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Adding lines to files based on their names

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# 1  
Old 06-24-2010
Adding lines to files based on their names
I have several files on a folder something like this:
Quote:
1a-Pat1.fas
1a-Pat32.fas
1b-Pat16.fas
6-Pat76.fas
4-Pat243.fas
3-Pat101.fas
5-Pat33.fas
6-Pat93.fas
2-Pat5.fas
If the file starts with 1a, I would like to add the following at the very beggining of the file
Quote:
>Reference1a
AGCATGACGATCAGTGTGCGGGTGA
If the file starts with 1b then I should add the following
Quote:
>Reference1b
AGCATGTGTGCGGGTGA
For files starting with 6
Quote:
>Reference6
AGCATGTGTGCGGGTGATTTTTT
So on and so forth. Thus, at the end each file will have a reference sequence at the very top 'matching' the beggining of the file name.
Thanks in advance.
# 2  
Old 06-24-2010
wrong solutions. deleted.
Last edited by rdcwayx; 06-25-2010 at 02:44 AM..
# 3  
Old 06-24-2010
Assuming that you have files which contain the data that needs to be added to each file named after the reference. For example, file "1a.header" contains the header for reference id "1a".
Code:
function add_reference
{
  typeset file=$1
  typeset ref_id=${file%%-*}
  typeset temp=${file}.tmp
  cat ${ref_id}.header $file > $temp
  mv $temp $file
}

for file in *.fas
do
  add_reference $file
done

If you want to keep all the reference strings within your script (instead of external files), you can use associative arrays. Since, ksh does not support associative arrays, you will have to use either ksh93 or awk.
# 4  
Old 06-24-2010
another way, you can build init files by name as 1a, 1b, 1 with related contents.

such as:

Code:
$ cat 1a
>Reference1a
AGCATGACGATCAGTGTGCGGGTGA

then use below scripts.
Code:
for file in `ls *.fas`
do
  str=`echo $file|cut -d \- -f1`
  cat $str $file >> $file_new
done

Last edited by rdcwayx; 06-25-2010 at 02:43 AM..
# 5  
Old 06-25-2010
I rather have all the References within my script (I really do not like the idea of having external files)
Code:
for file in `ls 1a*.fas`
do 
  echo ">Reference1a
AGCATGACGATCAGTGTGCGGGTGA " >> $file
done

I am not getting the expected result. ALl the information in the file is being replaced by the reference sequence.
Quote:
If you want to keep all the reference strings within your script (instead of external files), you can use associative arrays. Since, ksh does not support associative arrays, you will have to use either ksh93 or awk.
I have been trying with awk, I just cannot get it to do what I want.
# 6  
Old 06-25-2010
Quote:
Originally Posted by Xterra
I rather have all the References within my script (I really do not like the idea of having external files)
Code:
for file in `ls 1a*.fas`
do 
  echo ">Reference1a
AGCATGACGATCAGTGTGCGGGTGA " >> $file
done

I am not getting the expected result. ALl the information in the file is being replaced by the reference sequence.

I have been trying with awk, I just cannot get it to do what I want.
I am not big with awk, but the original code I posted can be modified to use ksh93 as follows:

Code:
#!/bin/ksh93

typeset -A reference_headers

##
## Add all the valid references in this associative array
##
reference_headers=(
[1a]=">Reference1a
AGCATGACGATCAGTGTGCGGGTGA"
[1b]=">Reference1b
AGCATGTGTGCGGGTGA"
);

function add_reference
{
  typeset file=$1
  typeset ref_id=${file%%-*}
  typeset temp=${file}.tmp
  (echo "${reference_headers[${ref_id}]}"; cat $file) > $temp
  mv $temp $file
}

for file in *.fas
do
  add_reference $file
done

Note that, on my Mac OS X, the default ksh shell itself is ksh93, but on lots of Unix systems there are separate executables for ksh and ksh93. If your system has only ksh, if the following command gives an output similar to what is shown, its ksh93, else not:
Code:
$ echo ${.sh.version}
Version M 1993-12-28 s+

# 7  
Old 06-25-2010
a_programmer
I will try that. Hopefully someone will post a code using awk to accomplish the same task.
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