diff snpEff_2_1a/scripts/download.sh @ 0:f8eaa3f8194b default tip

Uploaded snpEff_v2_1a_core.tgz from Pablo Cingolani

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/snpEff_2_1a/scripts/download.sh	Fri Apr 20 14:47:09 2012 -0400
@@ -0,0 +1,120 @@
+#!/bin/sh -e
+
+RELEASE=66
+
+# mkdir download
+cd download
+
+#---
+# Download
+#---
+
+# # Download GTF files (annotations)
+# wget -r -A "*gtf.gz" "ftp://ftp.ensembl.org/pub/release-$RELEASE/gtf/"
+# 
+# # Download FASTA files (reference genomes)
+# wget -r -A "*toplevel.fa.gz" "ftp://ftp.ensembl.org/pub/release-$RELEASE/fasta/"
+# 
+# # Download CDS sequences
+# wget -r -A "*cdna.all.fa.gz" "ftp://ftp.ensembl.org/pub/release-$RELEASE/fasta/"
+# 
+# # Download PROTEIN sequences
+# wget -r -A "*.pep.all.fa.gz" "ftp://ftp.ensembl.org/pub/release-$RELEASE/fasta/"
+
+#---
+# Create directory structure
+#---
+
+# # Move all downloaded file to this directory
+# mv `find ftp.ensembl.org -type f` .
+ 
+# # Gene annotations files
+# for gtf in *.gtf.gz
+# do
+# 	short=`../scripts/file2GenomeName.pl $gtf | cut -f 5`
+# 	echo ANNOTATIONS: $short
+# 
+# 	mkdir -p data/$short
+# 	cp $gtf data/$short/genes.gtf.gz
+# done
+#  
+# # Reference genomes files
+# mkdir -p data/genomes
+# for fasta in *.dna.toplevel.fa.gz
+# do
+# 	genome=`../scripts/file2GenomeName.pl $fasta | cut -f 5`
+# 	echo REFERENCE: $genome
+# 
+# 	cp $fasta data/genomes/$genome.fa.gz
+# done
+# 
+# # CDS genomes files
+# for fasta in *.cdna.all.fa.gz
+# do
+# 	genome=`../scripts/file2GenomeName.pl $fasta | cut -f 5`
+# 	echo CDS: $genome
+# 
+# 	cp $fasta data/$genome/cds.fa.gz
+# done
+# 
+# # Protein seuqence files
+# for pep in *.pep.all.fa.gz
+# do
+# 	short=`../scripts/file2GenomeName.pl $pep | cut -f 5`
+# 	echo PROTEIN: $short
+# 
+# 	mkdir -p data/$short
+# 	cp $pep data/$short/protein.fa.gz
+# done
+
+#---
+# Config file entries
+#---
+
+# for fasta in *.cdna.all.fa.gz
+# do
+# 	genome=`../scripts/file2GenomeName.pl $fasta | cut -f 4`
+# 	short=`../scripts/file2GenomeName.pl $fasta | cut -f 5`
+# 
+# 	# Individual genome entry
+# 	echo -e "$short.genome : $genome"
+# 	echo -e "$short.reference : ftp://ftp.ensembl.org/pub/release-$RELEASE/gtf/"
+# 	echo
+# done
+
+# Back to parent dir
+cd - > /dev/null
+
+#---
+# Create build queue entries
+#---
+
+# rm -vf queue_build.txt
+# 
+# # Build from TXT files
+# for genes in data/*/genes.txt*
+# do
+# 	dir=`dirname $genes`
+# 	genomeName=`basename $dir`
+# 	echo "./scripts/snpEffXL.sh build -v $genomeName"
+# done | sort >> queue_build.txt
+# 
+# # Build from GFF2 files
+# echo "./scripts/snpEffXL.sh build -v -gff2 amel2" >> queue_build.txt
+# 
+# # Build from GFF3 files
+# for genes in `ls data/*/genes.gff* | grep -v amel2`
+# do
+# 	dir=`dirname $genes`
+# 	genomeName=`basename $dir`
+# 	echo "./scripts/snpEffXL.sh build -v -gff3 $genomeName"
+# done | sort >> queue_build.txt
+# 
+# # Build from GTF22 files
+# for genes in data/*/genes.gtf*
+# do
+# 	dir=`dirname $genes`
+# 	genomeName=`basename $dir`
+# 	echo "./scripts/snpEffXL.sh build -v -gtf22 $genomeName"
+# done | sort >> queue_build.txt
+