_cds_0_0_chr13_112381695_f 0 + +chr12 38440094 38440321 CCDS8736.1_cds_0_0_chr12_38440095_r 0 - +chr11 1812377 1812407 CCDS7726.1_cds_0_0_chr11_1812378_f 0 + +chr11 116211733 116212337 CCDS8378.1_cds_0_0_chr11_116211734_r 0 - +chr11 116206508 116206563 CCDS8377.1_cds_0_0_chr11_116206509_f 0 + +chr11 116124407 116124501 CCDS8374.1_cds_0_0_chr11_116124408_r 0 - +chr10 55251623 55253124 CCDS7248.1_cds_0_0_chr10_55251624_r 0 - +chr1 148185136 148185276 CCDS996.1_cds_0_0_chr1_148185137_f 0 + +chr1 148078400 148078582 CCDS993.1_cds_0_0_chr1_148078401_r 0 - +chr1 147984545 147984630 CCDS990.1_cds_0_0_chr1_147984546_f 0 +chr1 147962192 147962580 CCDS989.1_cds_0_0_chr1_147962193_r 0 - \ No newline at end of file diff -r 3f0e0d4c15a9 -r 8928e6d1e7ba test-data/unix_awk_input1.txt --- a/test-data/unix_awk_input1.txt Wed Jan 07 11:15:41 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,10 +0,0 @@ -chr10 0.4 -chr1 1.4 -chrM 3e-1 -chr2 1.1e2 -chr15 3.14e-2 -chr15 0.0314 -chr4 0.1 -chr20 0.9 -chr22 +1.3 -chrX -0.3 diff -r 3f0e0d4c15a9 -r 8928e6d1e7ba test-data/unix_awk_output1.txt --- a/test-data/unix_awk_output1.txt Wed Jan 07 11:15:41 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -12.6 chr1 -990 chr2 -8.1 chr20 -11.7 chr22 diff -r 3f0e0d4c15a9 -r 8928e6d1e7ba test-data/unix_cut_input1.txt --- a/test-data/unix_cut_input1.txt Wed Jan 07 11:15:41 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -fruit color weight price -apple red 1.4 0.4 -orange orange 1.1 0.2 -banana yellow 0.9 0.35 diff -r 3f0e0d4c15a9 -r 8928e6d1e7ba test-data/unix_cut_output1.txt --- a/test-data/unix_cut_output1.txt Wed Jan 07 11:15:41 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -fruit weight price -apple 1.4 0.4 -orange 1.1 0.2 -banana 0.9 0.35 diff -r 3f0e0d4c15a9 -r 8928e6d1e7ba test-data/unix_grep_input1.txt --- a/test-data/unix_grep_input1.txt Wed Jan 07 11:15:41 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,152 +0,0 @@ ->FC0000042:5:1:220:1502 -AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA ->FC0000042:5:1:34:1398 -GATCTCAGTCCACCGCTGGGATTAACCTTGCCCCCC ->FC0000042:5:1:164:1396 -TATCTTATAGATATTTCCCTCTATACTAGTGACCCC ->FC0000042:5:1:333:925 -GAGCTTATAGCTTGTTATATACGTCAACCCCCCCCC ->FC0000042:5:1:204:1476 -GTACTTATATAGATACAAAATATGTATAGGATTGTC ->FC0000042:5:1:119:1511 -GATCTGCATGACCTGGGATTTGTTGGACCCCCCCCC ->FC0000042:5:1:202:1487 -CATGTATAGTCTCCAGTCTATACAACAACCCCCCCC ->FC0000042:5:1:182:1434 -GCTATAGAAATGTTAACATCGAATGTACATTATAAC ->FC0000042:5:1:627:866 -AATATAGATATGGGACAAAACACATTTAGACCCCCC ->FC0000042:5:1:24:1357 -GATATAATATCAATATCAATCCACGCTTGTTCCCCC ->FC0000042:5:1:187:1492 -TATAGAAGCAGAAGAAACAACCTACTTTCACATGTT ->FC0000042:5:1:45:1344 -CAGCTAACAATCAAGCGTTACAGATTAGCCCCCCCC ->FC0000042:5:1:87:1299 -AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA ->FC0000042:5:1:206:1341 -GATATATAGCAGTGACCACCTCTAAGCCCCCCCCCC ->FC0000042:5:1:144:929 -GCCCTGGCATATTGTCAATATCTTTAAACCCCCCCC ->FC0000042:5:1:662:820 -TGTCTTTTCGATTTTTTTCTTTGCGTCACCCCCCCC ->FC0000042:5:1:53:1507 -GACCTCACTGTGGCATGAATCATACATTCCCCCCCC ->FC0000042:5:1:182:1502 -AATGCTTGGCAAAGCTCAACTTCGTTGCCCCCCCCC ->FC0000042:5:1:194:1423 -GATCCTATAGGTCTCGATTGGTCTTTTATTCTTTTT ->FC0000042:5:1:35:1444 -GCTATAGCACGGCATAGTGCGATACTAGTACCCCCC ->FC0000042:5:1:667:872 -GACTATAGGCGGAATGATAATGTCAAATAAGTAGTT ->FC0000042:5:1:147:1438 -GATCAAGGAGACTAGGGAGGTAGGAGTTACTCCCCC ->FC0000042:5:1:467:510 -GAACCACTATAGTGACATGGAACACGCGTGAACCCC ->FC0000042:5:1:1553:1707 -TATAGTTACCCTACTGGGCCGACGATTCCCTTACGA ->FC0000042:5:1:207:964 -AATCTATAGATTTTTCTATTATTGTGTCCTCACCCC ->FC0000042:5:1:169:1468 -GCTCTATAGTTCGAGTTACCAAACTCTTCCCCCCCC ->FC0000042:5:1:42:1465 -GCTCTTTAGGTTTGAACCTGTAGACTTGAGGGGCAT ->FC0000042:5:1:55:1331 -GAACTTGCGTAACGTACAAAAATGCAAGCAAAAAGT ->FC0000042:5:1:175:1501 -GCTCTGTTAATCTAGAAAATGTGTCTCCCCCCCCCC ->FC0000042:5:1:221:1465 -TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT ->FC0000042:5:1:196:1450 -AATATAGTCTATCCAACAAGATGTAACCCCCCCCCC ->FC0000042:5:1:86:1413 -TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT ->FC0000042:5:1:453:514 -GATATCTTCGTTTTATATTGAAACTGGCCCCCCCCC ->FC0000042:5:1:150:1415 -TATAGGGCCCTGTATGGTTGCTTGACTAGGGGCTGC ->FC0000042:5:1:191:1475 -GATCCATCCCAATCTCTACGATTGAAAGCATCGGGA ->FC0000042:5:1:26:1407 -GTTATAGAGGCGGGAAGGTGAGAATGCCCCCCCCCC ->FC0000042:5:1:107:1407 -AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA ->FC0000042:5:1:388:780 -GATCTATAGCTTCTTTAGCTTGGAAACTGGTCAGCC ->FC0000042:5:1:223:1535 -AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA ->FC0000042:5:1:145:783 -AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA ->FC0000042:5:1:449:876 -GACCATCAATCAGGTGGAAAGCAGGGCCCCCCCCCC ->FC0000042:5:1:212:1325 -TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT ->FC0000042:5:1:194:1485 -GAACCGAATCCAACCTGTTTCATTCCTCAGATCCCC ->FC0000042:5:1:507:494 -GATCTTATAGAATTTTTGACAACATAAGTTACCCCC ->FC0000042:5:1:416:938 -AATCGTATAGCTCGGGCCGGATACTAGTACACCCCC ->FC0000042:5:1:633:480 -GAGCTGTGTGCATCTGTCCTGAGAGAGGCAAGATTT ->FC0000042:5:1:53:1443 -GTAATGTTATAGCTAGGATTTTGGAGTTTGGTCCTC ->FC0000042:5:1:45:915 -GTATAGCAGCCTAATAAGGAGCTGGGGACCCCCCCC ->FC0000042:5:1:39:1343 -GTTCTATTTTCGATAAAACTGAACCACCCCCCCCCC ->FC0000042:5:1:46:1501 -GATATAGTGGATAACTAATGCTCCCCCAGAACTGTT ->FC0000042:5:1:187:1507 -GAACTAATCCTGATTTATACAACGGCTCCCCCCCCC ->FC0000042:5:1:91:1364 -AATTTATAGCCACTCTAATTCCGTTTGGTTCCCCCC ->FC0000042:5:1:1542:1751 -AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA ->FC0000042:5:1:146:886 -GATCTACGATGTACCTTACGCCTCCGAGCATCCCCC ->FC0000042:5:1:615:861 -GATCTACATTATAGATAATGAAGTTCCATTTCCCCC ->FC0000042:5:1:52:792 -GATGTGGTATAGAGAGCAATTCGTTGGTTTTGCCCC ->FC0000042:5:1:153:1433 -GGTCTTTCTATAGAACGGAACGATATATTTTTCCCC ->FC0000042:5:1:540:800 -GAGCGAAAGTGATAGATGGAGGACTATATCTGCCCC ->FC0000042:5:1:160:1344 -GGTGTACTATAGCTATTAAGTCCAATCATGATAATA ->FC0000042:5:1:544:413 -GATCTCTGGAAAATATAAACCGGTGACCCCCCCCCC ->FC0000042:5:1:579:895 -AGTCTCGAATCAATGTATTTCATCGTGGTAATCCCC ->FC0000042:5:1:468:495 -TATTGATGCTCCCTGCCTGAAAGATACCCCCCCCCC ->FC0000042:5:1:383:831 -CTTCATGAATCTACTGTTGGCGTTTATTTTATCTGG ->FC0000042:5:1:112:1416 -TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT ->FC0000042:5:1:37:1299 -GATCGTGAGCTCTGTACCGGAAGTTCGTGGCTGCCA ->FC0000042:5:1:205:780 -TATAGTGTTCCACAAAGACTAGGTAACGCTTCATTT ->FC0000042:5:1:33:702 -GAACGGACTATAGCCGGTATCCAAACATAAATGTTC ->FC0000042:5:1:54:1019 -AATCGCAGCATTCTGACACACAGGTTTCGGATGTAC ->FC0000042:5:1:587:867 -TATCTAATGTCATATTTTCAGACAAATTACTAGAAA ->FC0000042:5:1:319:990 -GATTTGTAAATTACTTCGAACATAGAAGTTCCCCCC ->FC0000042:5:1:453:829 -GAACTTACGGCATTAAGTTTAATCTTCAGCCACCCC ->FC0000042:5:1:159:1470 -GATCTGATAGTGTTGCGACGTAAATAAGTCCCCCCC ->FC0000042:5:1:487:820 -GATCTCGCAGGGATCAGTTATCCAGGTATTCCCCCC ->FC0000042:5:1:48:371 -AATCTATAATCTTTACCCGAGTTTAAGTCCCCCCCC ->FC0000042:5:1:1346:1739 -GATATAGGTTATACGTTTTTAGTCTTAGAGAAGTTT ->FC0000042:5:1:661:459 -GATCTGCTTTAACGATTGAGGACGATGCCCCCCCCC diff -r 3f0e0d4c15a9 -r 8928e6d1e7ba test-data/unix_grep_output1.txt --- a/test-data/unix_grep_output1.txt Wed Jan 07 11:15:41 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,14 +0,0 @@ ->FC0000042:5:1:182:1434 -GCTATAGAAATGTTAACATCGAATGTACATTATAAC ->FC0000042:5:1:45:1344 -CAGCTAACAATCAAGCGTTACAGATTAGCCCCCCCC ->FC0000042:5:1:55:1331 -GAACTTGCGTAACGTACAAAAATGCAAGCAAAAAGT ->FC0000042:5:1:175:1501 -GCTCTGTTAATCTAGAAAATGTGTCTCCCCCCCCCC ->FC0000042:5:1:416:938 -AATCGTATAGCTCGGGCCGGATACTAGTACACCCCC ->FC0000042:5:1:46:1501 -GATATAGTGGATAACTAATGCTCCCCCAGAACTGTT ->FC0000042:5:1:33:702 -GAACGGACTATAGCCGGTATCCAAACATAAATGTTC diff -r 3f0e0d4c15a9 -r 8928e6d1e7ba test-data/unix_grep_output2.html --- a/test-data/unix_grep_output2.html Wed Jan 07 11:15:41 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,307 +0,0 @@ - - - - - - - -

-GCTATAGAAATGTTAACATCGAATGTACATTATAAC
---
-CAGCTAACAATCAAGCGTTACAGATTAGCCCCCCCC
---
-GAACTTGCGTAACGTACAAAAATGCAAGCAAAAAGT
---
-GCTCTGTTAATCTAGAAAATGTGTCTCCCCCCCCCC
---
-AATCGTATAGCTCGGGCCGGATACTAGTACACCCCC
---
-GATATAGTGGATAACTAATGCTCCCCCAGAACTGTT
---
-GAACGGACTATAGCCGGTATCCAAACATAAATGTTC
-

