formats.py 1.92 KB
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#
# Copyright (C) 2012 INRA
# 
# 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/>.
#

from jflow import seqio
import os
import sys


class Formats(object):
    ANY = "any"
    BAM = "bam"
    FASTQ = "fastq"
    FASTA = "fasta"
    SFF = "sff"
    

def fastq(ifile):
    try:
        reader = seqio.FastqReader(ifile)
        nb_seq = 0
        for id, desc, seq, qualities in reader:
            nb_seq += 1
            # only check the first 10 sequences
            if nb_seq == 10: break
    except: 
        sys.stderr.write("Error: The provided file '" + ifile + "' is not a fastq file!\n")
        sys.exit(1)
    
def fasta(ifile):
    try:
        reader = seqio.FastaReader(ifile, wholefile=True)
        nb_seq = 0
        for id, desc, seq, qualities in reader:
            nb_seq += 1
             # only check the first 10 sequences
            if nb_seq == 10: break
    except: 
        sys.stderr.write("Error: The provided file '" + ifile + "' is not a fasta file!\n")
        sys.exit(1)
    
def sff(ifile):
    try:
        reader = seqio.SFFReader(ifile)
        nb_seq = 0
        for id, desc, seq, qualities in reader:
            nb_seq += 1
            # only check the first 10 sequences
            if nb_seq == 10: break
    except: 
        sys.stderr.write("Error: The provided file '" + ifile + "' is not a sff file!\n")
        sys.exit(1)