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go_pass1 moved to bin

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Former-commit-id: 6be837df8518c9374c0a9de6ff717add6178d01b
Former-commit-id: b2e3e8200b9e14447b7eeedd70191e10cf4b8a58
This commit is contained in:
alain viari
2015-11-09 00:58:50 +01:00
parent 0066211385
commit c3c2be254f
7 changed files with 63 additions and 36 deletions
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2
TODO
View File

@ -12,3 +12,5 @@ o CDS speedup à tester
o CDS ajouter tools/dbchloro et tools/compare o CDS ajouter tools/dbchloro et tools/compare
o $red

3
detectors/cds/bin/go_cds.sh
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@ -15,6 +15,7 @@
#======================================================================================== #========================================================================================
# usage: go_cds.sh fasta # usage: go_cds.sh fasta
# #
unsetenv ORG_SOURCED
setenv ORG_HOME `dirname $0`/../../.. setenv ORG_HOME `dirname $0`/../../..
source $ORG_HOME/scripts/csh_init.sh source $ORG_HOME/scripts/csh_init.sh
@ -49,7 +50,7 @@ Notify "running pass1: exonerate of $Genome"
foreach f ($fams) foreach f ($fams)
set prot = `basename $f:r` set prot = `basename $f:r`
$LIB_DIR/go_pass1.sh $Fasta $prot $temp $PROG_DIR/go_pass1.sh $Fasta $prot $temp
end end
# #

1
detectors/cds/lib/go_filterbx.sh → detectors/cds/bin/go_filterbx.sh
View File

@ -7,6 +7,7 @@
# #
# usage: go_filterbx.sh dna_fasta prot_fasta [idmin nbmin nbmax] # usage: go_filterbx.sh dna_fasta prot_fasta [idmin nbmin nbmax]
# #
unsetenv ORG_SOURCED
setenv ORG_HOME `dirname $0`/../../.. setenv ORG_HOME `dirname $0`/../../..
source $ORG_HOME/scripts/csh_init.sh source $ORG_HOME/scripts/csh_init.sh

9
detectors/cds/lib/go_pass1.sh → detectors/cds/bin/go_pass1.sh
View File

@ -17,6 +17,7 @@
# #
# usage: go_pass1.sh fasta family [outdir] # usage: go_pass1.sh fasta family [outdir]
# #
unsetenv ORG_SOURCED
setenv ORG_HOME `dirname $0`/../../.. setenv ORG_HOME `dirname $0`/../../..
source $ORG_HOME/scripts/csh_init.sh source $ORG_HOME/scripts/csh_init.sh
@ -100,10 +101,10 @@ endif
if ($PASS1_SPEEDUP != 0) then if ($PASS1_SPEEDUP != 0) then
$LIB_DIR/go_filterbx.sh $GenoFile $ProtFile \ $PROG_DIR/go_filterbx.sh $GenoFile $ProtFile \
$PASS1_BLASTX_FILTER_IDMIN \ $PASS1_BLASTX_FILTER_IDMIN \
$PASS1_BLASTX_FILTER_NBMIN \ $PASS1_BLASTX_FILTER_NBMIN \
$PASS1_BLASTX_FILTER_NBMAX > D_$$ $PASS1_BLASTX_FILTER_NBMAX > D_$$
set n = `egrep "^>" D_$$ | wc -l` set n = `egrep "^>" D_$$ | wc -l`
if ($n > 0) then if ($n > 0) then

16
detectors/cds/test/go_test.sh
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@ -1,22 +1,26 @@
#!/bin/csh -f #!/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_SPEEDUP 1
setenv PASS1_SLOWDOWN 0 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 diff -q test.bak test.ref >& /dev/null
set stat = $status set stat = $status
if ($stat == 0) then if ($stat == 0) then
echo '+ CDS test Ok' echo "+ $VTC[3]CDS test Ok$VTC[1]"
\rm -r test.bak \rm -r test.bak test.tmp
else else
echo '* CDS test Failure' echo "* $VTC[2]CDS test Failure$VTC[1]"
endif endif
exit $stat exit $stat

