def test_two_mismatches(self):
""" Correct 2 mismatches in the same read. Useful for making sure that
the TE log string is correct. """
sam_fields = [
"test_read", "0", "chr1", "202892094", "255", "5M", "*", "0", "0",
"ACCGA", "*", "NM:i:2", "MD:Z:1A0A2", "jI:B:i,-1", "jM:B:c,-1"
]
genome = Fasta("input_files/hg38_chr1.fa")
spliceAnnot = None
variants = {}
logInfo = TC.init_log_info(sam_fields)
# Init transcript object
transcript = t2.Transcript(sam_fields, genome, spliceAnnot)
# Run correction
error_entries = TC.correctMismatches(transcript, genome, variants,
logInfo)
# Check to see if correction was successful
assert transcript.SEQ == "AAAGA"
assert transcript.CIGAR == "5M"
# Check the number and content of the transcript error entries
print(error_entries)
assert error_entries.count('\n') == 2
assert error_entries.count('Corrected') == 2
def test_fix_donor_case3(self):
""" Toy transcript with sequence AAGGT|GAA, where the splice motif
is noncanonical but located 2 bp from a canonical splice donor.
chr1: 23,071,357 - 23,072,126
So-called case #3
"""
# Process references
sjFile = "input_files/test_junctions.txt"
tmp_dir = "scratch/test/TC_tmp/"
chroms = set(["chr1"])
donors, acceptors, sjDict = TC.processSpliceAnnotation(sjFile, tmp_dir,
chroms)
genome = Fasta("input_files/hg38_chr1.fa")
# Init transcript object
sam_fields = ["test_read", "0", "chr1", "23071357", "255", "5M762N3M", "*",
"0", "0", "AAGGTGAA", "*", "NM:i:0", "MD:Z:8"]
transcript = t2.Transcript(sam_fields, genome, sjDict)
jnNumber = 0
maxDist = 5
donor = (transcript.spliceJunctions[jnNumber]).bounds[0]
# Attempt to correct the splice donor side of the junction (left)
new_seq, new_cigar = TC.fix_one_side_of_junction(transcript.CHROM,
transcript.POS, jnNumber,
donor, -2, genome,
transcript.SEQ,
transcript.CIGAR)
assert new_seq == "AAGGAA"
assert new_cigar == "3M764N3M"
def test_correct_jn(self):
""" Toy transcript with sequence A|GAA, where the splice motif
is noncanonical but located 2 bp from a canonical splice donor.
chr1: 23,071,357 - 23,072,126
"""
# Process references
sjFile = "input_files/test_junctions.txt"
outprefix = "scratch/test_jns/"
tmp_dir = "scratch/test_jns/TC_tmp/"
chroms = set(["chr1"])
donors, acceptors, sjAnnot = TC.processSpliceAnnotation(
sjFile, tmp_dir, chroms)
genome = Fasta("input_files/hg38_chr1.fa")
# Init transcript object
sam_fields = [
"test_read", "0", "chr1", "23071357", "255", "1M766N3M", "*", "0",
"0", "AGAA", "*", "NM:i:0", "MD:Z:4"
]
transcript = t2.Transcript(sam_fields, genome, sjAnnot)
jnNumber = 0
maxDist = 5
#donor = (transcript.spliceJunctions[jnNumber]).bounds[0]
# Attempt to correct the splice junction
correction_status, reason, dist = TC.attempt_jn_correction(
transcript, jnNumber, genome, donors, acceptors, sjAnnot, maxDist)
assert correction_status == True
assert reason == "NA"
assert dist == 2
def test_mark_canonical(self):
""" In this test, we check whether TC correctly detects the junction
and labels it canonical.
Toy transcript with sequence AAG|GAA, where the splice motif (GT-AG)
is canonical.
chr1: 23,071,357 - 23,072,126 """
sam_fields = [
"test_read", "0", "chr1", "23071357", "255", "3M764N3M", "*", "0",
"0", "AAGGAA", "*", "NM:i:0", "MD:Z:6"
]
genome = Fasta("input_files/hg38_chr1.fa")
maxLen = 5
spliceAnnot = {}
variants = {}
# Init transcript object
transcript = t2.Transcript(sam_fields, genome, spliceAnnot)
# Check if the intron bounds are correct
intronBounds = transcript.getAllIntronBounds()
assert intronBounds[0].pos == 23071360
assert intronBounds[1].pos == 23072123
# Check if the overall junction is labeled correctly
assert (transcript.spliceJunctions[0]).isCanonical == True
# Check if the overall transcript is labeled correctly
assert transcript.isCanonical == True
def test_mark_noncanonical(self):
""" In this test, we check whether TC correctly detects the junction
and labels it noncanonical.
Toy transcript with sequence GGT|GTG, where the splice motif (AA-CA)
is noncanonical.
chr1: 23,072,197 - 23,073,291. """
sam_fields = [
"test_read", "0", "chr1", "23072197", "255", "3M1091N3M", "*", "0",
"0", "GGTGTG", "*", "NM:i:0", "MD:Z:6"
]
genome = Fasta("input_files/hg38_chr1.fa")
maxLen = 5
spliceAnnot = {}
variants = {}
# Init transcript object
transcript = t2.Transcript(sam_fields, genome, spliceAnnot)
# Check if the intron bounds are correct
intronBounds = transcript.getAllIntronBounds()
assert intronBounds[0].pos == 23072200
assert intronBounds[1].pos == 23073290
# Check if the overall junction is labeled correctly
assert (transcript.spliceJunctions[0]).isCanonical == False
# Check if the overall transcript is labeled correctly
assert transcript.isCanonical == False
def test_correctable_deletion(self):
""" Toy transcript with sequence AA-GA, where the '-' is a deletion of
the base 'A'.
