diff options
author | V3n3RiX <venerix@redcorelinux.org> | 2017-10-09 18:53:29 +0100 |
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committer | V3n3RiX <venerix@redcorelinux.org> | 2017-10-09 18:53:29 +0100 |
commit | 4f2d7949f03e1c198bc888f2d05f421d35c57e21 (patch) | |
tree | ba5f07bf3f9d22d82e54a462313f5d244036c768 /sci-biology/glimmer/files/glimmer-3.02b-rename_extract.patch |
reinit the tree, so we can have metadata
Diffstat (limited to 'sci-biology/glimmer/files/glimmer-3.02b-rename_extract.patch')
-rw-r--r-- | sci-biology/glimmer/files/glimmer-3.02b-rename_extract.patch | 196 |
1 files changed, 196 insertions, 0 deletions
diff --git a/sci-biology/glimmer/files/glimmer-3.02b-rename_extract.patch b/sci-biology/glimmer/files/glimmer-3.02b-rename_extract.patch new file mode 100644 index 000000000000..6eebc5610414 --- /dev/null +++ b/sci-biology/glimmer/files/glimmer-3.02b-rename_extract.patch @@ -0,0 +1,196 @@ +diff -r -u glimmer3.02.old/docs/notes.tex glimmer3.02/docs/notes.tex +--- glimmer3.02.old/docs/notes.tex 2006-06-12 21:40:14.000000000 +0200 ++++ glimmer3.02/docs/notes.tex 2015-05-25 22:41:39.450340098 +0200 +@@ -306,7 +306,7 @@ + The script would then run the commands: + \BSV\begin{verbatim} + long-orfs -n -t 1.15 genom.seq run1.longorfs +- extract -t genom.seq run1.longorfs > run1.train ++ glimmer_extract -t genom.seq run1.longorfs > run1.train + build-icm -r run1.icm < run1.train + glimmer3 -o50 -g110 -t30 genom.seq run1.icm run1 + \end{verbatim}\ESV +@@ -330,9 +330,9 @@ + \end{verbatim}\ESV + The script would then run the commands: + \BSV\begin{verbatim} +- extract -t genom.seq train.coords > run2.train ++ glimmer_extract -t genom.seq train.coords > run2.train + build-icm -r run2.icm < run2.train +- upstream-coords.awk 25 0 train.coords | extract genom.seq - > run2.upstream ++ upstream-coords.awk 25 0 train.coords | glimmer_extract genom.seq - > run2.upstream + elph run2.upstream LEN=6 | get-motif-counts.awk > run2.motif + set startuse = `start-codon-distrib -3 genom.seq train.coords` + glimmer3 -o50 -g110 -t30 -b run2.motif -P $startuse genom.seq run2.icm run2 +@@ -358,11 +358,11 @@ + The script would then run the commands: + \BSV\begin{verbatim} + long-orfs -n -t 1.15 genom.seq run3.longorfs +- extract -t genom.seq run3.longorfs > run3.train ++ glimmer_extract -t genom.seq run3.longorfs > run3.train + build-icm -r run3.icm < run3.train + glimmer3 -o50 -g110 -t30 genom.seq run3.icm run3.run1 + tail +2 run3.run1.predict > run3.coords +- upstream-coords.awk 25 0 run3.coords | extract genom.seq - > run3.upstream ++ upstream-coords.awk 25 0 run3.coords | glimmer_extract genom.seq - > run3.upstream + elph run3.upstream LEN=6 | get-motif-counts.awk > run3.motif + set startuse = `start-codon-distrib -3 genom.seq run3.coords` + glimmer3 -o50 -g110 -t30 -b run3.motif -P $startuse genom.seq run3.icm run3 +@@ -1081,12 +1081,12 @@ + \Pg{entropy-score}\, [\Desc{options}] \Desc{sequence} \Desc{coords} + \eq + +-\subsubsection{\Pg{extract} Program} ++\subsubsection{\Pg{glimmer_extract} Program} + This program reads a genome sequence and a list of coordinates + for it and outputs a multi-fasta file of the regions specified + by the coordinates. Output goes to standard output. + \bq +- \Pg{extract}\, [\Desc{options}] \Desc{sequence} \Desc{coords} ++ \Pg{glimmer_extract}\, [\Desc{options}] \Desc{sequence} \Desc{coords} + \eq + + \subsubsection{\Pg{multi-extract} Program} +diff -r -u glimmer3.02.old/sample-run/g3-from-scratch.csh glimmer3.02/sample-run/g3-from-scratch.csh +--- glimmer3.02.old/sample-run/g3-from-scratch.csh 2006-06-12 21:46:35.000000000 +0200 ++++ glimmer3.02/sample-run/g3-from-scratch.csh 2015-05-25 22:40:18.450338748 +0200 +@@ -50,7 +50,7 @@ + step2: + # Extract the training sequences from the genome file + echo "Step 2 of ${numsteps}: Extracting training sequences" +-$glimmerpath/extract -t $genome $tag.longorfs > $tag.train ++$glimmerpath/glimmer_extract -t $genome $tag.longorfs > $tag.train + if ($status != 0) then + echo "Failed to extract training sequences" + exit +diff -r -u glimmer3.02.old/sample-run/g3-from-training.csh glimmer3.02/sample-run/g3-from-training.csh +--- glimmer3.02.old/sample-run/g3-from-training.csh 2006-06-12 21:46:35.000000000 +0200 ++++ glimmer3.02/sample-run/g3-from-training.csh 2015-05-25 22:40:18.450338748 +0200 +@@ -42,7 +42,7 @@ + step1: + # Extract the training sequences from the genome file + echo "Step 1 of ${numsteps}: Extracting training sequences" +-$glimmerpath/extract -t $genome $coords > $tag.train ++$glimmerpath/glimmer_extract -t $genome $coords > $tag.train + if ($status != 0) then + echo "Failed to extract training sequences" + exit +@@ -66,7 +66,7 @@ + # upstream of the start locations in $coords + echo "Step 3 of ${numsteps}: Making PWM from upstream regions" + $awkpath/upstream-coords.awk 25 0 $coords \ +- | $glimmerpath/extract $genome - > $tag.upstream ++ | $glimmerpath/glimmer_extract $genome - > $tag.upstream + $elphbin $tag.upstream LEN=6 | $awkpath/get-motif-counts.awk > $tag.motif + if ($status != 0) then + echo "Failed to create PWM" +diff -r -u glimmer3.02.old/sample-run/g3-iterated.csh glimmer3.02/sample-run/g3-iterated.csh +--- glimmer3.02.old/sample-run/g3-iterated.csh 2006-06-13 14:15:28.000000000 +0200 ++++ glimmer3.02/sample-run/g3-iterated.csh 2015-05-25 22:40:18.450338748 +0200 +@@ -57,7 +57,7 @@ + step2: + # Extract the training sequences from the genome file + echo "Step 2 of ${numsteps}: Extracting training sequences" +-$glimmerpath/extract -t $genome $tag.longorfs > $tag.train ++$glimmerpath/glimmer_extract -t $genome $tag.longorfs > $tag.train + if ($status != 0) then + echo "Failed to extract training sequences" + exit +@@ -103,7 +103,7 @@ + # upstream of the start locations in $tag.coords + echo "Step 6 of ${numsteps}: Making PWM from upstream regions" + $awkpath/upstream-coords.awk 25 0 $tag.coords \ +- | $glimmerpath/extract $genome - > $tag.upstream ++ | $glimmerpath/glimmer_extract $genome - > $tag.upstream + $elphbin $tag.upstream LEN=6 | $awkpath/get-motif-counts.awk > $tag.motif + if ($status != 0) then + echo "Failed to create PWM" +diff -r -u glimmer3.02.old/scripts/g3-from-scratch.csh glimmer3.02/scripts/g3-from-scratch.csh +--- glimmer3.02.old/scripts/g3-from-scratch.csh 2006-06-12 21:40:14.000000000 +0200 ++++ glimmer3.02/scripts/g3-from-scratch.csh 2015-05-25 22:44:44.190343177 +0200 +@@ -50,7 +50,7 @@ + step2: + # Extract the training sequences from the genome file + echo "Step 2 of ${numsteps}: Extracting training sequences" +-$glimmerpath/extract -t $genome $tag.longorfs > $tag.train ++$glimmerpath/glimmer_extract -t $genome $tag.longorfs > $tag.train + if ($status != 0) then + echo "Failed to extract training sequences" + exit +diff -r -u glimmer3.02.old/scripts/g3-from-training.csh