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197 lines
9.1 KiB
197 lines
9.1 KiB
diff -r -u glimmer3.02.old/docs/notes.tex glimmer3.02/docs/notes.tex
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--- glimmer3.02.old/docs/notes.tex 2006-06-12 21:40:14.000000000 +0200
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+++ glimmer3.02/docs/notes.tex 2015-05-25 22:41:39.450340098 +0200
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@@ -306,7 +306,7 @@
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The script would then run the commands:
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\BSV\begin{verbatim}
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long-orfs -n -t 1.15 genom.seq run1.longorfs
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- extract -t genom.seq run1.longorfs > run1.train
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+ glimmer_extract -t genom.seq run1.longorfs > run1.train
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build-icm -r run1.icm < run1.train
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glimmer3 -o50 -g110 -t30 genom.seq run1.icm run1
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\end{verbatim}\ESV
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@@ -330,9 +330,9 @@
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\end{verbatim}\ESV
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The script would then run the commands:
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\BSV\begin{verbatim}
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- extract -t genom.seq train.coords > run2.train
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+ glimmer_extract -t genom.seq train.coords > run2.train
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build-icm -r run2.icm < run2.train
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- upstream-coords.awk 25 0 train.coords | extract genom.seq - > run2.upstream
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+ upstream-coords.awk 25 0 train.coords | glimmer_extract genom.seq - > run2.upstream
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elph run2.upstream LEN=6 | get-motif-counts.awk > run2.motif
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set startuse = `start-codon-distrib -3 genom.seq train.coords`
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glimmer3 -o50 -g110 -t30 -b run2.motif -P $startuse genom.seq run2.icm run2
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@@ -358,11 +358,11 @@
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The script would then run the commands:
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\BSV\begin{verbatim}
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long-orfs -n -t 1.15 genom.seq run3.longorfs
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- extract -t genom.seq run3.longorfs > run3.train
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+ glimmer_extract -t genom.seq run3.longorfs > run3.train
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build-icm -r run3.icm < run3.train
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glimmer3 -o50 -g110 -t30 genom.seq run3.icm run3.run1
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tail +2 run3.run1.predict > run3.coords
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- upstream-coords.awk 25 0 run3.coords | extract genom.seq - > run3.upstream
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+ upstream-coords.awk 25 0 run3.coords | glimmer_extract genom.seq - > run3.upstream
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elph run3.upstream LEN=6 | get-motif-counts.awk > run3.motif
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set startuse = `start-codon-distrib -3 genom.seq run3.coords`
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glimmer3 -o50 -g110 -t30 -b run3.motif -P $startuse genom.seq run3.icm run3
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@@ -1081,12 +1081,12 @@
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\Pg{entropy-score}\, [\Desc{options}] \Desc{sequence} \Desc{coords}
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\eq
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-\subsubsection{\Pg{extract} Program}
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+\subsubsection{\Pg{glimmer_extract} Program}
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This program reads a genome sequence and a list of coordinates
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for it and outputs a multi-fasta file of the regions specified
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by the coordinates. Output goes to standard output.
