For loop for MUMmer

Question

[AP]

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

[lieven.sterck]

then what is the output you are getting?

I would personally already change the loop to this:

for  var in `cat file_list.txt`
    do

[AP]

I am getting the delta file as below

Nechacore-T2_AssemblyScaffolds_Repeatmasked.fasta-filtered.delta

instead of

Nechacore-T2-filtered.delta

but after this step, I am getting an error :

ERROR: Could not parse delta file, Nechacore-T2_AssemblyScaffolds_Repeatmasked.fasta.delta
error no: 400
ERROR: Could not parse delta file, Nechacore-T2_AssemblyScaffolds_Repeatmasked.fasta-filtered.delta
error no: 402

I think I am doing something wrong while calling the variable. The output files I am getting are also empty. When I run the code for individual files the code is alright. It runs perfectly, so the problem is definitely with the loop I made.

[lieven.sterck]

what would the cmdline for such a single job look like?

the file names you are getting is exactly what has been asked for in the loop. In the loop you request to use the whole filename of the input files for the new file names. Since the last part is always the same you need to create a new var, in the loop, that contains the T2 T16 and so. Something like this :

$base=${var%_*} 

this will remove everything from the first _ onward and thus retain only the T parts

[AP]

#running promer. this code generates delta file
promer --mum --prefix=Nechacore-T2 77-13-4_masked_core.fasta T2_AssemblyScaffolds_Repeatmasked.fasta

#filtering delta file
delta-filter -g Nechacore-T2.delta > Nechacore-T2-filtered.delta 

#making coordinate file out of filtered delta file
show-coords -rcl Nechacore-T2-filtered.delta > Nechacore-T2.coords

[lieven.sterck]

see my post above to figure out what the difference is with what you do in the loop

(top tip btw: including an echo of $var in your loop is a good idea to see what you're working with)

[AP]

I am sorry, since I am quite new to these for loops I could not figure out how and where to put this new variable in my code so that I can get the desired output. Could you please help!!

[cpad0112]

$ cat test.txt | while read var; do echo Nechacore-${var/_*/}; done

Nechacore-T161
Nechacore-T31
Nechacore-T299
Nechacore-T2

Answer 1

[lieven.sterck]

replace all ${var} with $base in your three cmdlines.

alternatively you can create a list that only contains those prefixes (in stead of the complete file names), for instance like this:

ls *_AssemblyScaffolds_Repeatmasked.fasta | sed 's/_.*$//' > file_list.txt

than in your file_list file you will only have the T2 T16 things and don't have to change anything else

[AP]

Thank you for your help, It is working now!!