46
detectors/cds/test/test.ref
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@ -6,7 +6,7 @@ FT /codon_start=1
FT /transl_table=11 FT /transl_table=11
FT /gene="ccsA" FT /gene="ccsA"
FT /locus_tag="" 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 /inference="similar to DNA sequence:AC_000188:LyesCp084"
FT /translation="MIFSTLEHILTHISFSIVSIVITIHLITFLVDEIVKLYDSSEKGI FT /translation="MIFSTLEHILTHISFSIVSIVITIHLITFLVDEIVKLYDSSEKGI
FT IVTFFCITGLLVTRWVSSGHFPLSDLYESLIFLSWSFSLIHIIPYFKKNVLILSKITGP FT IVTFFCITGLLVTRWVSSGHFPLSDLYESLIFLSWSFSLIHIIPYFKKNVLILSKITGP
@ -22,7 +22,7 @@ FT /codon_start=1
FT /transl_table=11 FT /transl_table=11
FT /gene="ndhA_1" FT /gene="ndhA_1"
FT /locus_tag="" 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 /inference="similar to DNA sequence:AC_000188:LyesCp085"
FT /translation="LSNSLSTVDIVEAQSKYGFWGWNLWRQPIGFIVFLISSLAECERL FT /translation="LSNSLSTVDIVEAQSKYGFWGWNLWRQPIGFIVFLISSLAECERL
FT PFDLPEAEEELVAGYQTEYSGIKFGLFYIASYLNLLVSSLFVTVLYLGGWNLSIPYIFV FT PFDLPEAEEELVAGYQTEYSGIKFGLFYIASYLNLLVSSLFVTVLYLGGWNLSIPYIFV
@ -36,7 +36,7 @@ FT /codon_start=1
FT /transl_table=11 FT /transl_table=11
FT /gene="ndhA_2" FT /gene="ndhA_2"
FT /locus_tag="" 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 /inference="similar to DNA sequence:AC_000188:LyesCp085"
FT /translation="MIIDTTEIETINSFSKLESLKEVYGIIWMLVPIVTLVLGITIGVL FT /translation="MIIDTTEIETINSFSKLESLKEVYGIIWMLVPIVTLVLGITIGVL
FT VIVWLEREISAGIQQRIGPEYAGPLGILQALADGTKLLLKENLIPSTGDTRLFSIGPSI FT VIVWLEREISAGIQQRIGPEYAGPLGILQALADGTKLLLKENLIPSTGDTRLFSIGPSI
@ -50,7 +50,7 @@ FT /codon_start=1
FT /transl_table=11 FT /transl_table=11
FT /gene="ndhB" FT /gene="ndhB"
FT /locus_tag="" 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 /inference="similar to DNA sequence:NC_008535:CoarCp067"
FT /translation="MIWHVQNENFILDSTRIFMKAFHLLLFDGSLIFPECILIFGLILL FT /translation="MIWHVQNENFILDSTRIFMKAFHLLLFDGSLIFPECILIFGLILL
FT LMIDSTSDQKDIPWLYFISSTSLVMSITALLFRWREEPMISFSGNFQTNNFNEIFQFLI FT LMIDSTSDQKDIPWLYFISSTSLVMSITALLFRWREEPMISFSGNFQTNNFNEIFQFLI
@ -78,7 +78,7 @@ FT /codon_start=1
FT /transl_table=11 FT /transl_table=11
FT /gene="ndhD" FT /gene="ndhD"
FT /locus_tag="" 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 /inference="similar to DNA sequence:NC_007898:LyesC2p017"
FT /translation="MNYFPWLTIIVVFPIFAGSLIFFLPHKGNRVIRWYTICICILELL FT /translation="MNYFPWLTIIVVFPIFAGSLIFFLPHKGNRVIRWYTICICILELL
FT LTTYAFCYHFQSDDPLIQLVEDYKWIDFFDFHWRLGIDGLSIGPILLTGFITTLATLAA FT LTTYAFCYHFQSDDPLIQLVEDYKWIDFFDFHWRLGIDGLSIGPILLTGFITTLATLAA
@ -97,8 +97,8 @@ FT /codon_start=1
FT /transl_table=11 FT /transl_table=11
FT /gene="ndhE" FT /gene="ndhE"
FT /locus_tag="" FT /locus_tag=""
FT /product=NADH dehydrogenase subunit 4L FT /product="NADH dehydrogenase subunit 4L"
