From efc7f8c5f919316793d69e9c79ac1d51c343239f Mon Sep 17 00:00:00 2001 From: martinahansen Date: Fri, 2 Nov 2012 13:33:34 +0000 Subject: [PATCH] added tests for find_pairs git-svn-id: http://biopieces.googlecode.com/svn/trunk@1987 74ccb610-7750-0410-82ae-013aeee3265d --- bp_test/in/find_pairs.in | 140 +++++++++++++++++++++++++++++++++++ bp_test/out/find_pairs.out.1 | 52 +++++++++++++ bp_test/test/test_find_pairs | 7 ++ 3 files changed, 199 insertions(+) create mode 100644 bp_test/in/find_pairs.in create mode 100644 bp_test/out/find_pairs.out.1 create mode 100755 bp_test/test/test_find_pairs diff --git a/bp_test/in/find_pairs.in b/bp_test/in/find_pairs.in new file mode 100644 index 0000000..f9a2a66 --- /dev/null +++ b/bp_test/in/find_pairs.in @@ -0,0 +1,140 @@ +SCORES: ffeaffd`ce`eecccKLT`bT^]bYHV^BBBBBBBBBBBBBBBBBBBBB +SEQ: GGGTCCGCTCCTTTCGCTAGCNGGGGACGCGGGGGGCTGAGGGGNNACGC +SEQ_LEN: 50 +SEQ_NAME: ILLUMINA-52179E_0004:2:1:1040:5263#TTAGGC/1 +--- +SCORES: BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB +SEQ: NNNNNGNNNNNNNTANACNNNNTNNNNNNNANNNNGNNNNNCNNNNNGNN +SEQ_LEN: 50 +SEQ_NAME: ILLUMINA-52179E_0004:2:1:1040:5263#TTAGGC/2 +--- +SCORES: BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB +SEQ: NNNNNNNNGGNNCNANNANNNNGTNNNTNGNANNNNCNNANTTGNNNNNN +SEQ_LEN: 50 +SEQ_NAME: ILLUMINA-52179E_0004:2:1:1041:14486#TTAGGC/2 +--- +SCORES: db`dadddddeeeeedeeeeccdddfffffcdaddbac`d_BBBBBBBBB +SEQ: GGGAGGGGGGCGGGCCAGGNTNCGGTTTTTCTCATAGATCCCCCTAGGGG +SEQ_LEN: 50 +SEQ_NAME: ILLUMINA-52179E_0004:2:1:1043:19446#TTAGGC/1 +--- +SCORES: BBBBGSSNONdddddBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB +SEQ: NANNNNNNNCANNNTCAANNNGCACNGGGTNATNNCNATTCNNNCGNCTN +SEQ_LEN: 50 +SEQ_NAME: ILLUMINA-52179E_0004:2:1:1043:19446#TTAGGC/2 +--- +SCORES: ffffcfffffded^eddddddbdcdeedcefecfefdffecabccBB`b` +SEQ: CCNAGGAGGAGNCAATAAGAGACCATTCGTATATGATCTCTCAGGAGAGC +SEQ_LEN: 50 +SEQ_NAME: ILLUMINA-52179E_0004:2:1:1044:7943#TTAGGC/1 +--- +SCORES: ceceeee\e``cd^^Yb`b`cc``c\accccZT`YTbYb`Y\VZYBBa\Y +SEQ: GCCGAGTAGCGTTCNTGGNTACCTTCCGATCCGCGGCCCGCCCCCTGTCT +SEQ_LEN: 50 +SEQ_NAME: ILLUMINA-52179E_0004:2:1:1045:16499#TTAGGC/1 +--- +SCORES: BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB +SEQ: AANAANANCTNCNNANCGNCGGTTTCGTNANNANNGGTTCGCANCGNNNC +SEQ_LEN: 50 +SEQ_NAME: ILLUMINA-52179E_0004:2:1:1045:16499#TTAGGC/2 +--- +SEQ_NAME: HWI-ST575:107:C0HE6ACXX:5:1101:1958:2175 2:N:0:TAGCTG +SEQ: CTACCTGTGCAAAAAGCACCAAGCAGAGCCATGCTNAACATGGACAGGCGAGCTGGTGTCATAAACATTTCCTGNTTTTANTCTATNGTAGNTANTAA +SEQ_LEN: 98 +SCORES: bbbeeeecggfeghfggfhihhieh]ffbeghiiiBOYcfghighfghghaedfeeV^abcccce`bdbdc```BKZ^aaBKW^^aBBBBBBBBBBBB +--- +SEQ_NAME: HWI-ST575:107:C0HE6ACXX:5:1101:2412:2210 2:N:0:TAGCTG +SEQ: CCGGGCTTGATGCCCTGGCATTGGAGCAATACGAGTTGTTGCTGGAAGAACAAGCCTATCCGTTTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT +SEQ_LEN: 98 +SCORES: ^^_eee^ccgeggiidfdd_ggfhhhfhifhhfgfggffgdeghe_ebfgedfXZcffdggdT`^aeeee^`bcacc\^Z^a[]Q[`b^]^aaBBBBB +--- +SEQ_NAME: HWI-ST575:107:C0HE6ACXX:5:1101:2110:2236 2:N:0:TAGCTG +SEQ: CCATCACGCAATCTGCTAACACCGACAGATAACGCTCGCGCCAACGCAGATCTGTATTGCGGGCATCCTGCATATTACTGTTAGGAATAGATCGGAAG +SEQ_LEN: 98 +SCORES: ZZac^cd`gf`eeifhh`dfbaafagha`g`_`e`a^cZ`edS\deedcc`^_]]bccRTZQW[T^bbb__bbbb__bc]bc_R^bc]_]bbba[[^R +--- +SEQ_NAME: HWI-ST575:107:C0HE6ACXX:5:1101:2326:2150 1:N:0:TAGCTG +SEQ: CATAGGCTTTTTTAACGGCCCAGCCAAAGGCGATCAGGCCAAATAGNANTACCCACCAGTACTGTTGCATNGTCTCAGAAATGNNCAATACAAATTGG +SEQ_LEN: 98 +SCORES: _[_cccccgcaeeaeJb`b^dd_cg]cZedbfU_eghhhddfg[f]BLBLTZ^abbb^aT]b_`]`b`Y`BKT^^ac_YYY_`BBJGQW_b]bbbbbb +--- +SEQ_NAME: HWI-ST575:107:C0HE6ACXX:5:1101:1832:2218 1:N:0:TAGCTG +SEQ: GCTTTGACATAGTCGCTCCAGAATTGCCAGCTAGGGTTAGCTTGGCAACTGCAGCGACGTAATGTGCTGTGGCAGATCAATTTATCTGTTTTGAATCA +SEQ_LEN: 98 +SCORES: ^P^PJ\Y`eea`e[daYdecggadgdXJIYVbdc`efg_cdedI^aXIO^abeb\eL_daQU^_V]``]UGTZ\^BBBBBBBBBBBBBBBBBBBBBBB +--- +SEQ_NAME: HWI-ST575:107:C0HE6ACXX:5:1101:2155:2169 2:N:0:TAGCTG +SEQ: AACAAACTGTTTTGCAGAATGTTATGAATGGTCCGNGCGCNTNAACCCAGATCGGAAGAGCGTCGTGTAGGGAANGANGGNNGNNCNCGGNNNNNGNC +SEQ_LEN: 98 +SCORES: a__eeecegcgegihhifhhfcgdghfffiibgheBPPYcBOBOXaffffgfhhhffa`bfe\^cR]Z]`baZ`BBBBBBBBBBBBBBBBBBBBBBBB +--- +SEQ_NAME: HWI-ST575:107:C0HE6ACXX:5:1101:2037:2173 1:N:0:TAGCTG +SEQ: