# Developed by Michael Cummings and Richard Joh
# Python 3.3.1

1)Generate primers for a given genomic feature
    Deletion
    C-terminus tagging (only for CDS)
2)Count and list all overlapping genes/CDSs/ncRNAs which will be disrupted upon deletion

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Syntax
python primer.py INPUT1 INPUT2 INPUT3

INPUT1: integer from 0 to 5
	0: pombe
	1: cerevisiae S288C
	2: cerevisiae RM11_1A
	3: cerevisiae SK1
	4: cerevisiae W303
	5: cerevisiae Y55
	#
	# To input custom library (e.g. another yeast strain), the following lines should be modified
	# 	1) Lines 102-123: Add additional sequence and annotation files
	# 	2) Lines 129-130: Define the output file name
	# 	3) Lines 159-160: Specify the new strain
	# 	4) Lines 186-215: Header lines of .fa files may have different
	# 	structures  
	# 	5) Line 232: Include other chromosomal sequences (e.g.
	# 	Mitochondria or chromosome 17+)
	# 	6) Lines 282-380: Extraction of each genomic feature depends on
	# 	each annotation file
	# 	7) Lines 389-430: Finding the systematic and common name for
	# 	each genomic feature depends on each annotation file

INPUT2: feature to delete
	1: CDS (also generate primers for C-terminal tagging)
	2: ncRNA
        3: 3'UTR (only for pombe)
        4: tRNA
	#
        # Other genomic features can be implemented and examples are shown in lines 134-140
	# Note that feature name might be different in each annotation file
	# (can be modified in lines 139-140)

INPUT3: the length of homology (any positive integer)
        80 recommended for pombe
        50 recommended for cerevisiae

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Example

python primer.py 0 1 80: primers for deletion/tagging CDS in pombe with 80bp homology


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Input files
	Whole genome sequence (.fa or equivalent)
        Annotation (.gff3 or equivalent)


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Output files
	Stat file
		Count all features within the genome (genes/CDSs/ncRNAs and the feature of interest)
                Header for the primer file
        Primer file
		Basic info of the feature: start/stop coordinate, directionality, chromosome and name
                Primers for deletion/tagging
                	One set only with the region of homology: Custom sequence need to be added for amplification of constructs
			Another set for pFA6a-based vectors.  The common MCS (or adh terminator for 3' UTR)  sequences are included as a part of primers, so that primers can directly amplify constructs from pFA6a-based vectors.
	Check file
		Basic info of the feature
                First and last 3bp: To check start/stop codons
                Region immediately upstream and downstream
                Feature sequence