#### obtain all the genes for the 'mito' browser

### This script will use the mito.chrom.sizes listing which defines
###  the species used in the mito browser.  It will parse the names
###  to determine if they are UCSC databse browsers or GenArk browsers.
###  Then, it will check those browser build directories to find the
###  appropriate gene definitions and gather them all together
###  in this /hive/data/genomes/mito/trackData/genes/<species>
###  directory.

#########################################################################
#!/bin/bash

mkdir -p /hive/data/genomes/mito/trackData/genes
cd /hive/data/genomes/mito/trackData/genes

for asmChr in `cut -f1 ../../mito.chrom.sizes`
do
  case "${asmChr}" in
      GC*)
        asmName=`echo $asmChr | cut -d'_' -f1-2 | sed -e 's/v/./;'`
        chrName=`echo $asmChr | cut -d'_' -f3-`
        gcX="${asmName:0:3}"
        d0="${asmName:4:3}"
        d1="${asmName:7:3}"
        d2="${asmName:10:3}"
        t=`ls -d /hive/data/genomes/asmHubs/allBuild/${gcX}/${d0}/${d1}/${d2}/${asmName}_*`
        if [ -d "${t}" ]; then
          buildDir=`realpath "${t}"`
          asmId=`basename "${buildDir}"`
          ncbiRefSeq="${buildDir}/trackData/ncbiRefSeq"
          if [ -d "${ncbiRefSeq}" ]; then
            if [ ! -s "${asmName}/${asmChr}.gp.gz" ]; then
              printf "%s %s %s\n" "${asmId}" "${asmChr}" "${chrName}"
              mkdir -p "${asmName}"
              if [ -s "${ncbiRefSeq}/process/${asmId}.other.gp" -a -s "${ncbiRefSeq}/process/${asmId}.ncbiRefSeq.gp" ]; then
              egrep -h -w "${chrName}" \
                "${ncbiRefSeq}/process/${asmId}.ncbiRefSeq.gp" \
                "${ncbiRefSeq}/process/${asmId}.other.gp" \
                  | sort -u | tawk -v chr="${asmChr}" '{$2=chr; print $0}' \
                     | gzip -c > "${asmName}/${asmChr}.gp.gz"
printf "# DBG proceess %s both\n" "${asmChr}" 1>&2
             elif [ -s "${ncbiRefSeq}/process/${asmId}.ncbiRefSeq.gp" ]; then
              egrep -h -w "${chrName}" \
                "${ncbiRefSeq}/process/${asmId}.ncbiRefSeq.gp" \
                  | sort -u | tawk -v chr="${asmChr}" '{$2=chr; print $0}' \
                     | gzip -c > "${asmName}/${asmChr}.gp.gz"
printf "# DBG proceess %s other\n" "${asmChr}" 1>&2
              elif [ -s "${ncbiRefSeq}/process/${asmId}.other.gp" ]; then
              egrep -h -w "${chrName}" \
                "${ncbiRefSeq}/process/${asmId}.other.gp" \
                  | sort -u | tawk -v chr="${asmChr}" '{$2=chr; print $0}' \
                     | gzip -c > "${asmName}/${asmChr}.gp.gz"
printf "# DBG %s\n" "${asmChr}" 1>&2
              else
                 printf "# can not find ncbiRefSeq.gp or other.gp\n"
              fi
            else
              printf "DONE\t%s %s %s\n" "${asmId}" "${asmChr}" "${chrName}"
            fi
          else
            printf "%s: no ncbiRefSeq\n" "${asmName}"
          fi
        else
          printf "%s: GCx missing buildDir\n" "${asmName}"
        fi
        ;;
      mm10_chrM)
        if [ ! -s "mm10/${asmChr}.gp.gz" ]; then
          printf "%s\n" "mm10/${asmChr}.gp.gz"
          mkdir -p mm10
          zcat /hive/data/genomes/mm10/bed/ncbiRefSeq.p6.2021-04-22/process/mm10.curated.gp.gz \
             | awk '$2 == "chrM"' \
                  | sed -e 's/chrM/mm10_chrM/;' \
                 | gzip -c > mm10/${asmChr}.gp.gz
