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Hi Everyone,

I am in a class on Biocomputing and we have a project due VERY soon. In part of it, we have to write a script and this is what we have to do:

It can execute in the shell, python, or perl. The script should do the following on an input file.
1. When the script is executed, it should as for the input file name.
2. perform a sanity check to ensure that the input file exists; otherwise, prints an error message and aborts
3. after a good sanity check, it passes the data from the input file to clustalw for sequence alignment
4. pass the alignment to collapse1.5
5. use seqret from EMBOSS to convert to file from PHYLIP to Nexus non-interleaved
6. clean up any intermediate files

I have done some of this, but I keep getting errors. Can anyone help me???
Please.... :(

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Last Post by jasimp
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Post this in the Software Development forum and post what you have done for coding so far. Also post what errors you are getting. They will not do your homework for you.

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This is what I have so far:

#!/bin/bash

PATH=/Users/MYNAMEHERE/Desktop/LASTNAME_Miniproject_2_Part_2

printf "\nWhat is the name of the input file? "
read Part_2_Seq.fasta.txt

if [ '$INPUT_FILE' = "Part_2_Seq.fasta.txt" ]
then
$INPUT_FILE | ./clustalw > $Part_2_Seq_clustalw.output
else
printf "\nNo matching file name!! Aborting!!\n\n"
exit 192
fi

collapse-1.5 $Part_2_Seq_clustalw.output [-g -p -d -n -v -m -z -w -h -t -l# -?] > $Part_2_Seq_collapse.output

This is the error message I get:
: command not founds.txt: line 4:

I know in class we were told to go into .bashrc and change the path to get around "command not found" but I do not know if that is what I need to do here or if I do, where do I change my path? beginning or end? I am confused.

Thanks for the help.

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