Usage: assembled_exons_to_fastas.py -l PLSX_list -f FASTA_file -d OUT_directory [-g] [-r] [-n reference_NAME]

assembled_exons_to_fastas.py -- Processes the BLAT output from several samples
    comparing reference-guided contig assemblies with the reference (probe)
    contigs. The output is a directory containing a fasta file for each
    reference contig holding the sequence for each sample.

Copyright (c) 2014 Kevin Weitemier
Version 1.0

This program is free software: you can redistribute it and/or modify it under
the terms of the GNU General Public License as published by the Free Software
Foundation, either version 3 of the License, or (at your option) any later
version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY
WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
PARTICULAR PURPOSE.  See the GNU General Public License for more details. You
should have received a copy of the GNU General Public License along with this
program.  If not, see <http://www.gnu.org/licenses/>.

If you find this program useful, please cite:

K. Weitemier, S.C.K. Straub, R. Cronn, M. Fishbein, R. Schmickl, A. McDonnell,
and A. Liston. 2014. Hyb-Seq: Combining target enrichment and genome skimming
for plant phylogenomics. Applications in Plant Sciences 2(9): 1400042.

Input - A file containing a list of every .pslx file to be processed (one file
    per line), and a fasta file of the targeted contigs or exons. The .pslx
    files to be processed need to have been created with the targeted exons
    input as the 'database' or 'targets.'

Options:
  -h, --help   show this help message and exit
  -l CONNAME   File containing a list of the .pslx files to process; one name
               per line
  -f FANAME    Fasta file of targeted contigs
  -d DIRNAME   Name of directory for output files
  -g           Insert gaps? If the sample sequence matches the reference
               across two or more blocks, a string of Ns will be inserted
               equal to the size of the gap(s). In certain cases this may
               match the size of introns. Without this separate blocks will be
               concatenated. Default=False
  -r           Output the reference sequence as an entry in each sequence
               alignment? default=False
  -n REF_NAME  If the reference sequence is output (-r), what name will be
               given to this sample in the alignment files? Default=Reference