def generate_gene_table(table_path, name):
loader = GeneTableLoader()
table = loader.createTable(name, loader.loadUnprocessed(table_path))
rows = []
for key, value in table:
start, end, strand = key.split(Table.ID_DELIMITER)[:3]
row = [value["unique_id"],
value["name"],
value["blattner-id"],
value["unique-id"],
int(start),
int(end),
strand]
synonyms = [""] * 4
for index, name in enumerate(value["other_names"]):
synonyms[index] = name
row.extend(synonyms)
rows.append(row)
# for row in rows:
# print row
db = MySQLdb.connect(host="localhost",user="******",db="article_refactor_24_3_2016")
cur = db.cursor(MySQLdb.cursors.DictCursor)
key_list = ["unique_id",
"name",
"blattner_id",
"gene_unique_id",
"start",
"end",
"strand",
"synonym_1",
"synonym_2",
"synonym_3",
"synonym_4"]
fields = ", ".join("%s VARCHAR(200)" % key for key in key_list)
cur.execute("CREATE TABLE %s (%s)" % (table.get_name(), fields))
for row in rows:
values = ",".join("%s" % db.literal(str(val)) for val in row )
cur.execute("INSERT INTO %s VALUES (%s)" % (table.get_name(), values))
db.commit()
def generate_gene_table(table_path, name):
loader = GeneTableLoader()
table = loader.createTable(name, loader.loadUnprocessed(table_path))
rows = []
for key, value in table:
start, end, strand = key.split(Table.ID_DELIMITER)[:3]
row = [
value["unique_id"], value["name"], value["blattner-id"],
value["unique-id"],
int(start),
int(end), strand
]
synonyms = [""] * 4
for index, name in enumerate(value["other_names"]):
synonyms[index] = name
row.extend(synonyms)
rows.append(row)
# for row in rows:
# print row
db = MySQLdb.connect(host="localhost",
user="******",
db="article_refactor_24_3_2016")
cur = db.cursor(MySQLdb.cursors.DictCursor)
key_list = [
"unique_id", "name", "blattner_id", "gene_unique_id", "start", "end",
"strand", "synonym_1", "synonym_2", "synonym_3", "synonym_4"
]
fields = ", ".join("%s VARCHAR(200)" % key for key in key_list)
cur.execute("CREATE TABLE %s (%s)" % (table.get_name(), fields))
for row in rows:
values = ",".join("%s" % db.literal(str(val)) for val in row)
cur.execute("INSERT INTO %s VALUES (%s)" % (table.get_name(), values))
db.commit()
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 lybecker_update(file_name,
show_warnings=True,
overlap_delimiter="/",
overlap_field="annotation of overlapping genes",
adjacent_field="adjacent genes",
loader_type=LybeckerS2TableLoader):
geneLoader = GeneTableLoader()
gene_table = geneLoader.createTable("genes", geneLoader.loadUnprocessed("./genes.col"))
loader = loader_type()
table = loader.createTable("lybecker", loader.load("lybecker/final/%s" % file_name))
new_table_raw = []
for id, info in table:
dct = {}
info.pop(Table.UNIQUE_ID_FIELD)
start, end, strand = id.split(";")[:3]
# print info["name"]
start = int(start)
end = int(end)
result = gene_table.is_overlaps(start, end, "none")
if show_warnings:
print id
overlaps = [gene for gene in info[overlap_field].split(overlap_delimiter) if gene != ""]
print overlaps
for index, gene in enumerate(result):
print "%d: %s" % (index, gene[1][1]["name"])
if gene[1][1]["name"] not in overlaps:
print "[warning] older name is being used"
if len(overlaps) > len(result):
print "[warning] missing overlapping gene"
if len(overlaps) < len(result):
print "[warning] extra overlapping gene"
# Set the record location
dct[TableGlobals.FIRST_START_BASE_KEY], dct[TableGlobals.FIRST_END_BASE_KEY], \
