2 This program takes as input a multifasta file (with sequences already aligned together formated in fasta in the same file), considers the first sequence as the reference sequence, infers polymorphims and generates output files in GnpSNP exchange format.
33 - For several input files, create a directory in the root of the uncompressed package and put your input files in it. Then use this type of command line:
42 They show the command lines to use in order to set up environment variables and then to run the parser on our sample input file (Example_multifasta_input.fasta).
47 When the launcher is called for several input files (with -d option), the parser should be able to generate only one set of files describing all the batches (one batch per input file).
52 # RUNNING METHOD: Add the run_several_batches(directory) method that will browse the input files and iterate over them to run each of them successively (see runSeveralInputFile() method of the launcher)
55 # BATCH MANAGEMENT: Modify createBatchDict() to create one batch per file in the dictionary and add a class variable to point toward the current batch (ex: self._iCurrentLineNumber)
56 # BATCH-LINE MANAGEMENT: Modify _completeBatchLineListWithCurrentIndividual method to allow several batch and link lines to batches (for the moment hard coded batch no1)
57 # SUBSNP MANAGEMENT: check that all elements (dSUbSNP) added in SubSNP list (lSubSNPFileResults) is linked to the current batch (for the moment hard coded batch no1)
