Parse text files on in nested Unix directories and create one formatted text file

Create a script (preferably in perl) called create_illumina that will parse through all files in a directory with the following nested structure: /home/data/agencourt_crsp/CRSP_agencourt and parse through all subdirectories which look something like: /home/data/agencourt_crsp/CRSP_agencourt/20080320_Amplicons/Plate3/Chromatograms/0_11367_01/Pila/edit_dir In each edit_dir, read the *[url removed, login to view] file For each line that ends with 'G' in the final column, grab that line and format the information to adhere to the format found in the following attached file. One input to the script should be the 4 letter species code to generate a file from. The options in this case are: Piel, Psme, Paab, Pila, Pipn, Pira, Pisy In this illumina output file, the all the header lines will be the same as the sample here with the exception of line 13, 2nd column where the value will be CRSP-speciescode where species code will be the same as what the user entered at command line. Also, line 16, column two will have the number of lines with G in them for that speciescode that will be populated into that same file. After the header (starting with line 22) Each G line will be formatted according to a set style. The following lines in *[url removed, login to view] [url removed, login to view] CL2272Contig1_02 40 GTAAAACGACGGCCAGTCCTCACCAATTCCAAGAACAGC[G/T]ACATTGCAATTAGAACCATTCAGTTTTCCTTCTGCTAATGCTTCCCTGAC pp/pb 98 1.00 G Will translate to this line in the illumina_input file: CL2272Contig1_02-40 GTAAAACGACGGCCAGTCCTCACCAATTCCAAGAACAGC[G/T]ACATTGCAATTAGAACCATTCAGTTTTCCTTCTGCTAATGCTTCCCTGAC 0 0 0 0 0 0 haploid speciescode Forward Please note, project is to be completed within the same day bidding is accepted (worked on immediately - Thanks!)

## Deliverables

1) Complete and fully-functional working program(s) in executable form as well as complete source code of all work done.

2) Deliverables must be in ready-to-run condition, as follows (depending on the nature of the deliverables):

a) For web sites or other server-side deliverables intended to only ever exist in one place in the Buyer's environment--Deliverables must be installed by the Seller in ready-to-run condition in the Buyer's environment.

b) For all others including desktop software or software the buyer intends to distribute: A software installation package that will install the software in ready-to-run condition on the platform(s) specified in this bid request.

3) All deliverables will be considered "work made for hire" under U.S. Copyright law. Buyer will receive exclusive and complete copyrights to all work purchased. (No GPL, GNU, 3rd party components, etc. unless all copyright ramifications are explained AND AGREED TO by the buyer on the site per the coder's Seller Legal Agreement).

## Platform


Habilidades: Engenharia, Mac OS, MySQL, Perl, PHP, Arquitetura de software, Teste de Software

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ID do Projeto: #3025597

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