FT /inference="similar to DNA sequence:AC_000188:LyesCp080" FT /inference="similar to DNA sequence:NC_001879:NitaCp085"
FT /translation="MILEHVLVLSAYLFSIGIYGLITSRNMVRALMCLELILNAVNINF FT /translation="MILEHVLVLSAYLFSIGIYGLITSRNMVRALMCLELILNAVNINF
FT VTFSDFFDNRQLKGDIFSIFVIAIAAAEAAIGLAIVSSIYRNRKSTRINQSNLLNN" FT VTFSDFFDNRQLKGDIFSIFVIAIAAAEAAIGLAIVSSIYRNRKSTRINQSNLLNN"
FT gene complement(11509..13722) FT gene complement(11509..13722)
@ -109,7 +109,7 @@ FT /codon_start=1
FT /transl_table=11 FT /transl_table=11
FT /gene="ndhF" FT /gene="ndhF"
FT /locus_tag="" 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 /inference="similar to DNA sequence:AC_000188:LyesCp073"
FT /translation="MEQTYEYAWIIPFIPLPVPMLIGAGLILFPTATKRFRRMWAFQSV FT /translation="MEQTYEYAWIIPFIPLPVPMLIGAGLILFPTATKRFRRMWAFQSV
FT LLLSIVMIFSIYLSIQQINSSSVYQYVWSWIINNDFSLDFGYLIDPLTSIMSILITTVG FT LLLSIVMIFSIYLSIQQINSSSVYQYVWSWIINNDFSLDFGYLIDPLTSIMSILITTVG
@ -132,7 +132,7 @@ FT /codon_start=1
FT /transl_table=11 FT /transl_table=11
FT /gene="ndhG" FT /gene="ndhG"
FT /locus_tag="" 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 /inference="similar to DNA sequence:AC_000188:LyesCp077"
FT /translation="MDLSEPIHDFLLVFLGSGLILGGLGVVLLPNPIYSAFSLGLVLVC FT /translation="MDLSEPIHDFLLVFLGSGLILGGLGVVLLPNPIYSAFSLGLVLVC
FT TSLFYILSNAYFVAAAQLLIYVGAINVLIIFAVMFMNGSEYYKDFHLWTVGDGITSMVC FT TSLFYILSNAYFVAAAQLLIYVGAINVLIIFAVMFMNGSEYYKDFHLWTVGDGITSMVC
@ -146,7 +146,7 @@ FT /codon_start=1
FT /transl_table=11 FT /transl_table=11
FT /gene="ndhH" FT /gene="ndhH"
FT /locus_tag="" 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 /inference="similar to DNA sequence:AC_000188:LyesCp078"
FT /translation="MTAPTTRKDLMIVNMGPQHPSMHGVLRLIVTLDGEDVVDCEPILG FT /translation="MTAPTTRKDLMIVNMGPQHPSMHGVLRLIVTLDGEDVVDCEPILG
FT YLHRGMEKIAENRTIIQYLPYVTRWDYLATMFTEAITINGPEQLGNIQVPKRASYIRVI FT YLHRGMEKIAENRTIIQYLPYVTRWDYLATMFTEAITINGPEQLGNIQVPKRASYIRVI
@ -163,7 +163,7 @@ FT /codon_start=1
FT /transl_table=11 FT /transl_table=11
FT /gene="ndhI" FT /gene="ndhI"
FT /locus_tag="" 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 /inference="similar to DNA sequence:AC_000188:LyesCp076"
FT /translation="MLPMITEFINYGQQTIRAARYIGQGFMITLSHANRLPVTIQYPYE FT /translation="MLPMITEFINYGQQTIRAARYIGQGFMITLSHANRLPVTIQYPYE
FT KLITSERFRGRIHFEFDKCIACEVCVRVCPIDLPVVDWKLETDIRKKRLLNYSIDFGIC FT KLITSERFRGRIHFEFDKCIACEVCVRVCPIDLPVVDWKLETDIRKKRLLNYSIDFGIC
@ -177,8 +177,8 @@ FT /codon_start=1
FT /transl_table=11 FT /transl_table=11
FT /gene="psaC" FT /gene="psaC"
FT /locus_tag="" FT /locus_tag=""
FT /product=photosystem I subunit VII FT /product="photosystem I subunit VII"
FT /inference="similar to DNA sequence:NC_022409:CEXI_CP_p076" FT /inference="similar to DNA sequence:NC_023792:CP89_p014"