- - diff -r 3f0e0d4c15a9 -r 8928e6d1e7ba test-data/unix_sed_input1.txt --- a/test-data/unix_sed_input1.txt Wed Jan 07 11:15:41 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -This is a header line -Lorem ipsum dolor foo sit amet foo, -consectetur adipiscing elit. -Nam foo ut nulla non neque faucibus commodo diff -r 3f0e0d4c15a9 -r 8928e6d1e7ba test-data/unix_sed_output1.txt --- a/test-data/unix_sed_output1.txt Wed Jan 07 11:15:41 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,3 +0,0 @@ -Lorem ipsum dolor bar sit amet foo, -consectetur adipiscing elit. -Nam bar ut nulla non neque faucibus commodo diff -r 3f0e0d4c15a9 -r 8928e6d1e7ba test-data/unix_sed_output2.txt --- a/test-data/unix_sed_output2.txt Wed Jan 07 11:15:41 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,2 +0,0 @@ -Lorem ipsum dolor baz sit amet baz, -Nam baz ut nulla non neque faucibus commodo diff -r 3f0e0d4c15a9 -r 8928e6d1e7ba test-data/unix_sort_input1.txt --- a/test-data/unix_sort_input1.txt Wed Jan 07 11:15:41 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,11 +0,0 @@ -chrom value -chr10 0.4 -chr1 1.4 -chrM 3e-1 -chr2 1.1e2 -chr15 3.14e-2 -chr15 0.0314 -chr4 0.1 -chr20 0.9 -chr22 +1.3 -chrX -0.3 diff -r 3f0e0d4c15a9 -r 8928e6d1e7ba test-data/unix_sort_input2.txt --- a/test-data/unix_sort_input2.txt Wed Jan 07 11:15:41 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,11 +0,0 @@ -Chrom Value -chr10 0.4 -chr1 1.4 -chrM 3e-1 -chr2 1.1e2 -chr15 3.14e-2 -chr15 0.0314 -chr4 0.1 -chr20 0.9 -chr22 +1.3 -chrX -0.3 diff -r 3f0e0d4c15a9 -r 8928e6d1e7ba test-data/unix_sort_output1.txt --- a/test-data/unix_sort_output1.txt Wed Jan 07 11:15:41 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,11 +0,0 @@ -chrom value -chr2 1.1e2 -chr1 1.4 -chr22 +1.3 -chr20 0.9 -chr10 0.4 -chrM 3e-1 -chr4 0.1 -chr15 0.0314 -chr15 3.14e-2 -chrX -0.3 diff -r 3f0e0d4c15a9 -r 8928e6d1e7ba test-data/unix_sort_output2.txt --- a/test-data/unix_sort_output2.txt Wed Jan 07 11:15:41 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,10 +0,0 @@ -chrom value -chrX -0.3 -chr15 3.14e-2 -chr4 0.1 -chrM 3e-1 -chr10 0.4 -chr20 0.9 -chr22 +1.3 -chr1 1.4 -chr2 1.1e2 diff -r 3f0e0d4c15a9 -r 8928e6d1e7ba test-data/unix_sort_output3.txt --- a/test-data/unix_sort_output3.txt Wed Jan 07 11:15:41 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,11 +0,0 @@ -chrom value -chr1 1.4 -chr2 1.1e2 -chr4 0.1 -chr10 0.4 -chr15 0.0314 -chr15 3.14e-2 -chr20 0.9 -chr22 +1.3 -chrM 3e-1 -chrX -0.3 diff -r 3f0e0d4c15a9 -r 8928e6d1e7ba tool_test_output.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_test_output.html Thu Jan 08 09:07:31 2015 -0500 @@ -0,0 +1,356 @@ + + + + + + + Tool Test Results (powered by Planemo) + + + + + + + + + + + + + + +

+ +

Overview

Tests

The remainder of this contains a description for each test executed to run these jobs.

