view rankfilter_GCMS/pdftotabular.py @ 49:f772a5caa86a

Added more options and better documentation. Added MsClust support for parsing XCMS alignment results. Improved output reports for XCMS wrappers. New tools.

"""
Copyright (C) 2013, Pieter Lukasse, Plant Research International, Wageningen

Licensed under the Apache License, Version 2.0 (the "License");
you may not use this software except in compliance with the License.
You may obtain a copy of the License at

http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.

"""

import sys
import pdfread
from subprocess import call


def convert_pdftotext(filename, output_file):
    '''
    Converts PDF file to text
    @param filename: PDF file to parse
    @param output_file: output text file for the hits    
    '''
    
    try:
        call(["pdftotext", filename, output_file])
    except:
        raise Exception("Error while trying to convert PDF to text")
   
   


if __name__ == '__main__':
    pdf_as_text = sys.argv[1]+".txt"
    convert_pdftotext(sys.argv[1], pdf_as_text)
    pdfread.convert_pdftotext2tabular(pdf_as_text, sys.argv[2], sys.argv[3], False)