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Assign sets of values from each row of a table separately to a command in bash

debugcn Published at Dev
5
hola

I have a txt file (input.txt) with 3 columns separated by \t.

62M__29_length_73210_cov_19.6684    28981-31993    minus
61M__32_length_66572_cov_22.1672    22311-25323    minus
60M__65_length_73281_cov_15.6315    28978-31990    minus
59M__78_length_80030_cov_19.1814    28973-31985    minus
58M__28_length_80029_cov_24.2362    28972-31984    minus
57M__31_length_73253_cov_24.4297    41300-44312    plus
56M__32_length_73450_cov_26.6071    28975-31987    minus
55M__29_length_73232_cov_26.5615    41244-44256    plus
54M__38_length_66570_cov_23.8255    41307-44319    plus

I need to run a command using the values from each row in this way:

blastdbcmd -db mydatabase -entry "row_1_column_1" -range "row_1_column_2" -strand "row_1_column_3" -out out.fa

For example, for row 1 it would be:

blastdbcmd -db mydatabase -entry 62M__29_length_73210_cov_19.6684 -range 28981-31993 -strand minus -out out.fa
Freddy

With bash:

while IFS=$'\t' read -r entry range strand; do
  blastdbcmd -db mydatabase -entry "$entry" -range "$range" -strand "$strand" -out out.fa
done <input.txt

Read the input file linewise and split each line into three variables separated by a tab. Then run the command using these variables.

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