+ + + + + + + diff -r 3f0e0d4c15a9 -r 8928e6d1e7ba tool_test_output.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_test_output.json Thu Jan 08 09:07:31 2015 -0500 @@ -0,0 +1,1 @@ +{"tests": [{"data": {"status": "success", "inputs": {"token_set_0|line": "freedom"}, "job": {"inputs": {}, "update_time": "2015-01-08T12:53:15.015881", "tool_id": "tp_text_file_with_recurring_lines", "outputs": {"outfile": {"src": "hda", "id": "2891970512fa2d5a"}}, "stdout": "", "command_line": "times=10; yes -- \"freedom\" 2>/dev/null | head -n $times >> /tmp/tmp2u132Ifiles/000/dataset_1.dat;", "exit_code": 0, "state": "ok", "create_time": "2015-01-08T12:53:12.504736", "params": {"token_set": "[{\"__index__\": 0, \"line\": \"freedom\", \"repeat_select\": {\"repeat_select_opts\": \"user\", \"__current_case__\": 0, \"times\": \"10\"}}]", "chromInfo": "\"/home/bag/projects/code/galaxy-central/tool-data/shared/ucsc/chrom/?.len\"", "dbkey": "\"?\""}, "stderr": "", "job_metrics": [], "model_class": "Job", "id": "2891970512fa2d5a"}}, "id": "functional.test_toolbox.TestForTool_tp_text_file_with_recurring_lines.test_tool_000000", "has_data": true}, {"data": {"status": "failure", "inputs": {"token_set_1|line": "war is over", "token_set_0|line": "freedom"}, "output_problems": ["History item different than expected, difference (using diff):\n( /home/bag/projects/code/galaxytools/text_processing/text_processing/test-data/recurring_result2.txt v. /tmp/tmp2u132I/tmp/tmpg7l0Jdrecurring_result2.txt )\n--- local_file\n+++ history_data\n@@ -8,3 +8,13 @@\n freedom\n freedom\n freedom\n+war is over\n+war is over\n+war is over\n+war is over\n+war is over\n+war is over\n+war is over\n+war is over\n+war is over\n+war is over\n"], "job": {"inputs": {}, "update_time": "2015-01-08T12:53:19.516495", "tool_id": "tp_text_file_with_recurring_lines", "outputs": {"outfile": {"src": "hda", "id": "5729865256bc2525"}}, "stdout": "", "command_line": "times=10; yes -- \"freedom\" 2>/dev/null | head -n $times >> /tmp/tmp2u132Ifiles/000/dataset_2.dat; times=10; yes -- \"war is over\" 2>/dev/null | head -n $times >> /tmp/tmp2u132Ifiles/000/dataset_2.dat;", "exit_code": 0, "state": "ok", "create_time": "2015-01-08T12:53:17.104670", "params": {"token_set": "[{\"__index__\": 0, \"line\": \"freedom\", \"repeat_select\": {\"repeat_select_opts\": \"user\", \"__current_case__\": 0, \"times\": \"10\"}}, {\"__index__\": 1, \"line\": \"war is over\", \"repeat_select\": {\"repeat_select_opts\": \"user\", \"__current_case__\": 0, \"times\": \"10\"}}]", "chromInfo": "\"/home/bag/projects/code/galaxy-central/tool-data/shared/ucsc/chrom/?.len\"", "dbkey": "\"?