fasta-tool

This perl script can be used to parse the FASTA file for various respects of processing.

Date: 2016/11/7
Upgrade: 2017/7/12
Author: Jeff

Usage: fasta_tool.pl [OPTIONS] < in.fa

Options:
-h, -?, --help
        This help message.
-p, --prerequisite-process
        If the input of FASTA file doesn't be represented the format of each sequence on a single line, the flag must be used to convert the regular FASTA file. Each sequence will be re-labelled as the following format:seq1, seq2, seq3 and so on.
-c, --count-bases
        Calculate the ratio of bases.
-f, --fetch-seq
        Fetch the applicable sequences that match the forward/reverse primers in the 5'/3' end, and then trim primers.
-g, --get-seq
        Get target sequences from the label list. The label of target sequences need be listed per line in a file, furthermore, the file must be named seq_label.txt.
-l, --cal-len
        Print the length of sequence.
-m, --format-output-fasta
        Convert the input of FASTA file to standard FASTA format, that is represented as a series of lines, each of which be 70 nucleotides.
-s, --fetch-subseq
        Fetch specified region of sequence from the input FASTA file.
-sn, --search-nu-seq-occu [sequence pattern]
        Retrieve the position of last occurrence of a match of nucleotide sequence.
-sa, --sort-asc-by-length
        Sort the length of sequences by ascending order.
-sd, --sort-desc-by-length
        Sort the length of sequences by descending order.

If the flag of -f is used, please provide the primer file including forward and reserve sequences.
        Please refer the example file, i.e. primer.txt.

If the flag of -s is used, please provide the specified region of sequences.
        Please refer the example file, i.e. chr_position.txt.

If the flag of -g is used, please provide the label of target sequences.
        Please refer the example file, i.e. seq_label.txt.