FT /translation="MSHSVKIYDTCIGCTQCVRACPTDVLEMIPWDGCKAKQIASAPRT FT /translation="MSHSVKIYDTCIGCTQCVRACPTDVLEMIPWDGCKAKQIASAPRT
FT EDCVGCKRCESACPTDFLSVRVYLWHETTRSMGLAY" FT EDCVGCKRCESACPTDFLSVRVYLWHETTRSMGLAY"
FT gene 53817..55307 FT gene 53817..55307
@ -189,8 +189,8 @@ FT /codon_start=1
FT /transl_table=11 FT /transl_table=11
FT /gene="rpl2" FT /gene="rpl2"
FT /locus_tag="" FT /locus_tag=""
FT /product=ribosomal protein L2 FT /product="ribosomal protein L2"
FT /inference="similar to DNA sequence:AC_000188:LyesCp030" FT /inference="similar to DNA sequence:NC_007898:LyesC2p002"
FT /translation="MAIHLYKTSTPSTRNGTVDSQVKSNPRNNLIYGQRRCGKGRNARG FT /translation="MAIHLYKTSTPSTRNGTVDSQVKSNPRNNLIYGQRRCGKGRNARG
FT IITARHRGGGHKRLYRKIDFRRNEKDIYGRIVTIEYDPNRNAYICLIHYGDGEKRYILH FT IITARHRGGGHKRLYRKIDFRRNEKDIYGRIVTIEYDPNRNAYICLIHYGDGEKRYILH
FT PRGAIIGDTIVSGTEVPIKMGNALPSTDMPLGTAIHNIEITLGKGGQLARAAGAVAKLI FT PRGAIIGDTIVSGTEVPIKMGNALPSTDMPLGTAIHNIEITLGKGGQLARAAGAVAKLI
@ -212,8 +212,8 @@ FT /codon_start=1
FT /transl_table=11 FT /transl_table=11
FT /gene="rpl23" FT /gene="rpl23"
FT /locus_tag="" FT /locus_tag=""
FT /product=ribosomal protein L23 FT /product="ribosomal protein L23"
FT /inference="similar to DNA sequence:AC_000188:LyesCp026" FT /inference="similar to DNA sequence:NC_007898:LyesC2p003"
FT /translation="MDGIKYAVFTDKSIRLLGKNQYTSNVESGSTRTEIKHWVELFFGV FT /translation="MDGIKYAVFTDKSIRLLGKNQYTSNVESGSTRTEIKHWVELFFGV
FT KVIAMNSHRLPGKSRRMGPIMGHTMHYRRMIITLQPGYSIPPLRKKRT" FT KVIAMNSHRLPGKSRRMGPIMGHTMHYRRMIITLQPGYSIPPLRKKRT"
FT gene 14505..14672 FT gene 14505..14672
@ -224,7 +224,7 @@ FT /codon_start=1
FT /transl_table=11 FT /transl_table=11
FT /gene="rpl32" FT /gene="rpl32"
FT /locus_tag="" FT /locus_tag=""
FT /product=ribosomal protein L32 FT /product="ribosomal protein L32"
FT /inference="similar to DNA sequence:AC_000188:LyesCp036" FT /inference="similar to DNA sequence:AC_000188:LyesCp036"
FT /translation="MAVPKKRTSTSKKRIRKNIWKRKGYWVALKAFSLAKSLSTGNSKS FT /translation="MAVPKKRTSTSKKRIRKNIWKRKGYWVALKAFSLAKSLSTGNSKS
FT FFVRQTKINK" FT FFVRQTKINK"
@ -236,7 +236,7 @@ FT /codon_start=1
FT /transl_table=11 FT /transl_table=11
FT /gene="rps15" FT /gene="rps15"
FT /locus_tag="" FT /locus_tag=""
FT /product=ribosomal protein S15 FT /product="ribosomal protein S15"
FT /inference="similar to DNA sequence:AC_000188:LyesCp029" FT /inference="similar to DNA sequence:AC_000188:LyesCp029"
FT /translation="MVKNSVISVISQEEKKGSVEFQVFNFTNKIRRLTSHLELHKKDYL FT /translation="MVKNSVISVISQEEKKGSVEFQVFNFTNKIRRLTSHLELHKKDYL
FT SQRGLKKILGKRQRLLAYLAKKNRVRYKELINRLDIRETKTR" FT SQRGLKKILGKRQRLLAYLAKKNRVRYKELINRLDIRETKTR"
@ -248,8 +248,8 @@ FT /codon_start=1
FT /transl_table=11 FT /transl_table=11