\""}, "stderr": "", "job_metrics": [], "model_class": "Job", "id": "5729865256bc2525"}, "problem_log": "Traceback (most recent call last):\n File \"/usr/lib/python2.7/unittest/case.py\", line 329, in run\n testMethod()\n File \"/home/bag/projects/code/galaxy-central/test/functional/test_toolbox.py\", line 182, in test_tool\n self.do_it( td )\n File \"/home/bag/projects/code/galaxy-central/test/functional/test_toolbox.py\", line 65, in do_it\n raise e\nJobOutputsError: History item different than expected, difference (using diff):\n( /home/bag/projects/code/galaxytools/text_processing/text_processing/test-data/recurring_result2.txt v. /tmp/tmp2u132I/tmp/tmpg7l0Jdrecurring_result2.txt )\n--- local_file\n+++ history_data\n@@ -8,3 +8,13 @@\n freedom\n freedom\n freedom\n+war is over\n+war is over\n+war is over\n+war is over\n+war is over\n+war is over\n+war is over\n+war is over\n+war is over\n+war is over\n\n-------------------- >> begin captured logging << --------------------\nrequests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\ngalaxy.web.framework.webapp: INFO: Session authenticated using Galaxy master api key\nrequests.packages.urllib3.connectionpool: DEBUG: \"GET /api/users?key=test_key HTTP/1.1\" 200 None\nrequests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\ngalaxy.web.framework.webapp: INFO: Session authenticated using Galaxy master api key\nrequests.packages.urllib3.connectionpool: DEBUG: \"POST /api/users/2891970512fa2d5a/api_key HTTP/1.1\" 200 None\nrequests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nrequests.packages.urllib3.connectionpool: DEBUG: \"POST /api/histories HTTP/1.1\" 200 None\nrequests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\ngalaxy.jobs: DEBUG: (2) Working directory for job is: /tmp/tmp2u132I/job_working_directory/000/2\nrequests.packages.urllib3.connectionpool: DEBUG: \"POST /api/tools HTTP/1.1\" 200 None\nrequests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\ngalaxy.jobs.handler: DEBUG: (2) Dispatching to local runner\nrequests.packages.urllib3.connectionpool: DEBUG: \"GET /api/jobs/5729865256bc2525?key=4ae730223dcd94beeb67e4990d1568f0 HTTP/1.1\" 200 None\ngalaxy.jobs: DEBUG: (2) Persisting job destination (destination id: local:///)\ngalaxy.jobs.handler: INFO: (2) Job dispatched\nrequests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nrequests.packages.urllib3.connectionpool: DEBUG: \"GET /api/jobs/5729865256bc2525?key=4ae730223dcd94beeb67e4990d1568f0 HTTP/1.1\" 200 None\ngalaxy.jobs.runners: DEBUG: (2) command is: times=10; yes -- \"freedom\" 2>/dev/null | head -n $times >> /tmp/tmp2u132Ifiles/000/dataset_2.dat; times=10; yes -- \"war is over\" 2>/dev/null | head -n $times >> /tmp/tmp2u132Ifiles/000/dataset_2.dat; return_code=$?; cd /home/bag/projects/code/galaxy-central; /home/bag/projects/code/galaxy-central/set_metadata.sh /tmp/tmp2u132Ifiles /tmp/tmp2u132I/job_working_directory/000/2 . /tmp/tmps7TGPy/functional_tests_wsgi.ini /tmp/tmp2u132I/tmp/tmplMl0my /tmp/tmp2u132I/job_working_directory/000/2/galaxy.json /tmp/tmp2u132I/job_working_directory/000/2/metadata_in_HistoryDatasetAssociation_2_3vVc3k,/tmp/tmp2u132I/job_working_directory/000/2/metadata_kwds_HistoryDatasetAssociation_2_yZP_M2,/tmp/tmp2u132I/job_working_directory/000/2/metadata_out_HistoryDatasetAssociation_2_Xs7G1C,/tmp/tmp2u132I/job_working_directory/000/2/metadata_results_HistoryDatasetAssociation_2_DTBxkX,,/tmp/tmp2u132I/job_working_directory/000/2/metadata_override_HistoryDatasetAssociation_2_nGbyiQ; sh -c \"exit $return_code\"\ngalaxy.jobs.runners.local: DEBUG: (2) executing job script: /tmp/tmp2u132I/job_working_directory/000/2/galaxy_2.sh\ngalaxy.jobs: DEBUG: (2) Persisting job destination (destination id: local:///)\nrequests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\ngalaxy.jobs.runners.local: DEBUG: execution finished: /tmp/tmp2u132I/job_working_directory/000/2/galaxy_2.sh\ngalaxy.datatypes.metadata: DEBUG: loading metadata from file for: HistoryDatasetAssociation 2\ngalaxy.jobs: DEBUG: job 2 ended\nrequests.packages.urllib3.connectionpool: DEBUG: \"GET /api/jobs/5729865256bc2525?key=4ae730223dcd94beeb67e4990d1568f0 HTTP/1.1\" 200 None\nrequests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nrequests.packages.urllib3.connectionpool: DEBUG: \"GET /api/jobs/5729865256bc2525?key=4ae730223dcd94beeb67e4990d1568f0 HTTP/1.1\" 200 None\nrequests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nrequests.packages.urllib3.connectionpool: DEBUG: \"GET /api/histories/5729865256bc2525/contents/5729865256bc2525/display?raw=true&key=4ae730223dcd94beeb67e4990d1568f0 HTTP/1.1\" 200 None\nbase.twilltestcase: DEBUG: keepoutdir: /tmp/tmp2u132I/jobfiles, ofn: /tmp/tmp2u132I/jobfiles/recurring_result2.txt\nbase.twilltestcase: DEBUG: ## GALAXY_TEST_SAVE=/tmp/tmp2u132I/jobfiles. saved /tmp/tmp2u132I/jobfiles/recurring_result2.txt\nbase.twilltestcase: INFO: ## files diff on /home/bag/projects/code/galaxytools/text_processing/text_processing/test-data/recurring_result2.txt and /tmp/tmp2u132I/tmp/tmpg7l0Jdrecurring_result2.txt lines_diff=0, found diff = 10\nrequests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): localhost\nrequests.packages.urllib3.connectionpool: DEBUG: \"GET /api/jobs/5729865256bc2525?full=true&key=4ae730223dcd94beeb67e4990d1568f0 HTTP/1.1\" 200 None\n--------------------- >> end captured logging << ---------------------\n", "problem_type": "functional.test_toolbox.JobOutputsError"}, "id": "functional.test_toolbox.TestForTool_tp_text_file_with_recurring_lines.test_tool_000001", "has_data": true}], "version": "0.1", "summary": {"num_skips": 0, "num_errors": 0, "num_failures": 1, "num_tests": 2}} \ No newline at end of file diff -r 3f0e0d4c15a9 -r 8928e6d1e7ba unfold_column.xml --- a/unfold_column.xml Wed Jan 07 11:15:41 2015 -0500 +++ b/unfold_column.xml Thu Jan 08 09:07:31 2015 -0500 @@ -26,7 +26,7 @@ - + diff -r 3f0e0d4c15a9 -r 8928e6d1e7ba unsorted_uniq.xml --- a/unsorted_uniq.xml Wed Jan 07 11:15:41 2015 -0500 +++ b/unsorted_uniq.xml Thu Jan 08 09:07:31 2015 -0500 @@ -37,7 +37,7 @@ - +