def addDirectionalityToPdfTables():
loader = GeneTableLoader()
geneTable = loader.createTable("geneDB", loader.loadUnprocessed("our_files/genes.col"))
pdfLoader = PDFTableLoader()
# handling table 2 (not from supplementary)
result = pdfLoader.loadUnprocessed("./parsed_files/2.table")
# match for each entry in the in s5 table a strand
for entry in result:
id, data = geneTable.findByField(Table.NAME_FIELD, entry["name"])
strand = None
# if there is no data look in the old names
if (id == None):
id, data = geneTable.findByOtherNames(entry["name"])
if (data != None):
strand = id.split(Table.ID_DELIMITER)[2]
entry[TableGlobals.FIRST_STRAND_KEY] = strand
entry[TableGlobals.SECOND_STRAND_KEY] = strand
pdfTable = pdfLoader.createTable("dummy", result)
pdfTable.dump("./final_format/2_directed.table")
# S5 handling
result = pdfLoader.loadUnprocessed("./parsed_files/s5.table")
# match for each entry in the in s5 table a strand
for entry in result:
id, data = geneTable.findByField(Table.NAME_FIELD, entry["name"])
strand = None
# if there is no data look in the old names
if (id == None):
id, data = geneTable.findByOtherNames(entry["name"])
if (data != None):
strand = id.split(Table.ID_DELIMITER)[2]
entry[TableGlobals.FIRST_STRAND_KEY] = strand
entry[TableGlobals.SECOND_STRAND_KEY] = strand
pdfTable = pdfLoader.createTable("dummy", result)
pdfTable.dump("./final_format/s5_directed.table")
# S8 handling
result = pdfLoader.loadUnprocessed("./parsed_files/s8.table")
# match for each entry in the in s5 table a strand
for entry in result:
id, data = geneTable.findByField(Table.NAME_FIELD, entry["name"])
strand = None
# if there is no data look in the old names
if (id == None):
id, data = geneTable.findByOtherNames(entry["name"])
if (data != None):
print "[warning] using by old name"
strand = id.split(Table.ID_DELIMITER)[2]
entry[TableGlobals.FIRST_STRAND_KEY] = strand
entry[TableGlobals.SECOND_STRAND_KEY] = strand
pdfTable = pdfLoader.createTable("dummy", result)
pdfTable.dump("./final_format/s8_directed.table")
#S7 handling
result = pdfLoader.loadUnprocessed("./parsed_files/s7.table")
for entry in result:
strand = entry.pop("strand")
if (strand == "f"):
strand = Table.POS_STRAND
elif (strand == "r"):
strand = Table.NEG_STRAND
entry[TableGlobals.FIRST_STRAND_KEY] = strand
entry[TableGlobals.SECOND_STRAND_KEY] = entry[TableGlobals.FIRST_STRAND_KEY]
pdfTable = pdfLoader.createTable("dummy", result)
pdfTable.dump("./final_format/s7_directed.table")
# S6 handling
result = pdfLoader.loadUnprocessed("./parsed_files/s6.table")
pdfLoader.createTable("dummy", result).dump("./final_format/s6_directed.table")
def printMatchAnalysis():
"""
This function is used to print the matched directions for the know rna from
the pdf so we can make sure the direction we matched them is valid and there
was no problems with the name (since there are new and old ones and the article
is from 2012).
:return: None
"""
loader = GeneTableLoader()
result = loader.loadUnprocessed("genes.col")
table = loader.createTable("geneDB", result)
count = {}
for entry in result:
name = entry["NAME".lower()].lower()
if not count.has_key(name):
count[name] = 1
else:
count[name] += 1
if count[name] > 1:
print "warning"
old_count = {}
warnings = ""
old_warnings = ""
for entry in result:
for name in entry["other_names"]:
lower_name = name.lower()
if count.has_key(lower_name):
count[lower_name] += 1
warnings += ("warning: %s is an old name of %s = %d\n" % (lower_name, entry["NAME".lower()], count[lower_name]))
elif (old_count.has_key(lower_name)):
old_count[lower_name] += 1
old_warnings += ("warning: old multiplicity for %s = %d\n" % (lower_name, old_count[lower_name]))
else:
old_count[lower_name] = 1
print "-" * 100
print "counting instances of major names and old names"
print "-" * 100
print warnings
print "-" * 100
print "counting instances of old names between themselves"
print "-" * 100
print old_warnings
print "-" * 100
# matches = table.is_overlaps(510860, 510863, "+")
#
# for match in matches:
# res, id = match
# print res, table.findById(id)
#
# print table.findByName("ybaS")
pdfLoader = PDFTableLoader()
result = pdfLoader.loadUnprocessed("./parsed_files/s5.table")
pdfTable = pdfLoader.createTable("s5", result)
print "-" * 100
print "print matches to majors"
print "-" * 100
other_name_matches = ""
total_count = {}
total_count.update(count)
total_count.update(old_count)
#table_name = "srna-name"
table_name = "name"
# find matching candidates to copy their directionality
for entry in result:
match = table.findByField("name", entry[table_name])
if (match != (None, None)):
first_entry_start, first_entry_end, dummy_a,\
second_entry_start, second_entry_end, dummy_b = \
pdfTable.findByField(table_name, entry[table_name])[0].split(";")
startDiff = int(first_entry_start)
endDiff = int(first_entry_end)
first_entry_start, first_entry_end, dummy_a,\
second_entry_start, second_entry_end, dummy_b = match[0].split(";")
startDiff -= int (int(first_entry_start))
endDiff -= int(first_entry_end)
print "%s from PDF match to: %s diff is: %d;%d" % (entry[table_name], match[0], startDiff, endDiff)
if(total_count[entry[table_name].lower()] > 1):
print "%s has multiple instances" % entry[table_name]
else:
match = table.findByOtherNames(entry[table_name])
other_name_matches += "%s match to other names: %s\n" % (entry[table_name], match[0])
if (match[0] != None):
first_entry_start, first_entry_end, dummy_a,\
second_entry_start, second_entry_end, dummy_b = \
pdfTable.findByField(table_name, entry[table_name])[0].split(";")
startDiff = int(first_entry_start)
endDiff = int(first_entry_end)
first_entry_start, first_entry_end, dummy_a,\
second_entry_start, second_entry_end, dummy_b = match[0].split(";")
startDiff -= int (int(first_entry_start))
endDiff -= int(first_entry_end)
other_name_matches += "the diff is %d;%d\n" % (startDiff, endDiff)
if (total_count.has_key(entry[table_name])):
other_name_matches += "%s appears %d in countings\n" % \
(entry[table_name], total_count[entry[table_name]])
print "-" * 100
print "matches to old names (in case of no match to major)"
print "-" * 100
print other_name_matches