Added shell script for generating the download page

download.html

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+
+<h4><p><b>Potential functional motifs per tissue type</b></p></h4><hr/><ul>
+<li><a href='bed/blood.funmotifs.bed.tar.gz' download>blood.funmotifs</a><br/></li>
+<li><a href='bed/brain.funmotifs.bed.tar.gz' download>brain.funmotifs</a><br/></li>
+<li><a href='bed/breast.funmotifs.bed.tar.gz' download>breast.funmotifs</a><br/></li>
+<li><a href='bed/cervix.funmotifs.bed.tar.gz' download>cervix.funmotifs</a><br/></li>
+<li><a href='bed/colon.funmotifs.bed.tar.gz' download>colon.funmotifs</a><br/></li>
+<li><a href='bed/esophagus.funmotifs.bed.tar.gz' download>esophagus.funmotifs</a><br/></li>
+<li><a href='bed/kidney.funmotifs.bed.tar.gz' download>kidney.funmotifs</a><br/></li>
+<li><a href='bed/liver.funmotifs.bed.tar.gz' download>liver.funmotifs</a><br/></li>
+<li><a href='bed/lung.funmotifs.bed.tar.gz' download>lung.funmotifs</a><br/></li>
+<li><a href='bed/myeloid.funmotifs.bed.tar.gz' download>myeloid.funmotifs</a><br/></li>
+<li><a href='bed/pancreas.funmotifs.bed.tar.gz' download>pancreas.funmotifs</a><br/></li>
+<li><a href='bed/prostate.funmotifs.bed.tar.gz' download>prostate.funmotifs</a><br/></li>
+<li><a href='bed/skin.funmotifs.bed.tar.gz' download>skin.funmotifs</a><br/></li>
+<li><a href='bed/stomach.funmotifs.bed.tar.gz' download>stomach.funmotifs</a><br/></li>
+<li><a href='bed/uterus.funmotifs.bed.tar.gz' download>uterus.funmotifs</a><br/></li>
+</ul>
+<hr/><h4><p><b>Annotated variatns using funMotifsDB</b></p></h4><hr/>
+<ul>
+<li>Putative regulatory variants from the 1000 Genomes project: <a href='../1000GenomeProject/functional/candidates1000G_tfexpr_entropyabs0.3_dnase_tfbindOrFscore2.55_grouped.tar.gz' download>candidate_variants_1000G.tar.gz</a>.</li>
+<li>Putative regulatory variants from the GTEx project (eQTLs): <a href='../GTEx_eQTLs/GTEx_eQTLs_candidates.tar.gz' download>GTEx_eQTLs_candidates.tar.gz</a>.</li>
+<li>Putative regulatory variants from GWAS : <a href='../GWAS_data/GWAS_SNPs_LD_candiadtes.tar.gz' download>GWAS_SNPs_LD_candiadtes.tar.gz</a>.</li>
+
+</ul>
+<br/><hr/><h4><p><b>All scored motifs per tissue type</b></p></h4><hr/>
+<ul><li><a href='bed/all_tissues.bed.tar.gz' download>All motifs: fscore per tissue type</a></li></ul><br/>
+<hr/><h4><p><b>Data files used to build funMotifsDB</b></p></h4><hr/><ul><li><a href='../datafiles.tar.gz' download>datafiles.tar.gz</a>: information about the contents of this archive is listed <a href='https://github.com/husensofteng/funMotifs/tree/master/ReadMe'>here</a>.</li></ul>

