retrieve_seq_from_fasta_usage.txt

Usage:
     retrieve_seq_from_fasta.pl [arguments] <regionfile>

     Optional arguments:
            -v, --verbose                   use verbose output
            -h, --help                      print help message
            -m, --man                       print complete documentation
                --format <string>           format of the regionfile
                --outfile <file>            output file name (default: input.fa)
                --seqdir <directory>        directory containing sequence files for genomes
                --seqfile <file>            sequence file name
                --tabout                    use tab-delimited output (default is FASTA file)
                --altchr                    process alternative haplotype chromosome (default: OFF)
                --[no]addchr                add chr prefix to region specification (default: ON)

     Function: reformat sequences at specific genomic positions from whole-genome FASTA files

     Example: retrieve_seq_from_fasta.pl -format tab -seqdir humandb/ region.tabinput
              retrieve_seq_from_fasta.pl -format tab -seqfile chrall.fa region.tabinput
              retrieve_seq_from_fasta.pl -format simple -seqdir humandb/ region.input
              retrieve_seq_from_fasta.pl -format refGene -seqdir humandb hg18_refGenet.txt
              retrieve_seq_from_fasta.pl -format genericGene -seqdir humandb/ hg18_gencodeGene.txt

     Version:$Date: 2015-12-14 13:51:19 -0800 (Mon, 14 Dec 2015) $

Options:
    --help  print a brief help message and exit

    --man   print the complete manual of how to use the program

    --verbose
            use verbose output

    --format
            specify the format of the input file (default: tab). Other
            supported formats include simple, refGene, knownGene, ensGene,
            genericGene and many other format support will be added in the
            future.

    --outfile
            specify the output file name (default: <input>.fa)

    --seqdir
            specify the directory of the sequence files (usually these
            sequence files are organized by chromosomes, and that the file
            name represent the chromosome).

    --seqfile
            specify the sequence file name (assuming that all sequences are
            stored within a single file).

    --tabout
            use tab-delimited output. By default, FASTA file will be printed
            out.

    --altchr
            process alternative haplotype chromosome, that look like
            chr6_cox_hap1. By default this will not be processed.

    --(no)addchr
            add chr prefix to region if it is not present (default: ON)