From c3c2be254f045d0944f4088a60f99c689b56cc69 Mon Sep 17 00:00:00 2001 From: alain viari Date: Mon, 9 Nov 2015 00:58:50 +0100 Subject: [PATCH] go_pass1 moved to bin Former-commit-id: 6be837df8518c9374c0a9de6ff717add6178d01b Former-commit-id: b2e3e8200b9e14447b7eeedd70191e10cf4b8a58 --- TODO | 2 + detectors/cds/bin/go_cds.sh | 3 +- detectors/cds/{lib => bin}/go_filterbx.sh | 1 + detectors/cds/{lib => bin}/go_pass1.sh | 9 +++-- detectors/cds/test/go_test.sh | 16 +++++--- detectors/cds/test/test.ref | 46 +++++++++++------------ scripts/csh_init.sh | 22 ++++++++++- 7 files changed, 63 insertions(+), 36 deletions(-) rename detectors/cds/{lib => bin}/go_filterbx.sh (98%) rename detectors/cds/{lib => bin}/go_pass1.sh (95%) diff --git a/TODO b/TODO index e466767..062a3fa 100644 --- a/TODO +++ b/TODO @@ -12,3 +12,5 @@ o CDS speedup à tester o CDS ajouter tools/dbchloro et tools/compare +o $red + diff --git a/detectors/cds/bin/go_cds.sh b/detectors/cds/bin/go_cds.sh index b3ba093..2dae666 100755 --- a/detectors/cds/bin/go_cds.sh +++ b/detectors/cds/bin/go_cds.sh @@ -15,6 +15,7 @@ #======================================================================================== # usage: go_cds.sh fasta # +unsetenv ORG_SOURCED setenv ORG_HOME `dirname $0`/../../.. source $ORG_HOME/scripts/csh_init.sh @@ -49,7 +50,7 @@ Notify "running pass1: exonerate of $Genome" foreach f ($fams) set prot = `basename $f:r` - $LIB_DIR/go_pass1.sh $Fasta $prot $temp + $PROG_DIR/go_pass1.sh $Fasta $prot $temp end # diff --git a/detectors/cds/lib/go_filterbx.sh b/detectors/cds/bin/go_filterbx.sh similarity index 98% rename from detectors/cds/lib/go_filterbx.sh rename to detectors/cds/bin/go_filterbx.sh index 1379767..7213fa3 100755 --- a/detectors/cds/lib/go_filterbx.sh +++ b/detectors/cds/bin/go_filterbx.sh @@ -7,6 +7,7 @@ # # usage: go_filterbx.sh dna_fasta prot_fasta [idmin nbmin nbmax] # +unsetenv ORG_SOURCED setenv ORG_HOME `dirname $0`/../../.. source $ORG_HOME/scripts/csh_init.sh diff --git a/detectors/cds/lib/go_pass1.sh b/detectors/cds/bin/go_pass1.sh similarity index 95% rename from detectors/cds/lib/go_pass1.sh rename to detectors/cds/bin/go_pass1.sh index 15dbaa3..4f911a5 100755 --- a/detectors/cds/lib/go_pass1.sh +++ b/detectors/cds/bin/go_pass1.sh @@ -17,6 +17,7 @@ # # usage: go_pass1.sh fasta family [outdir] # +unsetenv ORG_SOURCED setenv ORG_HOME `dirname $0`/../../.. source $ORG_HOME/scripts/csh_init.sh @@ -100,10 +101,10 @@ endif if ($PASS1_SPEEDUP != 0) then - $LIB_DIR/go_filterbx.sh $GenoFile $ProtFile \ - $PASS1_BLASTX_FILTER_IDMIN \ - $PASS1_BLASTX_FILTER_NBMIN \ - $PASS1_BLASTX_FILTER_NBMAX > D_$$ + $PROG_DIR/go_filterbx.sh $GenoFile $ProtFile \ + $PASS1_BLASTX_FILTER_IDMIN \ + $PASS1_BLASTX_FILTER_NBMIN \ + $PASS1_BLASTX_FILTER_NBMAX > D_$$ set n = `egrep "^>" D_$$ | wc -l` if ($n > 0) then diff --git a/detectors/cds/test/go_test.sh b/detectors/cds/test/go_test.sh index f5de850..f778c9f 100755 --- a/detectors/cds/test/go_test.sh +++ b/detectors/cds/test/go_test.sh @@ -1,22 +1,26 @@ #!