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appris_feat_gencode_report
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appris_feat_gencode_report
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#!/bin/bash
# -----------------------------------------------------------------------------
# Load environmental variables
# If you do not trust the path, configure below:
SYSTEM=`uname -s`
if [ "$SYSTEM" = Darwin ]
then
source /etc/bashrc
source /etc/profile
source ${HOME}/.bash_profile
elif [ "$SYSTEM" = Linux ]
then
source /etc/profile
source /etc/bash.bashrc
source ${HOME}/.bashrc
fi
VER=0.1b
VERDATE="1-Apr-2013"
FILENAME=`basename $0`
FILENAME="${FILENAME%.*}"
DIRNAME=`dirname $0`
CONF_SPECIES=""
# -----------------------------------------------------------------------------
# Load external functions
source ${DIRNAME}/appris_env
# -----------------------------------------------------------------------------
# Usage
USAGE="
\n
APPRIS's binary package.\n
\n
Name:\n
\t appris_gencode_report\n
\n
Description:\n
\t Retrieve statistics from gencode report\n
\n
Required arguments:\n
\t -c [-conf]\n
\t\t Hsap - Homo sapiens -\n
\t\t Mmus - Mus musculus -\n
\t\t Rnor - Rattus norvegicus -\n
\t\t Drer - Danio rerio -\n
\t\t Sscr - Sus scrofa -\n
\t\t Ptro - Pan troglodytes -\n
\t\t Dmel - Drosophila melanogaster -\n
\t\t Cele - Caenorhabditis elegans -\n
\t\t Lpar - Lynx pardinus -\n
\n
\t\t Source file for species\n
\n
\t -v [version]\n
\t -h [help]\n
\n
\n
Author: Jose Manuel Rodriguez Carrasco [email protected] (INB-GN2,CNIO)\n
\n
"
# -----------------------------------------------------------------------------
# Get input parameters
while expr "//$1" : //- >/dev/null
do
case "$1" in
-c | -conf )
CONF_SPECIES=$2
shift
;;
-h | -help )
echo -e $USAGE
exit
;;
-v | -version )
echo "$VER", "$VERDATE"
exit
;;
* )
echo Unknown option: "$1"
echo -e $USAGE
exit 1
;;
esac
shift
done
if [ "${CONF_SPECIES}" == "" ]; then
echo You must specify at least one config file for SPECIES!
echo -e $USAGE
exit 1
fi
# -----------------------------------------------------------------------------
# Prepare Environment from config file for SPECIES
load_appris_specie_env "${CONF_SPECIES}"
# -----------------------------------------------------------------------------
# Check gene and transcripts numbers
echo "---------------------------"
echo "Check gene and transcripts numbers:"
echo ""
echo "NAME,NUM"
awk 'BEGIN {num_g=0; num_t=0;} {if ( $3=="gene" && $2=="HAVANA"){num_g++} else {if ( $3=="transcript" && $2=="HAVANA" ){num_t++} }} END { print "HAVANA_GENES," num_g "\nHAVANA_TRANSCRIPTS," num_t }' ${GENCODE_ANNOTATION_FILE}
awk 'BEGIN {num_g=0; num_t=0;} {if ( $3=="gene" && $2=="ENSEMBL"){num_g++} else {if ( $3=="transcript" && $2=="ENSEMBL" ){num_t++} }} END { print "ENSEMBL_GENES," num_g "\nENSEMBL_TRANSCRIPTS," num_t }' ${GENCODE_ANNOTATION_FILE}
awk 'BEGIN {num_g=0; num_t=0;} {if ( $3=="gene" ){num_g++} else {if ( $3=="transcript" ){num_t++} }} END {print "GENES," num_g "\nTRANSCRIPTS," num_t }' ${GENCODE_ANNOTATION_FILE}
echo ""
# -----------------------------------------------------------------------------
# Count gene and transcript for chromosome
echo "---------------------------"
echo "Count gene and transcript for chromosome:"
echo ""
echo "CHR,N_GENES,N_TRANSC"
CHROMOSOME=(${APPRIS_CHR_LIST//,/ })
INDEX=${#CHROMOSOME[@]}
for ((i=0;i<$INDEX;i++)); do
CHR="${CHROMOSOME[${i}]}"
POSITION="chr${CHR}"
