For loop for MUMmer

0

Hello everyone,

I am trying to run MUMmer codes in a list of files for which I tried to make a for loop, but this does not seem to work. Below are my codes and list of files:

#list of files
T161_AssemblyScaffolds_Repeatmasked.fasta
T31_AssemblyScaffolds_Repeatmasked.fasta
T299_AssemblyScaffolds_Repeatmasked.fasta
T2_AssemblyScaffolds_Repeatmasked.fasta


    ls *__AssemblyScaffolds_Repeatmasked.fasta > file_list.txt
    files=`cat file_list.txt`

    for  var in $files
    do

    promer --mum --prefix=Nechacore-${var} 77-13-4_masked_core.fasta ${var}_AssemblyScaffolds_Repeatmasked.fasta
    delta-filter -g Nechacore-${var}.delta > Nechacore-${var}-filtered.delta
    show-coords -rcl Nechacore-${var}-filtered.delta > Nechacore-${var}.coords

I want the output files with the following names for each different input files in each steps but that's not what I am getting

Nechacore-T2.delta
Nechacore-T2-filtered.delta
Nechacore-T2.coords
Nechacore-T161.delta
.., etc

Please help!! Thanks


shell


bash


forloop

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