Ic@sdZddlZddlZddlZddlmZmZdejfdYZdejfdYZ dejfd YZ e d krej d d Z ejd e ndS(s5Tests for Primer-based programs in the Emboss suite. iN(t PrimerSearchtPrimer3tPrimer3ParseTestcBs5eZdZdZdZdZdZRS(cCsgtjjddtjjddtjjddtjjddtjjddg|_dS(NtEmbosssbac_find.primer3scds_forward.primer3scds_reverse.primer3s short.primer3sinternal_oligo.primer3(tostpathtjoint test_files(tself((stest_EmbossPrimer.pytsetUps cCs>x7|jD],}t|d}tj||jq WdS(s7Make sure that we can parse all primer3 files. trN(RtopenRtreadtclose(Rtfileth((stest_EmbossPrimer.pyttest_simple_parses cCs|jd}t|d}tj|}|jt|jdksctdt|j|jdjdkst|jdj dkst|jdj d kst|jd j d kst|jd j d kst|jd j d ks t|jd jdks't|jdjdksCt|jdjdks_t|jdjdks{t|jdjdkstdS(sBMake sure we get the data from normal primer3 files okay. iR isWrong number of primers: %sitCCGGTTTCTCTGGTTGAAAAitTCACATTCCCAAATGTAGATCGiiipig)\M@gF@ii0igGzM@gGztD@N(RR RR R tlentprimerstAssertionErrort forward_seqt reverse_seqtsizet forward_starttforward_lengtht forward_tmt forward_gct reverse_starttreverse_lengtht reverse_tmt reverse_gc(Rt regular_fileRt primer_info((stest_EmbossPrimer.pyttest_indepth_regular_parses&    cCs|jd}t|d}tj|}|jt|jdksPt|jdjdkslt|jdj dkst|jdj dkstdS( s?Make sure we get info right from a single primer find. iR ititTGTGATTGCTTGAGCTGGACiN( RR RR R RRRRRR(RRRR"((stest_EmbossPrimer.pyttest_in_depth_single_parse9s  cCs|jd}t|d}tj|}|jt|jdksPt|jdjdkslt|jdj dkst|jdj d kst|jd j d kst|jdj d kstd S(s9 Make sure we can parse an internal oligo file correctly iR iiiitTTGCGCTTTAGTTTGAATTGAAig(\OM@iigA@N( RR RR R RRRtinternal_lengtht internal_seqt internal_tmtinternal_startt internal_gc(RRRR"((stest_EmbossPrimer.pyt test_internal_oligo_single_parseGs  (t__name__t __module__R RR#R&R-(((stest_EmbossPrimer.pyR s    tPrimersearchParseTestcBs#eZdZdZdZRS(cCstjjddg|_dS(NRsbac_find.psearch(RRRR(R((stest_EmbossPrimer.pyR XscCs>x7|jD],}t|d}tj||jq WdS(s<Make sure that we can parse all primersearch files. R N(RR RR R (RRR((stest_EmbossPrimer.pyR\s cCs|jd}t|d}tj|}|jt|jjdksVtd|jjksqtt|jddkst|jddj dkst|jddj dddd d d d kstd S(sIMake sure the output from a simple primersearch file is correct. iR itTestisAC074298 AC074298 s7 Telomere associated sequence for Arabidopsis thaliana s,TEL1N from chromosome I, complete sequence. s6 CCGGTTTCTCTGGTTGAAAA hits forward strand at 114 with s 0 mismatches s: TCACATTCCCAAATGTAGATCG hits reverse strand at [114] with s 0 mismatchesN( RR RR R Rt amplifierstkeysRtlengththit_info(RRRtamp_info((stest_EmbossPrimer.pyttest_in_depth_normal_parseds  ! (R.R/R RR7(((stest_EmbossPrimer.pyR0Ws  tPrimerSearchInputTestcBs eZdZdZdZRS(s0Test creating input files for primersearch. cCsdS(N((R((stest_EmbossPrimer.pyR }scCsXtj}|jddd|jdddt|}|ddksTtd S( s>Make sure we can output primer information correctly. R1tGATCtCATGtTest2tAATAtTTATsTest GATC CATG sTest2 AATA TTAT N(Rt InputRecordtadd_primer_settstrR(Rtp_infotoutput((stest_EmbossPrimer.pyttest_primer_representations   (R.R/t__doc__R RC(((stest_EmbossPrimer.pyR8zs t__main__t verbosityit testRunner(RDtsysRtunittestt Bio.EmbossRRtTestCaseRR0R8R.tTextTestRunnertrunnertmain(((stest_EmbossPrimer.pyts   J#