# Instantiate the fasta rec lists with BioPython Seq using geneID field of discriptor as key to seq objects
genomeOneFastasDict = SeqIO.to_dict(SeqIO.parse(open(genomeFileOne, "rU"), 'fasta'),
key_function = lambda rec : rec.description.split()[0])
genomeTwoFastasDict = SeqIO.to_dict(SeqIO.parse(open(genomeFileTwo, "rU"), 'fasta'),
key_function = lambda rec : rec.description.split()[0])
# Initiate resultList
resultList = []
# Explode orthologList into list of lists
JamesDefs.explodeDelimitedList(orthologList, '\t')
# Populate a list of GeneIDs in each genome's dict of boundary seqs
genomeOneGeneIDs = genomeOneFastasDict.keys()
genomeTwoGeneIDs = genomeTwoFastasDict.keys()
# Loop through orthologList and call each fasta in orthoPair, format
# the new comboFasta and append it to resultList
for orthoPair in orthologList:
# Test for orthoPair[0] in genomeOneFastasDict and same for orthoPair[1] in genomeTwoFastasDict
orthoPair_0_warn = None
orthoPair_1_warn = None
if orthoPair[0] not in genomeOneGeneIDs:
orthoPair_0_warn = 'Yes'
if orthoPair[1] not in genomeTwoGeneIDs:
else:
print "WARNING: boundaryRegion variable should only be 'up' or 'down'.\nScript exiting."
sys.exit()
#--------------------------------------------------
# Strip trailing newlines
codingBoundsList = map(string.strip, codingBoundsList)
resolvedConflictsList = map(string.strip, resolvedConflictsList)
# Convert these into lists of lists so that field vals can be interrogated and copied
# Explode tab delimited strings of each record into list of values
JamesDefs.explodeDelimitedList(codingBoundsList, '\t')
JamesDefs.explodeDelimitedList(resolvedConflictsList, '\t')
len_codingBoundsList = len(codingBoundsList)
len_resolvedConflictsList = len(resolvedConflictsList)
# Populate unUsableList
unUsableGeneNames = []
i = 0
while i < len_resolvedConflictsList:
if int(resolvedConflictsList[i][5]) < shortestUsableBdryReg:
unUseableGene = resolvedConflictsList.pop(i)