CTGGGTGCCACTGTCGCCACCCTGTTAAGTCGTGAACCCGTTACCATCAGCACTGATGCCAACGTCTGGCAGGCCGCCCAGCTAATGACCGAGCAAAA +SEQ_LEN: 98 +SCORES: _[_cccceeegggffhiiihdfdefhhafeff_efdfgfhifhghhfbgbgdggfdhihhegggeeeebdZ^aaa^_aaX``b]b_bcccXXaV_ccb +--- +SEQ_NAME: HWI-ST575:107:C0HE6ACXX:5:1101:2284:2226 1:N:0:TAGCTG +SEQ: CGCCTTTTCATCAGCAACAGACAGTTACGACGCATATCGCCACCCAAATGTTTGCCGAGGCTAAACGGGTATTGAAACGCGGTGGCCGCTTGCGTATT +SEQ_LEN: 98 +SCORES: ___eeeeegagffgghdefb_e_eggia`\egfdhhdf`gdfghihiiib_`gghf``cbcabcbc^^_KW`c]Y_bbcc[a[[_^aa]cccc]__ab +--- +SEQ_NAME: HWI-ST575:107:C0HE6ACXX:5:1101:2412:2210 1:N:0:TAGCTG +SEQ: AAACGGATAGGCTTGTTCTTCCAGCAACAACTCGTATTGCTCCAATGCCAGGGCATCAAGCCCGGAGATCGGAAGAGCACACGTCTGAACTCCAGTCA +SEQ_LEN: 98 +SCORES: _bbaceceggeccgeZddghaegffiiWdghfff``ffgfacfcffhiihhfi\_e\egfcggde]acdccc^aa_`[`aca_a^b_`bbbbbbbS_b +--- +SEQ_NAME: HWI-ST575:107:C0HE6ACXX:5:1101:2284:2226 2:N:0:TAGCTG +SEQ: GGCCAAATAACCGCTGCAGTTGCTGCTGATAATTCAGGTGACGGTTAGCCACAATACGCAAGCGGCCACCGCGTTTCAATACCCGTTTAGCCTCGGCA +SEQ_LEN: 98 +SCORES: bbbeeeeegfgggiehihhef_gfgfhfghdffhihhfXc^egc_cgabgffghhfhfhfg`d^cba_ac^\_W]abcb_bccc]X`bQ]`b`^_a__ +--- +SEQ_NAME: HWI-ST575:107:C0HE6ACXX:5:1101:2037:2173 2:N:0:TAGCTG +SEQ: AGCCTGGCCCGGATATCCTTGTCAGTGATAATGCCNGTCAGATGCTGCTTGGCATCTAAAATAAGCAAGGATGANACCTTNTGNTCNGTCNNTANCTG +SEQ_LEN: 98 +SCORES: b__eeeeeggggcgghiiiihefggcgeffagdbfBOY^cffhfgbgfhdggXegghagghfffeggggeXV^_BKZ\_cBBBBBBBBBBBBBBBBBB +--- +SEQ_NAME: HWI-ST575:107:C0HE6ACXX:5:1101:1958:2175 1:N:0:TAGCTG +SEQ: TACCTAAAATAATTAATATCTACAATAGAATAAAATCAGGAAATGTTTATGACACCAGCTCGCCTGTCCATGTTCAGCATGGCTCTGCTTGGTGCTTT +SEQ_LEN: 98 +SCORES: __acceeegcgggiihihifiiiiiiiiiiefihhhhchhdhiafcghidffghhiihidfggighedhdhibdggegdgeeeedddcddccbcccab +--- +SEQ_NAME: HWI-ST575:107:C0HE6ACXX:5:1101:2155:2169 1:N:0:TAGCTG +SEQ: GGGTTCAGGCGCCCGGACCATTCATAACATTCTGCAAAACAGTTTGTTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACTAGCTGATCTCGTATG +SEQ_LEN: 98 +SCORES: ___J`cccgZccggghhhhffhbghhfeegffdghhfchhhfaffgbb]e`_c\a_\degdddbbb``^aY]bbb_bbbbbbb`bbbb_]`R]^[WR[ +--- +SEQ_NAME: HWI-ST575:107:C0HE6ACXX:5:1101:2326:2175 1:N:0:TAGCTG +SEQ: GTGCCAAAGAGGTACTGATGCTTTGTTGTTGTGGTTTAGCCGCACATTCAGCCTCGCTGACGGCAGCTAACTGCACATCTTTGGGGATATCCACCAGA +SEQ_LEN: 98 +SCORES: ^PWYP`R^cRcccgdghS`d_ebc[`ebffddb[ffffagf[O^_Uc`SabeffeegffW\\[XXR^bTGT__]b]_Y_]Zbbba][abb_cbba_aa +--- +SEQ_NAME: HWI-ST575:107:C0HE6ACXX:5:1101:2326:2175 2:N:0:TAGCTG +SEQ: GGTGGATATCCCCAAAGATGTGCAGTTAGCTGCCGNCAGCGAGGCTGAATGTGCGGCTAAACCACAACAACAAANCATCANTACCTNTTTGNCANAGA +SEQ_LEN: 98 +SCORES: ___cc\c`eggcghad`acabgfdg`g^daagaefBPYOafY_fYaa]e\aMWW__[W^Z_RZ^`aa__`Q[`^BBBBBBBBBBBBBBBBBBBBBBBB +--- +SEQ_NAME: HWI-ST575:107:C0HE6ACXX:5:1101:2139:2216 2:N:0:TAGCTG +SEQ: ATGTGTCGATGCTGGATAACGAATGGGGTATGTCGGTGTATCCGCTGGGGGCTGGTCATGAAGGGGTGGGGCATATTGCAGCTGTGGGTTCGGGGGCC +SEQ_LEN: 98 +SCORES: JJ\caa`^Ye`gW^[J[Q[`YJJ`dfa^PYbfX^^_H^^eh]fb`aefGZ_BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB +--- +SEQ_NAME: HWI-ST575:107:C0HE6ACXX:5:1101:2139:2216 1:N:0:TAGCTG +SEQ: CCACCTGCCCGGTTTTAAGATGACTGACCGCCGAACCCACAGCTGCAATATGCCCCACCACTTCATGACCAGCCACCAGCGGATACGCCGACATACCC +SEQ_LEN: 98 +SCORES: _Z_cccccaY_^cghhbagg[e]de][^ZcghfY_efgfbfdQ^^\bdZaaRMZZT\FRT\LLYYZTGT]_[^a^[^aBBBBBBBBBBBBBBBBBBBB +--- +SEQ_NAME: HWI-ST575:107:C0HE6ACXX:5:1101:2110:2236 1:N:0:TAGCTG +SEQ: ATTCCTAACAGTAATATGCAGGATGCCCGCAATACAGATCTGCGTTGGCGCGAGCGTTATCTGTCGGTGTTAGCAGATTTCGTGATGGAGATCGGAAG +SEQ_LEN: 98 +SCORES: ___cc`Sc^J[ecK``f]cY^RPbcRYJQQY^YccacfehhheU^^^eXFS_BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB +--- +SEQ_NAME: HWI-ST575:107:C0HE6ACXX:5:1101:2326:2150 2:N:0:TAGCTG +SEQ: CGGCCNNNACCCAATTTGNNTTGGGCATTTCTGANNNNNNNCNACNNTACTGNNGGGTANTGCTNNNTGNNNNGNNNNNNNNNNNNNNNNNNNNNNNN +SEQ_LEN: 98 +SCORES: WZ^ceBBBQQQQbffgggBBSQ`_fRZdegffdhBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB +--- +SEQ_NAME: HWI-ST575:107:C0HE6ACXX:5:1101:1832:2218 2:N:0:TAGCTG +SEQ: GGTTATCGATCTGGAAAAAGCAACTAAACCTAAAGCTAAACCACGTAGCGCCGGGTAAATGATTCAAAACAGATAAATTGATCTGCCACAGCACATTA +SEQ_LEN: 98 +SCORES: ^VYPJQ`c^JJ[b[efg^dHJ`aa`adXd_ZXXbIIIY[af_H^aWHWPZ[`gggFFZ^bd_Z]Zb_]ba\^ZGY_`TZ``cc[bbR]]^aaXQ[bbb +--- diff --git a/bp_test/out/find_pairs.out.1 b/bp_test/out/find_pairs.out.1 new file mode 100644 index 0000000..0611aa0 --- /dev/null +++ b/bp_test/out/find_pairs.out.1 @@ -0,0 +1,52 @@ +SEQ_NAME: ILLUMINA-52179E_0004:2:1:1040:5263#TTAGGC/1 +--- +SEQ_NAME: ILLUMINA-52179E_0004:2:1:1040:5263#TTAGGC/2 +--- +SEQ_NAME: ILLUMINA-52179E_0004:2:1:1043:19446#TTAGGC/1 +--- +SEQ_NAME: ILLUMINA-52179E_0004:2:1:1043:19446#TTAGGC/2 +--- +SEQ_NAME: ILLUMINA-52179E_0004:2:1:1045:16499#TTAGGC/1 +--- +SEQ_NAME: ILLUMINA-52179E_0004:2:1:1045:16499#TTAGGC/2 +--- +SEQ_NAME: HWI-ST575:107:C0HE6ACXX:5:1101:2412:2210 1:N:0:TAGCTG +--- +SEQ_NAME: HWI-ST575:107:C0HE6ACXX:5:1101:2412:2210 2:N:0:TAGCTG +--- +SEQ_NAME: HWI-ST575:107:C0HE6ACXX:5:1101:2284:2226 1:N:0:TAGCTG +--- +SEQ_NAME: HWI-ST575:107:C0HE6ACXX:5:1101:2284:2226 2:N:0:TAGCTG +--- +SEQ_NAME: HWI-ST575:107:C0HE6ACXX:5:1101:2037:2173 1:N:0:TAGCTG +--- +SEQ_NAME: HWI-ST575:107:C0HE6ACXX:5:1101:2037:2173 2:N:0:TAGCTG +--- +SEQ_NAME: HWI-ST575:107:C0HE6ACXX:5:1101:1958:2175 1:N:0:TAGCTG +--- +SEQ_NAME: HWI-ST575:107:C0HE6ACXX:5:1101:1958:2175 2:N:0:TAGCTG +--- +SEQ_NAME: HWI-ST575:107:C0HE6ACXX:5:1101:2155:2169 1:N:0:TAGCTG +--- +SEQ_NAME: HWI-ST575:107:C0HE6ACXX:5:1101:2155:2169 2:N:0:TAGCTG +--- +SEQ_NAME: HWI-ST575:107:C0HE6ACXX:5:1101:2326:2175 1:N:0:TAGCTG +--- +SEQ_NAME: HWI-ST575:107:C0HE6ACXX:5:1101:2326:2175 2:N:0:TAGCTG +--- +SEQ_NAME: HWI-ST575:107:C0HE6ACXX:5:1101:2139:2216 1:N:0:TAGCTG +--- +SEQ_NAME: HWI-ST575:107:C0HE6ACXX:5:1101:2139:2216 2:N:0:TAGCTG +--- +SEQ_NAME: HWI-ST575:107:C0HE6ACXX:5:1101:2110:2236 1:N:0:TAGCTG +--- +SEQ_NAME: HWI-ST575:107:C0HE6ACXX:5:1101:2110:2236 2:N:0:TAGCTG +--- +SEQ_NAME: HWI-ST575:107:C0HE6ACXX:5:1101:2326:2150 1:N:0:TAGCTG +--- +SEQ_NAME: HWI-ST575:107:C0HE6ACXX:5:1101:2326:2150 2:N:0:TAGCTG +--- +SEQ_NAME: HWI-ST575:107:C0HE6ACXX:5:1101:1832:2218 1:N:0:TAGCTG +--- +SEQ_NAME: HWI-ST575:107:C0HE6ACXX:5:1101:1832:2218 2:N:0:TAGCTG +--- diff --git a/bp_test/test/test_find_pairs b/bp_test/test/test_find_pairs new file mode 100755 index 0000000..61c5709 --- /dev/null +++ b/bp_test/test/test_find_pairs @@ -0,0 +1,7 @@ +#!/bin/bash + +source "$BP_DIR/bp_test/lib/test.sh" + +run "$bp -I $in -O $tmp" +assert_no_diff $tmp $out.1 +clean -- 2.39.5