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\bq
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- \Pg{extract}\, [\Desc{options}] \Desc{sequence} \Desc{coords}
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+ \Pg{glimmer_extract}\, [\Desc{options}] \Desc{sequence} \Desc{coords}
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\eq
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\subsubsection{\Pg{multi-extract} Program}
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diff -r -u glimmer3.02.old/sample-run/g3-from-scratch.csh glimmer3.02/sample-run/g3-from-scratch.csh
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--- glimmer3.02.old/sample-run/g3-from-scratch.csh 2006-06-12 21:46:35.000000000 +0200
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+++ glimmer3.02/sample-run/g3-from-scratch.csh 2015-05-25 22:40:18.450338748 +0200
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@@ -50,7 +50,7 @@
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step2:
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# Extract the training sequences from the genome file
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echo "Step 2 of ${numsteps}: Extracting training sequences"
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-$glimmerpath/extract -t $genome $tag.longorfs > $tag.train
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+$glimmerpath/glimmer_extract -t $genome $tag.longorfs > $tag.train
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if ($status != 0) then
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echo "Failed to extract training sequences"
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exit
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diff -r -u glimmer3.02.old/sample-run/g3-from-training.csh glimmer3.02/sample-run/g3-from-training.csh
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--- glimmer3.02.old/sample-run/g3-from-training.csh 2006-06-12 21:46:35.000000000 +0200
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+++ glimmer3.02/sample-run/g3-from-training.csh 2015-05-25 22:40:18.450338748 +0200
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@@ -42,7 +42,7 @@
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step1:
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# Extract the training sequences from the genome file
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echo "Step 1 of ${numsteps}: Extracting training sequences"
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-$glimmerpath/extract -t $genome $coords > $tag.train
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+$glimmerpath/glimmer_extract -t $genome $coords > $tag.train
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if ($status != 0) then
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echo "Failed to extract training sequences"
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exit
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@@ -66,7 +66,7 @@
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# upstream of the start locations in $coords
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echo "Step 3 of ${numsteps}: Making PWM from upstream regions"
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$awkpath/upstream-coords.awk 25 0 $coords \
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- | $glimmerpath/extract $genome - > $tag.upstream
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+ | $glimmerpath/glimmer_extract $genome - > $tag.upstream
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$elphbin $tag.upstream LEN=6 | $awkpath/get-motif-counts.awk > $tag.motif
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if ($status != 0) then
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echo "Failed to create PWM"
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diff -r -u glimmer3.02.old/sample-run/g3-iterated.csh glimmer3.02/sample-run/g3-iterated.csh
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--- glimmer3.02.old/sample-run/g3-iterated.csh 2006-06-13 14:15:28.000000000 +0200
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+++ glimmer3.02/sample-run/g3-iterated.csh 2015-05-25 22:40:18.450338748 +0200
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@@ -57,7 +57,7 @@
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step2:
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# Extract the training sequences from the genome file
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echo "Step 2 of ${numsteps}: Extracting training sequences"
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-$glimmerpath/extract -t $genome $tag.longorfs > $tag.train
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+$glimmerpath/glimmer_extract -t $genome $tag.longorfs > $tag.train
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if ($status != 0) then
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echo "Failed to extract training sequences"
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exit
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@@ -103,7 +103,7 @@
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# upstream of the start locations in $tag.coords
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echo "Step 6 of ${numsteps}: Making PWM from upstream regions"
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$awkpath/upstream-coords.awk 25 0 $tag.coords \
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- | $glimmerpath/extract $genome - > $tag.upstream
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+ | $glimmerpath/glimmer_extract $genome - > $tag.upstream
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$elphbin $tag.upstream LEN=6 | $awkpath/get-motif-counts.awk > $tag.motif
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if ($status != 0) then
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echo "Failed to create PWM"
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diff -r -u glimmer3.02.old/scripts/g3-from-scratch.csh glimmer3.02/scripts/g3-from-scratch.csh
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--- glimmer3.02.old/scripts/g3-from-scratch.csh 2006-06-12 21:40:14.000000000 +0200
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+++ glimmer3.02/scripts/g3-from-scratch.csh 2015-05-25 22:44:44.190343177 +0200
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@@ -50,7 +50,7 @@
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step2:
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# Extract the training sequences from the genome file
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echo "Step 2 of ${numsteps}: Extracting training sequences"
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-$glimmerpath/extract -t $genome $tag.longorfs > $tag.train
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+$glimmerpath/glimmer_extract -t $genome $tag.longorfs > $tag.train
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if ($status != 0) then
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echo "Failed to extract training sequences"
