GNU awk é usado. Eu coloquei este comando no script bash. Será mais conveniente.
Uso: ./join_files.sh ou, para uma impressão bonita, faça: ./join_files.sh | column -t .
#!/bin/bash
gawk '
NR == 1 {
PROCINFO["sorted_in"] = "@ind_num_asc";
header = $1;
}
FNR == 1 {
file = gensub(/.*\/([^.]*)\..*/, "\1", "g", FILENAME);
header = header OFS file;
}
FNR > 1 {
arr[$1] = arr[$1] OFS $5;
}
END {
print header;
for(i in arr) {
print i arr[i];
}
}' results/*.genes.results
Saída (criei três arquivos com o mesmo conteúdo para teste)
$ ./join_files.sh | column -t
gene_id TB1 TB2 TB3
ENSG00000000003 1.00 1.00 1.00
ENSG00000000005 0.00 0.00 0.00
ENSG00000000419 1865.00 1865.00 1865.00
ENSG00000000457 1521.00 1521.00 1521.00
ENSG00000000460 1860.00 1860.00 1860.00
ENSG00000000938 6846.00 6846.00 6846.00
ENSG00000000971 0.00 0.00 0.00
ENSG00000001036 1358.00 1358.00 1358.00
ENSG00000001084 1178.00 1178.00 1178.00
Explicação - o mesmo código com comentários adicionados. Além disso, veja o man gawk .
gawk '
# NR - the total number of input records seen so far.
# If the total line number is equal 1
NR == 1 {
# If the "sorted_in" element exists in PROCINFO, then its value controls
# the order in which array elements are traversed in the (for in) loop.
# else the order is undefined.
PROCINFO["sorted_in"] = "@ind_num_asc";
# Each field in the input record may be referenced by its position: $1, $2, and so on.
# $1 - is the first field or the first column.
# The first field in the first line is the "gene_id" word;
# Assign it to the header variable.
header = $1;
}
# FNR - the input record number in the current input file.
# NR is the total lines counter, FNR is the current file lines counter.
# FNR == 1 - if it is the first line of the current file.
FNR == 1 {
# remove from the filename all unneeded parts by the "gensub" function
# was - results/TB1.genes.results
# become - TB1
file = gensub(/.*\/([^.]*)\..*/, "\1", "g", FILENAME);
# and add it to the header variable, concatenating it with the
# previous content of the header, using OFS as delimiter.
# OFS - the output field separator, a space by default.
header = header OFS file;
}
# some trick is used here.
# $1 - the first column value - "gene_id"
# $5 - the fifth column value - "expected_count"
FNR > 1 {
# create array with "gene_id" indexes: arr["ENSG00000000003"], arr["ENSG00000000419"], so on.
# and add "expected_count" values to it, separated by OFS.
# each time, when the $1 equals to the specific "gene_id", the $5 value will be
# added into this array item.
# Example:
# arr["ENSG00000000003"] = 1.00
# arr["ENSG00000000003"] = 1.00 2.00
# arr["ENSG00000000003"] = 1.00 2.00 3.00
arr[$1] = arr[$1] OFS $5;
}
END {
print header;
for(i in arr) {
print i arr[i];
}
}' results/*.genes.results