awk -v CHR="${POSITION}" 'BEGIN {num_g=0; num_t=0;} {if ( $1==CHR && $3=="gene" ){num_g++} else {if ( $1==CHR && $3=="transcript" ){num_t++} }} END {print CHR "," num_g "," num_t }' ${GENCODE_ANNOTATION_FILE}
done
echo ""
# -----------------------------------------------------------------------------
# Count number of sequences
echo "---------------------------"
echo "Count number of transcript sequences:"
echo ""
echo -n "N_TRANSC," && grep -c ">" ${GENCODE_TRANSCRIPT_FILE}
echo ""
echo "---------------------------"
echo "Count number of translation sequences:"
echo ""
echo -n "N_TRANSL," && grep -c ">" ${GENCODE_TRANSLATION_FILE}
echo ""
echo "---------------------------"
echo "Check total number of cds and exons:"
echo ""
awk '{if ( $3=="CDS" ){num_c++} else {if ( $3=="exon" ){num_e++} }} END {print "N_CDS," num_c "\nN_EXON," num_e }' ${GENCODE_ANNOTATION_FILE}
echo ""
# -----------------------------------------------------------------------------
# Count the number of sequences by chromosome
echo "---------------------------"
echo "Count the number of gene/transcript sequences by chromosome:"
echo ""
echo "CHR,N_GENES,N_TRANSC"
CHROMOSOME=(${APPRIS_CHR_LIST//,/ })
INDEX=${#CHROMOSOME[@]}
for ((i=0;i<$INDEX;i++)); do
CHR="${CHROMOSOME[${i}]}"
POSITION="chr${CHR}"
N_GENES=$(awk -v CHR="${POSITION}" '{if ( $1==CHR && $3=="gene" ){print $10} }' ${GENCODE_ANNOTATION_FILE} | uniq | sed 's/[\"|\;]//g' | fgrep -f - ${GENCODE_TRANSCRIPT_FILE} | awk -F "|" '{print $2}' | uniq | wc -l )
N_TRANSC=$(awk -v CHR="${POSITION}" '{if ( $1==CHR && $3=="transcript" ){print $12} }' ${GENCODE_ANNOTATION_FILE} | uniq | sed 's/[\"|\;]//g' | fgrep -f - ${GENCODE_TRANSCRIPT_FILE} | awk -F "|" '{print $1}' | uniq | wc -l)
echo "${POSITION},${N_GENES},${N_TRANSC}"
done
echo ""
echo "---------------------------"
echo "Count the number of gene/transcript translations by chromosome:"
echo ""
echo "CHR,N_GENES,N_TRANSL"
CHROMOSOME=(${APPRIS_CHR_LIST//,/ })
INDEX=${#CHROMOSOME[@]}
for ((i=0;i<$INDEX;i++)); do
CHR="${CHROMOSOME[${i}]}"
POSITION="chr${CHR}"
N_GENES=$(awk -v CHR="${POSITION}" '{if ( $1==CHR && $3=="gene" ){print $10} }' ${GENCODE_ANNOTATION_FILE} | uniq | sed 's/[\"|\;]//g' | fgrep -f - ${GENCODE_TRANSLATION_FILE} | awk -F "|" '{print $3}' | uniq | wc -l )
N_TRANSC=$(awk -v CHR="${POSITION}" '{if ( $1==CHR && $3=="transcript" ){print $12} }' ${GENCODE_ANNOTATION_FILE} | uniq | sed 's/[\"|\;]//g' | fgrep -f - ${GENCODE_TRANSLATION_FILE} | awk -F "|" '{print $2}' | uniq | wc -l)
echo "${POSITION},${N_GENES},${N_TRANSC}"
done
echo ""
# -----------------------------------------------------------------------------
# Count gene types
echo "---------------------------"
echo "Count gene types:"
echo ""
echo "TYPE,NUM"
eval TYPE=( $(awk '{ if($3=="gene"){print $14}}' ${GENCODE_ANNOTATION_FILE} | sed -e 's/[\"|\;]//g' | sort | uniq) )
INDEX=${#TYPE[@]}
for ((i=0;i<$INDEX;i++)); do
N=$(awk '{ if($3=="gene" && $13=="gene_type"){print $14}}' ${GENCODE_ANNOTATION_FILE} | grep -c "\"${TYPE[${i}]}\"")
echo "${TYPE[${i}]},$N"
done
echo ""
# -----------------------------------------------------------------------------
# Count transcript types
echo "---------------------------"
echo "Count transcript types:"
echo ""
echo "TYPE,NUM"
eval TYPE=( $(awk '{ if($3=="transcript"){print $20}}' ${GENCODE_ANNOTATION_FILE} | sed -e 's/[\"|\;]//g' | sort | uniq) )
INDEX=${#TYPE[@]}
for ((i=0;i<$INDEX;i++)); do
N=$(awk '{ if ($3=="transcript" && $19=="transcript_type"){print $20}}' ${GENCODE_ANNOTATION_FILE} | grep -c "\"${TYPE[${i}]}\"")
echo "${TYPE[${i}]},$N"
done
echo ""