FT /gene="rps7" FT /gene="rps7"
FT /locus_tag="" FT /locus_tag=""
FT /product=ribosomal protein S7 FT /product="ribosomal protein S7"
FT /inference="similar to DNA sequence:AC_000188:LyesCp008" FT /inference="similar to DNA sequence:NC_007898:LyesC2p007"
FT /translation="MSRRGTAEKKTAKSDPIYRNRLVNMLVNRILKHGKKSLAYQIIYR FT /translation="MSRRGTAEKKTAKSDPIYRNRLVNMLVNRILKHGKKSLAYQIIYR
FT AVKKIQQKTETNPLSVLRQAIRGVTPDITVKARRVGGSTHQVPIEIGSTQGKALAIRWL FT AVKKIQQKTETNPLSVLRQAIRGVTPDITVKARRVGGSTHQVPIEIGSTQGKALAIRWL
FT LAASRKRPGRNMAFKLSSELVDAAKGSGDAIRKKEETHRMAEANRAFAHFR" FT LAASRKRPGRNMAFKLSSELVDAAKGSGDAIRKKEETHRMAEANRAFAHFR"
@ -261,7 +261,7 @@ FT /codon_start=1
FT /transl_table=11 FT /transl_table=11
FT /gene="ycf1" FT /gene="ycf1"
FT /locus_tag="" FT /locus_tag=""
FT /product=hypothetical chloroplast RF1 FT /product="hypothetical chloroplast RF1"
FT /inference="similar to DNA sequence:AC_000188:LyesCp019" FT /inference="similar to DNA sequence:AC_000188:LyesCp019"
FT /translation="MIFQSFLLGNLVSLCMKIINSVVVVGLYYGFLTTFSIGPSYLFLL FT /translation="MIFQSFLLGNLVSLCMKIINSVVVVGLYYGFLTTFSIGPSYLFLL
FT RALVMEEGTEKKVSATTGFITGQLMMFISIYYAPLHLALGRPHTITVLALPYLLFHFFW FT RALVMEEGTEKKVSATTGFITGQLMMFISIYYAPLHLALGRPHTITVLALPYLLFHFFW
@ -304,7 +304,7 @@ FT /codon_start=1
FT /transl_table=11 FT /transl_table=11
FT /gene="ycf2" FT /gene="ycf2"
FT /locus_tag="" FT /locus_tag=""
FT /product=Ycf2 FT /product="Ycf2"
FT /inference="similar to DNA sequence:AC_000188:LyesCp004" FT /inference="similar to DNA sequence:AC_000188:LyesCp004"
FT /translation="MRGHQFKSWIFELREILREIKNSHHFLDSWTQFNSVGSFIHIFFH FT /translation="MRGHQFKSWIFELREILREIKNSHHFLDSWTQFNSVGSFIHIFFH
FT QERFLKLFDPRIWSILLSRNSQGSPSNRYFTIKGVILFVVAVLIYRINNRNMVERKNLY FT QERFLKLFDPRIWSILLSRNSQGSPSNRYFTIKGVILFVVAVLIYRINNRNMVERKNLY

22
scripts/csh_init.sh
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@ -44,8 +44,15 @@ if ($?ORG_SOURCED == 0) then
setenv PROG_DIR `dirname $0` # Directory containing setenv PROG_DIR `dirname $0` # Directory containing
setenv PROG_DIR `cd $PROG_DIR && pwd -P` # the main script file setenv PROG_DIR `cd $PROG_DIR && pwd -P` # the main script file
setenv LIB_DIR "$PROG_DIR/../lib" # Directory containing if (-d "$PROG_DIR/../lib") then
setenv LIB_DIR `cd $LIB_DIR && pwd -P` # the main script libraries setenv LIB_DIR "$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 setenv CALL_DIR `pwd -P` # Directory from where the
# main script is called # main script is called
@ -121,6 +128,17 @@ alias Cat 'awk '"'"'{print "# " $0}'"'"' \!:*'
alias AssignUndef 'if ($?\!:1 == 0) set \!:1=\!:2-*' 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 # reset Stat each time
# -------------------------------------- # --------------------------------------