glimmer3.02/scripts/g3-from-training.csh +--- glimmer3.02.old/scripts/g3-from-training.csh 2006-06-12 21:40:14.000000000 +0200 ++++ glimmer3.02/scripts/g3-from-training.csh 2015-05-25 22:44:44.190343177 +0200 +@@ -42,7 +42,7 @@ + step1: + # Extract the training sequences from the genome file + echo "Step 1 of ${numsteps}: Extracting training sequences" +-$glimmerpath/extract -t $genome $coords > $tag.train ++$glimmerpath/glimmer_extract -t $genome $coords > $tag.train + if ($status != 0) then + echo "Failed to extract training sequences" + exit +@@ -66,7 +66,7 @@ + # upstream of the start locations in $coords + echo "Step 3 of ${numsteps}: Making PWM from upstream regions" + $awkpath/upstream-coords.awk 25 0 $coords \ +- | $glimmerpath/extract $genome - > $tag.upstream ++ | $glimmerpath/glimmer_extract $genome - > $tag.upstream + $elphbin $tag.upstream LEN=6 | $awkpath/get-motif-counts.awk > $tag.motif + if ($status != 0) then + echo "Failed to create PWM" +diff -r -u glimmer3.02.old/scripts/g3-iterated.csh glimmer3.02/scripts/g3-iterated.csh +--- glimmer3.02.old/scripts/g3-iterated.csh 2006-06-13 14:15:46.000000000 +0200 ++++ glimmer3.02/scripts/g3-iterated.csh 2015-05-25 22:44:44.190343177 +0200 +@@ -57,7 +57,7 @@ + step2: + # Extract the training sequences from the genome file + echo "Step 2 of ${numsteps}: Extracting training sequences" +-$glimmerpath/extract -t $genome $tag.longorfs > $tag.train ++$glimmerpath/glimmer_extract -t $genome $tag.longorfs > $tag.train + if ($status != 0) then + echo "Failed to extract training sequences" + exit +@@ -103,7 +103,7 @@ + # upstream of the start locations in $tag.coords + echo "Step 6 of ${numsteps}: Making PWM from upstream regions" + $awkpath/upstream-coords.awk 25 0 $tag.coords \ +- | $glimmerpath/extract $genome - > $tag.upstream ++ | $glimmerpath/glimmer_extract $genome - > $tag.upstream + $elphbin $tag.upstream LEN=6 | $awkpath/get-motif-counts.awk > $tag.motif + if ($status != 0) then + echo "Failed to create PWM" +diff -r -u glimmer3.02.old/src/Util/Makefile glimmer3.02/src/Util/Makefile +--- glimmer3.02.old/src/Util/Makefile 2006-06-12 21:40:14.000000000 +0200 ++++ glimmer3.02/src/Util/Makefile 2015-05-25 22:43:12.760341653 +0200 +@@ -8,7 +8,7 @@ + SOURCES = $(UTIL_SRCS) + OBJECTS = $(UTIL_OBJS) + +-PROGS = entropy-profile entropy-score extract multi-extract start-codon-distrib \ ++PROGS = entropy-profile entropy-score glimmer_extract multi-extract start-codon-distrib \ + uncovered window-acgt + + LIBRARIES = +diff -r -u glimmer3.02.old/src/Util/extract.cc glimmer3.02/src/Util/extract.cc +--- glimmer3.02.old/src/Util/extract.cc 2006-06-12 21:40:14.000000000 +0200 ++++ glimmer3.02/src/Util/extract.cc 2015-05-25 22:44:01.760342470 +0200 +@@ -297,7 +297,7 @@ + + { + fprintf (stderr, +- "USAGE: extract [options] <sequence-file> <coords>\n" ++ "USAGE: glimmer_extract [options] <sequence-file> <coords>\n" + "\n" + "Read fasta-format <sequence-file> and extract from it the\n" + "subsequences specified by <coords>. By default, <coords>\n" +--- glimmer3.02.old/src/Util/Makefile 2015-05-25 22:43:12.760341653 +0200 ++++ glimmer-3.02-r3/work/glimmer3.02/src/Util/Makefile 2015-05-25 23:13:34.230372010 +0200 +@@ -21,7 +21,7 @@ + + entropy-score: entropy-score.o libGLMcommon.a + +-extract: extract.o libGLMcommon.a ++glimmer_extract: extract.o libGLMcommon.a + + multi-extract: multi-extract.o libGLMcommon.a + |