/bin/csh -f -echo "+ [testing CDS]" +setenv ORG_HOME `dirname $0`/../../.. +source $ORG_HOME/scripts/csh_init.sh +echo "+ testing CDS" + +setenv TMP_CLEANUP 0 setenv PASS1_SPEEDUP 1 setenv PASS1_SLOWDOWN 0 -setenv PASS1_BLASTX_FILTER_NBMAX 50 +setenv PASS1_BLASTX_FILTER_NBMAX 10 -../bin/go_cds.sh test.fst > test.bak +`dirname $0`/../bin/go_cds.sh test.fst > test.bak diff -q test.bak test.ref >& /dev/null set stat = $status if ($stat == 0) then - echo '+ CDS test Ok' - \rm -r test.bak + echo "+ $VTC[3]CDS test Ok$VTC[1]" + \rm -r test.bak test.tmp else - echo '* CDS test Failure' + echo "* $VTC[2]CDS test Failure$VTC[1]" endif exit $stat diff --git a/detectors/cds/test/test.ref b/detectors/cds/test/test.ref index 758afc9..7449c64 100644 --- a/detectors/cds/test/test.ref +++ b/detectors/cds/test/test.ref @@ -6,7 +6,7 @@ FT /codon_start=1 FT /transl_table=11 FT /gene="ccsA" FT /locus_tag="" -FT /product=cytochrome c biogenesis protein +FT /product="cytochrome c biogenesis protein" FT /inference="similar to DNA sequence:AC_000188:LyesCp084" FT /translation="MIFSTLEHILTHISFSIVSIVITIHLITFLVDEIVKLYDSSEKGI FT IVTFFCITGLLVTRWVSSGHFPLSDLYESLIFLSWSFSLIHIIPYFKKNVLILSKITGP @@ -22,7 +22,7 @@ FT /codon_start=1 FT /transl_table=11 FT /gene="ndhA_1" FT /locus_tag="" -FT /product=NADH dehydrogenase subunit 1 +FT /product="NADH dehydrogenase subunit 1" FT /inference="similar to DNA sequence:AC_000188:LyesCp085" FT /translation="LSNSLSTVDIVEAQSKYGFWGWNLWRQPIGFIVFLISSLAECERL FT PFDLPEAEEELVAGYQTEYSGIKFGLFYIASYLNLLVSSLFVTVLYLGGWNLSIPYIFV @@ -36,7 +36,7 @@ FT /codon_start=1 FT /transl_table=11 FT /gene="ndhA_2" FT /locus_tag="" -FT /product=NADH dehydrogenase subunit 1 +FT /product="NADH dehydrogenase subunit 1" FT /inference="similar to DNA sequence:AC_000188:LyesCp085" FT /translation="MIIDTTEIETINSFSKLESLKEVYGIIWMLVPIVTLVLGITIGVL FT VIVWLEREISAGIQQRIGPEYAGPLGILQALADGTKLLLKENLIPSTGDTRLFSIGPSI @@ -50,7 +50,7 @@ FT /codon_start=1 FT /transl_table=11 FT /gene="ndhB" FT /locus_tag="" -FT /product=NADH dehydrogenase subunit 2 +FT /product="NADH dehydrogenase subunit 2" FT /inference="similar to DNA sequence:NC_008535:CoarCp067" FT /translation="MIWHVQNENFILDSTRIFMKAFHLLLFDGSLIFPECILIFGLILL FT LMIDSTSDQKDIPWLYFISSTSLVMSITALLFRWREEPMISFSGNFQTNNFNEIFQFLI @@ -78,7 +78,7 @@ FT /codon_start=1 FT /transl_table=11 FT /gene="ndhD" FT /locus_tag="" -FT /product=NADH dehydrogenase subunit 4 +FT /product="NADH dehydrogenase subunit 4" FT /inference="similar to DNA sequence:NC_007898:LyesC2p017" FT /translation="MNYFPWLTIIVVFPIFAGSLIFFLPHKGNRVIRWYTICICILELL FT LTTYAFCYHFQSDDPLIQLVEDYKWIDFFDFHWRLGIDGLSIGPILLTGFITTLATLAA @@ -97,8 +97,8 @@ FT /codon_start=1 FT /transl_table=11 FT /gene="ndhE" FT /locus_tag="" -FT /product=NADH dehydrogenase subunit 4L -FT /inference="similar to DNA sequence:AC_000188:LyesCp080" +FT /product="NADH dehydrogenase subunit 4L" +FT /inference="similar to DNA sequence:NC_001879:NitaCp085" FT /translation="MILEHVLVLSAYLFSIGIYGLITSRNMVRALMCLELILNAVNINF