generate_download_files.sh

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+downloadhtmlfile="../../download.html"
+db_name="funmotifsdb"
+tables_db_filename="table_names_funmotifsdb.txt"
+output_dir="www/"
+output_dir2="bed/"
+motifs_table="motifs"
+all_tissues_table="all_tissues"
+col_names_motifs="chr,motifstart,motifend,name,score,pval,strand"
+col_names_all_tissues="blood,brain,breast,cervix,colon,esophagus,kidney,liver,lung,myeloid,pancreas,prostate,skin,stomach,uterus"
+col_names_tissue_table="fscore, chromhmm, contactingdomain, dnase__seq, fantom, loopdomain, numothertfbinding, othertfbinding, replidomain, tfbinding, tfexpr"
+limit_stmt=""
+
+cd $output_dir$output_dir2
+#get tissue names from the database
+psql -d $db_name -c "SELECT distinct(table_name) as table_name FROM information_schema.tables where table_schema='public' and table_name not like '%motif%' order by table_name;" | awk '$0!~"table" && $0!~"---" && $0!~"row" && $0!="" && $0!~"all_tissues"'> $tables_db_filename
+
+echo "" > $downloadhtmlfile
+#GENERATE filtered output (potential functional motifs)
+echo "<h4><p><b>Potential functional motifs per tissue type</b></p></h4><hr/><ul>" >> $downloadhtmlfile 
+#export a file for each tissue table
+while read -r name
+do
+        echo $output_dir$name.funmotifs
+        psql -d $db_name -A -F $'\t' --pset footer -c "select $col_names_motifs,$col_names_tissue_table from $motifs_table,$name where $motifs_table.mid=$name.mid and dnase__seq>0 and (tfexpr>0 or tfexpr='nan') and (fscore>2.55 or (tfbinding>0 and tfbinding!='NaN'))$limit_stmt;" -o $name.funmotifs.bed
+tar -czvf $name.funmotifs.bed.tar.gz $name.funmotifs.bed
+echo "<li><a href='$output_dir2$name.funmotifs.bed.tar.gz' download>$name.funmotifs</a><br/></li>" >> $downloadhtmlfile
+done < $tables_db_filename
+echo "</ul>" >>  $downloadhtmlfile
+
+
+
+#get tissue names
+tissues=$(
+while read line
+do
+  echo -n ",${line}"
+done < $tables_db_filename)
+
+########variants######
+echo "<hr/><h4><p><b>Annotated variatns using funMotifsDB</b></p></h4><hr/>
+<ul>
+<li>Putative regulatory variants from the 1000 Genomes project: <a href='../1000GenomeProject/functional/candidates1000G_tfexpr_entropyabs0.3_dnase_tfbindOrFscore2.55_grouped.tar.gz' download>candidate_variants_1000G.tar.gz</a>.</li>
+<li>Putative regulatory variants from the GTEx project (eQTLs): <a href='../GTEx_eQTLs/GTEx_eQTLs_candidates.tar.gz' download>GTEx_eQTLs_candidates.tar.gz</a>.</li>
+<li>Putative regulatory variants from GWAS : <a href='../GWAS_data/GWAS_SNPs_LD_candiadtes.tar.gz' download>GWAS_SNPs_LD_candiadtes.tar.gz</a>.</li>
+
+</ul>" >> $downloadhtmlfile
+
+##########get motif tables
+tables_motifs_db_filename="motifs_tables.txt"
+psql -d $db_name --pset footer -c "SELECT distinct(table_name) as table_name FROM information_schema.tables where table_schema='public' and table_name like '%motif%' and table_name like '%chr%' order by table_name;" | awk '$0~"chr" && $0~"motifs"' > $tables_motifs_db_filename
+
+echo "<br/><hr/><h4><p><b>All scored motifs per tissue type</b></p></h4><hr/>" >> $downloadhtmlfile
+
+#write the column headers to an outputfile
+psql -d $db_name -A -F $'\t' --pset footer -c "select $col_names_motifs$tissues from $motifs_table,$all_tissues_table where $motifs_table.mid=$all_tissues_table.mid limit 0;" > $all_tissues_table.bed
+
+while read -r name
+do
+        echo $output_dir$name
+psql -d $db_name -A -F $'\t' -t -c "select $col_names_motifs$tissues from $name,$all_tissues_table where $name.mid=$all_tissues_table.mid$limit_stmt;" >> $all_tissues_table.bed
+done < $tables_motifs_db_filename
+tar -czvf $all_tissues_table.bed.tar.gz $all_tissues_table.bed
+
+
+echo "<ul><li><a href='$output_dir2$all_tissues_table.bed.tar.gz' download>All motifs: fscore per tissue type</a></li></ul><br/>" >> $downloadhtmlfile
+
+
+
+#####data_files.tar.gz
+echo "<hr/><h4><p><b>Data files used to build funMotifsDB</b></p></h4><hr/><ul><li><a href='../datafiles.tar.gz' download>datafiles.tar.gz</a>: information about the contents of this archive is listed <a href='https://github.com/husensofteng/funMotifs/tree/master/ReadMe'>here</a>.</li></ul>" >> $downloadhtmlfile
+
+
+