dct[TableGlobals.FIRST_STRAND_KEY], dct[TableGlobals.SECOND_START_BASE_KEY], \
dct[TableGlobals.SECOND_END_BASE_KEY], dct[TableGlobals.SECOND_STRAND_KEY] = id.split(Table.ID_DELIMITER)
# Assume unknown strand
dct[TableGlobals.FIRST_STRAND_KEY] = "none"
dct[TableGlobals.SECOND_STRAND_KEY] = "none"
is_valid = result[0][0]
overlap_names = info[overlap_field].split(overlap_delimiter)
# Check if major in overlapping names
if not is_valid:
is_valid = False
# print "major names", [gene[1][1]["name"] for gene in result]
for first in [gene[1][1]["name"] for gene in result]:
for second in overlap_names:
if first in second:
is_valid = True
break
if is_valid:
break
# check if minor in overlapping names
if not is_valid:
is_valid = False
other_names = []
for gene in result:
other_names.extend(gene[1][1]["other_names"])
# print "old names", other_names
for first in other_names:
for second in overlap_names:
if first in second:
is_valid = True
break
if is_valid:
break
if "intergenic" == info["category"]:
is_valid = False
adjacent_genes = [val for val in info[adjacent_field].split(overlap_delimiter) if val != ""]
first = gene_table.findByName(adjacent_genes[0])
second = gene_table.findByName(adjacent_genes[1])
if first == (None, None):
first = gene_table.findByOtherNames(adjacent_genes[0])
if second == (None, None):
second = gene_table.findByOtherNames(adjacent_genes[1])
if first != (None, None):
representing = first
elif second != (None, None):
representing = second
else:
raise BaseException("No presenting gene found")
strand = representing[0].split(Table.ID_DELIMITER)[2]
if strand == TableGlobals.STRAND_POSITIVE:
dct[TableGlobals.FIRST_STRAND_KEY] = TableGlobals.STRAND_NEGATIVE
dct[TableGlobals.SECOND_STRAND_KEY] = TableGlobals.STRAND_NEGATIVE
else:
dct[TableGlobals.FIRST_STRAND_KEY] = TableGlobals.STRAND_POSITIVE
dct[TableGlobals.SECOND_STRAND_KEY] = TableGlobals.STRAND_POSITIVE
if is_valid:
is_valid = "divergent" not in info["category"] and \
"convergent" not in info["category"]
# Update the record name if gene was found
if is_valid:
info["name"] = "overlapping_"
else:
name_id = id.split(Table.ID_DELIMITER)[:2]
name_id.append(dct[TableGlobals.FIRST_STRAND_KEY])
info["name"] = "lybecker_%s_%s" % (info["category"], Table.ID_DELIMITER.join(name_id))
pos_count = 0
neg_count = 0
if is_valid:
# for each gene match
for entry in result:
# exact match add name
info["name"] += "%s." % entry[1][1]["name"]
strand = entry[1][0].split(Table.ID_DELIMITER)[2]
if TableGlobals.STRAND_NEGATIVE == strand:
neg_count += 1
if TableGlobals.STRAND_POSITIVE == strand:
pos_count += 1
if neg_count == 0:
dct[TableGlobals.FIRST_STRAND_KEY] = TableGlobals.STRAND_NEGATIVE
dct[TableGlobals.SECOND_STRAND_KEY] = TableGlobals.STRAND_NEGATIVE
elif pos_count == 0:
dct[TableGlobals.FIRST_STRAND_KEY] = TableGlobals.STRAND_POSITIVE
dct[TableGlobals.SECOND_STRAND_KEY] = TableGlobals.STRAND_POSITIVE
else:
print "no strand match: %s" % entry[1][1]["name"]
# remove extra . from name if match found
if is_valid:
info["name"] = info["name"][:-1]
dct.update(info)
new_table_raw.append(dct)
if show_warnings:
print 20 * "*"
# for row in new_table_raw:
# print row
TableLoader().createTable("updated_lybecker", new_table_raw).dump("lybecker/final/updated_%s" % file_name)
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