FT VTFSDFFDNRQLKGDIFSIFVIAIAAAEAAIGLAIVSSIYRNRKSTRINQSNLLNN" FT gene complement(11509..13722) @@ -109,7 +109,7 @@ FT /codon_start=1 FT /transl_table=11 FT /gene="ndhF" FT /locus_tag="" -FT /product=NADH dehydrogenase subunit 5 +FT /product="NADH dehydrogenase subunit 5" FT /inference="similar to DNA sequence:AC_000188:LyesCp073" FT /translation="MEQTYEYAWIIPFIPLPVPMLIGAGLILFPTATKRFRRMWAFQSV FT LLLSIVMIFSIYLSIQQINSSSVYQYVWSWIINNDFSLDFGYLIDPLTSIMSILITTVG @@ -132,7 +132,7 @@ FT /codon_start=1 FT /transl_table=11 FT /gene="ndhG" FT /locus_tag="" -FT /product=NADH dehydrogenase subunit 6 +FT /product="NADH dehydrogenase subunit 6" FT /inference="similar to DNA sequence:AC_000188:LyesCp077" FT /translation="MDLSEPIHDFLLVFLGSGLILGGLGVVLLPNPIYSAFSLGLVLVC FT TSLFYILSNAYFVAAAQLLIYVGAINVLIIFAVMFMNGSEYYKDFHLWTVGDGITSMVC @@ -146,7 +146,7 @@ FT /codon_start=1 FT /transl_table=11 FT /gene="ndhH" FT /locus_tag="" -FT /product=NADH dehydrogenase subunit 7 +FT /product="NADH dehydrogenase subunit 7" FT /inference="similar to DNA sequence:AC_000188:LyesCp078" FT /translation="MTAPTTRKDLMIVNMGPQHPSMHGVLRLIVTLDGEDVVDCEPILG FT YLHRGMEKIAENRTIIQYLPYVTRWDYLATMFTEAITINGPEQLGNIQVPKRASYIRVI @@ -163,7 +163,7 @@ FT /codon_start=1 FT /transl_table=11 FT /gene="ndhI" FT /locus_tag="" -FT /product=NADH dehydrogenase subunit I +FT /product="NADH dehydrogenase subunit I" FT /inference="similar to DNA sequence:AC_000188:LyesCp076" FT /translation="MLPMITEFINYGQQTIRAARYIGQGFMITLSHANRLPVTIQYPYE FT KLITSERFRGRIHFEFDKCIACEVCVRVCPIDLPVVDWKLETDIRKKRLLNYSIDFGIC @@ -177,8 +177,8 @@ FT /codon_start=1 FT /transl_table=11 FT /gene="psaC" FT /locus_tag="" -FT /product=photosystem I subunit VII -FT /inference="similar to DNA sequence:NC_022409:CEXI_CP_p076" +FT /product="photosystem I subunit VII" +FT /inference="similar to DNA sequence:NC_023792:CP89_p014" FT /translation="MSHSVKIYDTCIGCTQCVRACPTDVLEMIPWDGCKAKQIASAPRT FT EDCVGCKRCESACPTDFLSVRVYLWHETTRSMGLAY" FT gene 53817..55307 @@ -189,8 +189,8 @@ FT /codon_start=1 FT /transl_table=11 FT /gene="rpl2" FT /locus_tag="" -FT /product=ribosomal protein L2 -FT /inference="similar to DNA sequence:AC_000188:LyesCp030" +FT /product="ribosomal protein L2" +FT /inference="similar to DNA sequence:NC_007898:LyesC2p002" FT /translation="MAIHLYKTSTPSTRNGTVDSQVKSNPRNNLIYGQRRCGKGRNARG FT IITARHRGGGHKRLYRKIDFRRNEKDIYGRIVTIEYDPNRNAYICLIHYGDGEKRYILH FT PRGAIIGDTIVSGTEVPIKMGNALPSTDMPLGTAIHNIEITLGKGGQLARAAGAVAKLI @@ -212,8 +212,8 @@ FT /codon_start=1 FT /transl_table=11 FT /gene="rpl23" FT /locus_tag="" -FT /product=ribosomal protein L23 -FT /inference="similar to DNA sequence:AC_000188:LyesCp026" +FT /product="ribosomal protein L23" +FT /inference="similar to DNA sequence:NC_007898:LyesC2p003" FT /translation="MDGIKYAVFTDKSIRLLGKNQYTSNVESGSTRTEIKHWVELFFGV FT KVIAMNSHRLPGKSRRMGPIMGHTMHYRRMIITLQPGYSIPPLRKKRT" FT gene 14505..14672 @@ -224,7 +224,7 @@ FT /codon_start=1 FT /transl_table=11 FT /gene="rpl32" FT /locus_tag="" -FT /product=ribosomal protein L32 +FT /product="ribosomal protein L32" FT /inference="similar to DNA sequence:AC_000188:LyesCp036" FT /translation="MAVPKKRTSTSKKRIRKNIWKRKGYWVALKAFSLAKSLSTGNSKS FT FFVRQTKINK" @@ -236,7 +236,7 @@ FT /codon_start=1 FT /transl_table=11 FT /gene="rps15" FT /locus_tag="" -FT /product=ribosomal protein S15 +FT /product="ribosomal protein S15" FT /inference="similar to DNA sequence:AC_000188:LyesCp029" FT /translation="MVKNSVISVISQEEKKGSVEFQVFNFTNKIRRLTSHLELHKKDYL FT SQRGLKKILGKRQRLLAYLAKKNRVRYKELINRLDIRETKTR" @@ -248,8 +248,8 @@ FT /codon_start=1 FT /transl_table=11 FT /gene="rps7" FT /locus_tag="" -FT /product=ribosomal protein S7 -FT /inference="similar to DNA sequence:AC_000188:LyesCp008" +FT /product="ribosomal protein S7" +FT /inference="similar to DNA sequence:NC_007898:LyesC2p007" FT /translation="MSRRGTAEKKTAKSDPIYRNRLVNMLVNRILKHGKKSLAYQIIYR FT AVKKIQQKTETNPLSVLRQAIRGVTPDITVKARRVGGSTHQVPIEIGSTQGKALAIRWL FT LAASRKRPGRNMAFKLSSELVDAAKGSGDAIRKKEETHRMAEANRAFAHFR" @@ -261,7 +261,7 @@ FT /codon_start=1 FT /transl_table=11 FT /gene="ycf1" FT /locus_tag="" -FT /product=hypothetical chloroplast RF1 +FT /product="hypothetical chloroplast RF1" FT /inference="similar to DNA sequence:AC_000188:LyesCp019" FT /translation="MIFQSFLLGNLVSLCMKIINSVVVVGLYYGFLTTFSIGPSYLFLL FT RALVMEEGTEKKVSATTGFITGQLMMFISIYYAPLHLALGRPHTITVLALPYLLFHFFW @@ -304,7 +304,7 @@ FT /codon_start=1 FT /transl_table=11 FT /gene="ycf2" FT /locus_tag="" -FT /product=Ycf2 +FT /product="Ycf2" FT /inference="similar to DNA sequence:AC_000188:LyesCp004" FT /translation="MRGHQFKSWIFELREILREIKNSHHFLDSWTQFNSVGSFIHIFFH FT QERFLKLFDPRIWSILLSRNSQGSPSNRYFTIKGVILFVVAVLIYRINNRNMVERKNLY diff --git a/scripts/csh_init.sh b/scripts/csh_init.sh index 3669b8e..779d30c 100644 --- a/scripts/csh_init.sh +++ b/scripts/csh_init.sh @@ -44,8 +44,15 @@ if ($?ORG_SOURCED == 0) then setenv PROG_DIR `dirname $0` # Directory containing setenv PROG_DIR `cd $PROG_DIR && pwd -P` # the main script file - setenv LIB_DIR "$PROG_DIR/../lib" # Directory containing - setenv LIB_DIR `cd $LIB_DIR && pwd -P` # the main script libraries + if (-d "$PROG_DIR/../lib") then + setenv LIB_DIR "$PROG_DIR/../lib" # Directory containing + setenv LIB_DIR `cd $LIB_DIR && pwd -P` # the main script libraries + else if (-d "$PROG_DIR/lib") then + setenv LIB_DIR "$PROG_DIR/lib" # alternate location + setenv LIB_DIR `cd $LIB_DIR && pwd -P` # + else + setenv LIB_DIR "$PROG_DIR" # alternate location + endif setenv CALL_DIR `pwd -P` # Directory from where the # main script is called @@ -121,6 +128,17 @@ alias Cat 'awk '"'"'{print "# " $0}'"'"' \!:*' alias AssignUndef 'if ($?\!:1 == 0) set \!:1=\!:2-*' +# -------------------------------------- +# VT100 color codes +# 1: normal 2: red 3: green 4: blue 5: magenta +# -------------------------------------- + +if ($?ORG_NO_COLOR != 0) then + set VTC = ('' '' '' '' '') +else + set VTC = ('' '' '' '' '') +endif + # -------------------------------------- # reset Stat each time # --------------------------------------