Shell Programming and Scripting

So basically what I want to do is pull out DNA sequences for a particular gene name.

I have 2 files (FILE1 and FILE2) and I want an output into a separate file (FILE3).

FILE1 and 2 are MASSIVE so I am only posting examples from each file.

So FILE1 looks like this (tab deliminted, 4 columns):

##gff-version 1

1154 10 + AAD6
418 7429 + AAH1
702 759 + AAT1
584 10 - ABF2
642 4894 - ACC1
651 7213 - ACN9
1055 3454 - ADE1

The next file, FILE2, looks like this:


>1154
ATCTCACTCGTAATTCTACATAATTTTGTTTATGCTTTTATTGTCATTTTATATATTGTCAGTCATTATCCTATTACATTATCAATCCTTGCATTTCAGC TTCCACTTATTTCGATGACCGCTTCTCATAACTTATGTCATCTTCTAACACCGTATATGATAATGTACCAGTAGTATGAC
>584
GCAAGCTTTATAGTGACAACAATAAGGTATCACTCGGTTACAATTACCCCCACTTCCCCT


What I want to do is identify column 1 of FILE1 with the ># on FILE2. So for example, 1154 from FILE1 will match up with 1154 from FILE2. Next, I want it to identify the value on column 2 (so for 1154, it will identify the 10th letter which happens to be G). So if column 3 of FILE1 is + then it will print the first 8 letters in from of it (i.e. the 8 letters in front of G would be TCTCACTC). But if is it - on column 3, then it will take the reverse. So for ABF2 on “584” it will take the top 8 sequences starting from the reverse end. So instead of starting at “G” at >584, it will start at “T” (the end). So the position of ABF2 will be 25 letters away from “T” , so the letter will be “C”. Then it will take the values behind it... so CCACTTCC.

The output file will print out column 4 of FILE1, the top 8 letters from FILE2 and column 3 from FILE1.

The final file (FILE3) will look like this:

AAD6 TCTCACTC +
ABF2 CCACTTCC -


Could someone give me some help on this! I am new to perl and I am put in a situation where I have to program at a very high level.

Thanks

I am not clear on this part -

Try this.

Code:

awk 'FNR==NR{a[$1]=$2SUBSEP$3","$4;next}
/^>/{gsub(/>/,"",$1);s=$1;
if (s in a){
getline;
st=substr(a[s],1,index(a[s],SUBSEP)-1)
sg=substr(a[s],index(a[s],SUBSEP)+1,1)
if ( sg == "+")str=substr($0,st-8,8);else str=substr($0,length($0)-st,8);pt=substr(a[s],index(a[s],",")+1,length(a[s]))
print pt,str,sg;next
}}' file1 file2

cheers,
Devaraj Takhellambam

how MASSIVE is your file1 and file2, in terms of MB?? GB??
also, if you are new to Perl, then you should at least read up something on Perl before attempting this.