#!/bin/sh -e

usage="txGenbankData db


Get GenBankand RefSeq alignments and metadata, and ReqSeq peptide sequences
for input to the UCSC Genes pipeline.  Outputs the following files in the
current directory:

   mrna.psl
   mrna.ra
   mrna.fa
   refSeq.psl
   refSeq.ra
   refSeq.fa
   refPep.fa
   mgcStatus.tab
"

if [ $# != 1 ] ; then
    echo "Wrong # args: $usage" >&2
    exit 1
fi
db="$1"

gbRoot=/cluster/data/genbank
gbGetSeqs=${gbRoot}/bin/$(uname -m)/gbGetSeqs

# function to get alignments and metadata.
doGet() {
    local srcDb="$1" outPre="$2"
    (set -x ; $gbGetSeqs -inclVersion -gbRoot=$gbRoot -get=psl -db=$db -native $srcDb mrna $outPre.psl)
    (set -x ; $gbGetSeqs -inclVersion -gbRoot=$gbRoot -get=ra  -db=$db -native $srcDb mrna $outPre.ra)
    (set -x ; $gbGetSeqs -inclVersion -gbRoot=$gbRoot -get=seq -db=$db -native $srcDb mrna $outPre.fa)
}

doGet refseq refSeq
(set -x ; $gbGetSeqs -inclVersion -gbRoot=$gbRoot -get=seq -db=$db -native refseq pep refPep.fa)
doGet genbank mrna

# create mgcStatus.tab, in the format of the retired mgcFullStatus table, from
# the mrna.ra file.  This has two columns, the acc and a status of either
# fullLength or fullLengthSynthetic.
awk '
BEGIN {OFS="\t"}

$1=="acc" {
    acc = $2;
    isMgc = isSyn = 0;
}
/^key .*mgc(\.$|;.*)/ {
    isMgc = 1;
}
/^org synthetic/ {
    isSyn = 1;
}
/^$/ && isMgc {
    if (isSyn) {
        print acc,"fullLengthSynthetic";
    } else {
        print acc,"fullLength";
    }
}
' mrna.ra >mgcStatus.tab.tmp
mv -f mgcStatus.tab.tmp mgcStatus.tab