Changeset 414

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Timestamp:
06/23/10 23:29:14 (20 months ago)
Author:
AlexanderPico
Message:

added funcgen dl

Location:
trunk/dbbuilder/src/org/bridgedb/download
Files:
2 modified

Legend:

Unmodified
Added
Removed

  • trunk/dbbuilder/src/org/bridgedb/download/bacteria_download.sh

    r413 r414  
    6464  rm -R ./${mysql_db_name}/ 
    6565 
     66##FUNCGEN 
     67  export species_name="$species_name"; var=`echo "ls -l /pub/bacteria/release-${release}/mysql/" | ncftp ${ftp_site} | perl -ane 'if ( $_ =~ /$Logged in to/ ) { $go=1; next } if ( $go ) { @a=split; $fileName=$a[ scalar( @a ) - 1]; $compareStr=$ENV{ species_name }."_funcgen"; if ( $fileName =~/^$compareStr/) { print $fileName."\n"; } }'`; set -- $var; mysql_efg_name=$1 
     68 
     69  # check variable before proceeding 
     70  if [[ $mysql_efg_name =~ 'species_list' || $mysql_efg_name == '' ]] 
     71  then 
     72        echo "Skip!:  $species_name not found at $ftp_site. Please fix file: $species_list" 
     73        continue 
     74  fi 
     75 
     76  echo "** $mysql_efg_name **" 
     77  mkdir ./${mysql_efg_name} 
     78 
     79 
     80  # get raw tables from ftp site 
     81  ncftpget ${ftp_site} ./${mysql_efg_name} /pub/bacteria/release-${release}/mysql/${mysql_efg_name}/*.txt.gz 
     82  for q in ./${mysql_efg_name}/*.txt.gz 
     83  do 
     84    gunzip $q 
     85  done 
     86 
     87  ncftpget ${ftp_site} ./ /pub/bacteria/release-${release}/mysql/${mysql_efg_name}/${mysql_efg_name}.sql.gz 
     88  gunzip ./${mysql_efg_name}.sql.gz 
     89 
     90  #rename 3-name databases 
     91  mysql_efg_name_local=${mysql_efg_name/escherichia_shigella/escherichia} 
     92 
     93  #create local mysql db 
     94  echo "create database if not exists ${mysql_efg_name_local}" | ${mysql} -u genmapp -pfun4genmapp 
     95  #create schema 
     96  ${mysql} -u genmapp -pfun4genmapp ${mysql_efg_name_local} < ./${mysql_efg_name}.sql 
     97   # place in own scope, due to "cd" command 
     98  ( 
     99    cd ./${mysql_efg_name}; for table_name in *.txt 
     100    do 
     101      ${mysqlimport} -u genmapp -pfun4genmapp ${mysql_efg_name_local} `pwd`/${table_name} 
     102    done 
     103  ) 
     104 
     105  # zip, archive and clean up 
     106  gzip ./${mysql_efg_name}.sql 
     107  tar cvzf ./${mysql_efg_name}.txt.tgz ./${mysql_efg_name}/* 
     108  rm -R ./${mysql_efg_name}/ 
     109 
    66110done 
    67111 

  • trunk/dbbuilder/src/org/bridgedb/download/plants_download.sh

    r413 r414  
    6060  rm -R ./${mysql_db_name}/ 
    6161 
     62##FUNCGEN 
     63  export species_name="$species_name"; var=`echo "ls -l /pub/plants/release-${release}/mysql/" | ncftp ${ftp_site} | perl -ane 'if ( $_ =~ /$Logged in to/ ) { $go=1; next } if ( $go ) { @a=split; $fileName=$a[ scalar( @a ) - 1]; $compareStr=$ENV{ species_name }."_funcgen"; if ( $fileName =~/^$compareStr/) { print $fileName."\n"; } }'`; set -- $var; mysql_efg_name=$1 
     64 
     65  # check variable before proceeding 
     66  if [[ $mysql_efg_name =~ 'species_list' || $mysql_efg_name == '' ]] 
     67  then 
     68        echo "Skip!:  $species_name not found at $ftp_site. Please fix file: $species_list" 
     69        continue 
     70  fi 
     71 
     72  echo "** $mysql_efg_name **" 
     73  mkdir ./${mysql_efg_name} 
     74 
     75  # get raw tables from ftp site 
     76  ncftpget ${ftp_site} ./${mysql_efg_name} /pub/plants/release-${release}/mysql/${mysql_efg_name}/*.txt.gz 
     77  for q in ./${mysql_efg_name}/*.txt.gz 
     78  do 
     79    gunzip $q 
     80  done 
     81 
     82  ncftpget ${ftp_site} ./ /pub/plants/release-${release}/mysql/${mysql_efg_name}/${mysql_efg_name}.sql.gz 
     83  gunzip ./${mysql_efg_name}.sql.gz 
     84 
     85  #create local mysql db 
     86  echo "create database if not exists ${mysql_efg_name}" | ${mysql} -u genmapp -pfun4genmapp 
     87  #create schema 
     88  ${mysql} -u genmapp -pfun4genmapp ${mysql_efg_name} < ./${mysql_efg_name}.sql 
     89   # place in own scope, due to "cd" command 
     90  ( 
     91    cd ./${mysql_efg_name}; for table_name in *.txt 
     92    do 
     93      ${mysqlimport} -u genmapp -pfun4genmapp ${mysql_efg_name} `pwd`/${table_name} 
     94    done 
     95  ) 
     96 
     97  # zip, archive and clean up 
     98  gzip ./${mysql_efg_name}.sql 
     99  tar cvzf ./${mysql_efg_name}.txt.tgz ./${mysql_efg_name}/* 
     100  rm -R ./${mysql_efg_name}/ 
     101 
    62102done 
    63103