#!/bin/sh #$ -S /bin/sh # sh chipatlas/sh/refineSearchList.sh # experimentList.tab を JSON 形式に変換 # 簡易版 cat `ls -1 chipatlas/lib/metadata/NCBI_SRA_Metadata_Full_20*tab| tail -n1`| awk -F '\t' -v OFS='\t' '{ x[$1] = $12 } END { while ((getline < "chipatlas/lib/assembled_list/experimentList.tab") > 0) { $1 = $1 "\t" x[$1] if ($9 ~ /^GSM[0-9][0-9]/) { split($9, a, ":") $1 = $1 "\t" a[1] } else { $1 = $1 "\t-" } print } }'| cut -f1-8| awk -F '\t' -v OFS='\t' ' BEGIN { while ((getline < "chipatlas/sh/preferences.txt") > 0 && $1 == "Genome") { N = split($2, a, " ") for (i=1; i<=N; i++) { split(a[i], b, "=") M = split(b[1], c, ",") gsub(",", ", ", b[1]) for (j=1; j<=M; j++) g[c[j]] = b[1] } } } !x[$1]++ { $4 = g[$4] print }'| awk -F '\t' ' BEGIN { printf "{\"data\": [" } { printf "[" for (i=1; i chipatlas/lib/assembled_list/ExperimentList.json # Advanced 版 cat `ls -1 chipatlas/lib/metadata/NCBI_SRA_Metadata_Full_20*tab| tail -n1`| awk -F '\t' -v OFS='\t' '{ x[$1] = $12 } END { while ((getline < "chipatlas/lib/assembled_list/experimentList.tab") > 0) { $1 = $1 "\t" x[$1] if ($9 ~ /^GSM[0-9][0-9]/) { split($9, a, ":") $1 = $1 "\t" a[1] sub(": ", "\t", $9) } else { $1 = $1 "\t-" $9 = "-\t" $9 } gsub("\\\\", "", $0) gsub("\"", "\\\"", $0) print } }'| cut -f1-8,12-| awk -F '\t' -v OFS='\t' ' BEGIN { while ((getline < "chipatlas/sh/preferences.txt") > 0 && $1 == "Genome") { N = split($2, a, " ") for (i=1; i<=N; i++) { split(a[i], b, "=") M = split(b[1], c, ",") gsub(",", ", ", b[1]) for (j=1; j<=M; j++) g[c[j]] = b[1] } } } !x[$1]++ { $4 = g[$4] print }'| awk '{ gsub("\t", "__TAB__") for (i=1; i<=9; i++) sub("__TAB__", "\t", $0) print }'| awk -F '\t' '{ print (NF == 9) ? $0 "\t-" : $0 }'| awk -F '\t' ' BEGIN { printf "{\"data\": [" } { printf "[" for (i=1; i chipatlas/lib/assembled_list/ExperimentList_adv.json # HTML ファイルを作成 (簡易版) cat << 'DDD' > chipatlas/lib/assembled_list/refineSearchList.html ChIP-Atlas / Keyword search

ChIP-Atlas / Keyword search

Search for ChIP-seq data with keywords.

Simple search
Advanced search

DDD # HTML ファイルを作成 (advanced 版) cat << 'DDD' > chipatlas/lib/assembled_list/refineSearchList_advanced.html ChIP-Atlas / Keyword search

ChIP-Atlas / Advanced keyword search

Search for ChIP-seq data with keywords.

Simple search
Advanced search

DDD