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exit
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diff -r -u glimmer3.02.old/scripts/g3-from-training.csh glimmer3.02/scripts/g3-from-training.csh
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--- glimmer3.02.old/scripts/g3-from-training.csh 2006-06-12 21:40:14.000000000 +0200
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+++ glimmer3.02/scripts/g3-from-training.csh 2015-05-25 22:44:44.190343177 +0200
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@@ -42,7 +42,7 @@
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step1:
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# Extract the training sequences from the genome file
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echo "Step 1 of ${numsteps}: Extracting training sequences"
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-$glimmerpath/extract -t $genome $coords > $tag.train
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+$glimmerpath/glimmer_extract -t $genome $coords > $tag.train
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if ($status != 0) then
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echo "Failed to extract training sequences"
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exit
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@@ -66,7 +66,7 @@
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# upstream of the start locations in $coords
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echo "Step 3 of ${numsteps}: Making PWM from upstream regions"
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$awkpath/upstream-coords.awk 25 0 $coords \
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- | $glimmerpath/extract $genome - > $tag.upstream
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+ | $glimmerpath/glimmer_extract $genome - > $tag.upstream
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$elphbin $tag.upstream LEN=6 | $awkpath/get-motif-counts.awk > $tag.motif
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if ($status != 0) then
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echo "Failed to create PWM"
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diff -r -u glimmer3.02.old/scripts/g3-iterated.csh glimmer3.02/scripts/g3-iterated.csh
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--- glimmer3.02.old/scripts/g3-iterated.csh 2006-06-13 14:15:46.000000000 +0200
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+++ glimmer3.02/scripts/g3-iterated.csh 2015-05-25 22:44:44.190343177 +0200
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@@ -57,7 +57,7 @@
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step2:
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# Extract the training sequences from the genome file
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echo "Step 2 of ${numsteps}: Extracting training sequences"
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-$glimmerpath/extract -t $genome $tag.longorfs > $tag.train
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+$glimmerpath/glimmer_extract -t $genome $tag.longorfs > $tag.train
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if ($status != 0) then
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echo "Failed to extract training sequences"
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exit
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@@ -103,7 +103,7 @@
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# upstream of the start locations in $tag.coords
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echo "Step 6 of ${numsteps}: Making PWM from upstream regions"
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$awkpath/upstream-coords.awk 25 0 $tag.coords \
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- | $glimmerpath/extract $genome - > $tag.upstream
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+ | $glimmerpath/glimmer_extract $genome - > $tag.upstream
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$elphbin $tag.upstream LEN=6 | $awkpath/get-motif-counts.awk > $tag.motif
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if ($status != 0) then
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echo "Failed to create PWM"
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diff -r -u glimmer3.02.old/src/Util/Makefile glimmer3.02/src/Util/Makefile
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--- glimmer3.02.old/src/Util/Makefile 2006-06-12 21:40:14.000000000 +0200
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+++ glimmer3.02/src/Util/Makefile 2015-05-25 22:43:12.760341653 +0200
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@@ -8,7 +8,7 @@
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SOURCES = $(UTIL_SRCS)
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OBJECTS = $(UTIL_OBJS)
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-PROGS = entropy-profile entropy-score extract multi-extract start-codon-distrib \
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+PROGS = entropy-profile entropy-score glimmer_extract multi-extract start-codon-distrib \
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uncovered window-acgt
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LIBRARIES =
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diff -r -u glimmer3.02.old/src/Util/extract.cc glimmer3.02/src/Util/extract.cc
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--- glimmer3.02.old/src/Util/extract.cc 2006-06-12 21:40:14.000000000 +0200
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+++ glimmer3.02/src/Util/extract.cc 2015-05-25 22:44:01.760342470 +0200
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@@ -297,7 +297,7 @@
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{
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fprintf (stderr,
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- "USAGE: extract [options] <sequence-file> <coords>\n"
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+ "USAGE: glimmer_extract [options] <sequence-file> <coords>\n"
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"\n"
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"Read fasta-format <sequence-file> and extract from it the\n"
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"subsequences specified by <coords>. By default, <coords>\n"
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--- glimmer3.02.old/src/Util/Makefile 2015-05-25 22:43:12.760341653 +0200
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+++ glimmer-3.02-r3/work/glimmer3.02/src/Util/Makefile 2015-05-25 23:13:34.230372010 +0200
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@@ -21,7 +21,7 @@
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entropy-score: entropy-score.o libGLMcommon.a
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-extract: extract.o libGLMcommon.a
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+glimmer_extract: extract.o libGLMcommon.a
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multi-extract: multi-extract.o libGLMcommon.a
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