def add(self, contigfile, sampleid, species, bamfile=None, assembler=None, copy=False) : self.log.info("adding %s (%s, %s, %s, %s)" % (sampleid, species, contigfile, bamfile, assembler)) if self.contains(sampleid) : self.log.warn("%s is already present, overwriting..." % sampleid) contigfile = self.copy(contigfile) if copy else abspath(contigfile) bamfile = self.copy(bamfile) if copy else abspath(bamfile) if bamfile else bamfile self.params['samples'][sampleid] = { 'contigs' : contigfile, 'contigs_checksum' : md5(contigfile), 'species' : species, 'bam' : bamfile, 'bam_checksum' : md5(bamfile) if bamfile else None, 'assembler' : assembler } self.set_sample_checksum()
def checksum(self) : return md5(self.fname)