         else
          printf "DONE\t%s\n" "mm10/${asmChr}.gp.gz"
        fi
        ;;
      mm39_chrM)
        if [ ! -s "hg39/${asmChr}.gp.gz" ]; then
          mkdir -p mm39
          zcat /hive/data/genomes/mm39/bed/ncbiRefSeq.2023-04-19/process/mm39.other.gp.gz \
             | awk '$2 == "chrM"' \
                  | sed -e 's/chrM/mm39_chrM/;' \
                 | gzip -c > mm39/${asmChr}.gp.gz
        else
          printf "DONE\t%s\n" "mm39/${asmChr}.gp.gz"
        fi
        ;;
      hg19a_chrM)
        if [ ! -s "hg19/${asmChr}.gp.gz" ]; then
        mkdir -p hg19
        hgsql -N -e 'select * from ensGene where chrom="chrM";' hg19 \
           | cut -f2- | sed -e 's/chrM/hg19a_chrM/;' | gzip -c > hg19/${asmChr}.gp.gz
        else
          printf "DONE\t%s\n" "hg19/${asmChr}.gp.gz"
        fi
        ;;
      hg19b_chrMT)
        if [ ! -s "hg19/${asmChr}.gp.gz" ]; then
          mkdir -p hg19
          zcat /hive/data/genomes/hg38/bed/ncbiRefSeq.p14.2023-03-29/process/hg38.other.gp.gz \
             | awk '$2 == "chrM"' \
                  | sed -e "s/chrM/${asmChr}/;" \
                     | gzip > hg19/${asmChr}.gp.gz
        else
          printf "DONE\t%s\n" "hg19/${asmChr}.gp.gz"
        fi
        ;;
      hg38_chrM)
        if [ ! -s "hg38/${asmChr}.gp.gz" ]; then
        mkdir -p hg38
        zcat /hive/data/genomes/hg38/bed/ncbiRefSeq.p14.2023-03-29/process/hg38.other.gp.gz \
           | awk '$2 == "chrM"' \
               | sed -e 's/chrM/hg38_chrM/;' \
                  | gzip > hg38/${asmChr}.gp.gz
        else
          printf "DONE\t%s\n" "hg38/${asmChr}.gp.gz"
        fi
        ;;
      [a-z]*)
        asmName=`echo $asmChr | cut -d'_' -f1`
        chr=`echo $asmChr | cut -d'_' -f2-`
        buildDir="/hive/data/genomes/${asmName}"
        if [ -d "${buildDir}" ]; then
          printf "DBG %s:\t" "${asmChr}" 1>&2
          hgsql -N -e 'show tables;' $asmName | grep -i gene | while read tbl
          do
            printf " %s" "${tbl}"
          done
          printf "\n"
          # priority of gene tables
          for xTbl in ncbiRefSeq ensGene refGene augustusGene
          do
          hgsql -N -e 'show tables;' $asmName | grep -i gene | while read tbl
          do
             case "${tbl}" in
               $xTbl)
                 mkdir -p "${asmName}"
                 if [ ! -s "$asmName/${asmChr}.gp.gz" ]; then
printf "DBG select * from $tbl where chrom=\"$chr\"; $asmName\n" 1>&2
       hgsql -N -e "select * from $tbl where chrom=\"$chr\";" $asmName \
                   | cut -f2- | tawk -v chr="${asmChr}" '{$2=chr; print $0}' \
                      | gzip -c > $asmName/${asmChr}.gp.gz
                 C=`zgrep -c . "$asmName/${asmChr}.gp.gz"`
                 if [ "${C}" -eq 0 ]; then
                    rm -f "$asmName/${asmChr}.gp.gz"
                 fi
                 else
                   printf "DONE\t%s\n" "$asmName/${asmChr}.gp.gz"
                 fi
                  ;;
             esac
          done
          done
        else
          printf "%s: a-z missing\n" "${asmName}"
        fi
        ;;
  esac
done

exit $?
      9 refGene
     23 augustusGene
      9 ensGene
      9 ensemblToGeneName
      3 geneName
      2 geneid
      1 mgcGenes
      5 ncbiRefSeq
      5 no
      1 nscanGene
      1 sgpGene
      1 transMapAlnUcscGenes
      1 transMapInfoUcscGenes
     19 xenoRefGene