chr1: 202,892,094 - 202,892,098. Deletion is at 202,892,096 """
sam_fields = [
"test_read", "0", "chr1", "202892094", "255", "2M1D2M", "*", "0",
"0", "AAGA", "*", "NM:i:1", "MD:Z:2^A2", "jI:B:i,-1", "jM:B:c,-1"
]
genome = Fasta("input_files/hg38_chr1.fa")
maxLen = 5
spliceAnnot = None
variants = {}
logInfo = TC.init_log_info(sam_fields)
# Init transcript object
transcript = t2.Transcript(sam_fields, genome, spliceAnnot)
# Run correction
TE_entries = TC.correctDeletions(transcript, genome, variants, maxLen,
logInfo)
# Check to see if correction was successful
assert transcript.SEQ == "AAAGA"
assert transcript.CIGAR == "5M"
# Check TE log
expected_TE = "\t".join([
"test_read", "chr1_202892095_202892096", "Deletion", "1",
"Corrected", "NA"
]) + "\n"
assert TE_entries == expected_TE
def test_crash(self):
""" This is a Drosophila junction that borders a small match preceded by
a 7 bp deletion. It is supposed to crash correction, which will result
in a categorization of 'Other' in the log """
# Process references
sjFile = "input_files/drosophila_example/chr3R_SJs.tsv"
outprefix = "scratch/dmel_crash/"
tmp_dir = "scratch/dmel_crash/TC_tmp/"
chroms = set(["chr3R"])
donors, acceptors, sjAnnot = TC.processSpliceAnnotation(
sjFile, tmp_dir, chroms)
genome = Fasta("input_files/drosophila_example/chr3R.fa")
# Init transcript object
sam_fields = [
"test_read", "0", "chr3R", "14890420", "255", "7M7D2M264N7M", "*",
"0", "0", "GATCAAACAACAAGTC", "*"
]
transcript = t2.Transcript(sam_fields, genome, sjAnnot)
jnNumber = 0
maxDist = 5
# Attempt to correct the splice junction
correction_status, reason, dist = TC.attempt_jn_correction(
transcript, jnNumber, genome, donors, acceptors, sjAnnot, maxDist)
assert correction_status == False
assert reason == "Other"
assert dist == 5
def test_variant_insertion(self):
""" Toy transcript with sequence AAATTGA, where the Ts are a 2 bp
insertion that matches a known variant.
chr1: 202,892,094 - 202,892,098. Insertion is between position
202,892,096 and 202,892,097. The genomic position used to refer
to it is 202,892,097 """
sam_fields = [
"test_read", "0", "chr1", "202892094", "255", "3M2I2M", "*", "0",
"0", "AAATTGA", "*", "NM:i:2", "MD:Z:5", "jI:B:i,-1", "jM:B:c,-1"
]
genome = Fasta("input_files/hg38_chr1.fa")
maxLen = 5
spliceAnnot = None
variants = {"chr1_202892096_202892098": "TT"}
logInfo = TC.init_log_info(sam_fields)
# Init transcript object
transcript = t2.Transcript(sam_fields, genome, spliceAnnot)
# Run correction
TE_entries = TC.correctInsertions(transcript, genome, variants, maxLen,
logInfo)
# Check to see if correction was successful
assert transcript.SEQ == "AAATTGA"
assert transcript.CIGAR == "3M2I2M"
# Check the log entries
expected_log = "\t".join([
"test_read", "chr1_202892096_202892098", "Insertion", "2",
"Uncorrected", "VariantMatch"
]) + "\n"
assert TE_entries == expected_log
def main():
logging.debug("Main function called")
# this is the object that will hold all of the data
transcriptObj = transcript.Transcript()
# display menu and call appropriate function based on user input
while True:
# display menu
choice = menuPrompt()
logging.debug("User entered: " + choice)
# exit loop if user chooses 0
if choice == "0":
break
# if 1, prompt user for grade info and store in transcript object
elif choice == "1":
enterGrades(transcriptObj)
# if 2, print the transcript to the console
elif choice == "2":
transcriptObj.print()
else:
logging.debug("Invalid choice by user")
print("Invalid choice. Please try again.")
def test_no_correction(self):
""" Make sure that the attributes stay the same if no correction
was performed
"""
# Process references
sjFile = "input_files/test_junctions.txt"
tmp_dir = "scratch/test/TC_tmp/"
chroms = set(["chr1"])
donor, acceptor, sjDict = TC.processSpliceAnnotation(
sjFile, tmp_dir, chroms)
genome = Fasta("input_files/hg38_chr1.fa")
# Init transcript object
sam_fields = [
"test_read", "0", "chr1", "23071357", "255", "1M766N3M", "*", "0",
"0", "AGAA", "*", "NM:i:0", "MD:Z:4"
]
transcript = t2.Transcript(sam_fields, genome, sjDict)
jnNumber = 0
maxDist = 5
donor = (transcript.spliceJunctions[jnNumber]).bounds[0]
# Now test the update function
TC.update_post_ncsj_correction(transcript, jnNumber, genome, sjDict)
junction = transcript.spliceJunctions[jnNumber]
assert junction.motif_code == "0"
assert junction.isCanonical == False
assert transcript.MD == "MD:Z:4"
assert transcript.isCanonical == False
def test_not_correctable_deletion(self):
""" Same deletion again, but correction cutoff set to 0 """
sam_fields = [
"test_read", "0", "chr1", "202892094", "255", "2M1D2M", "*", "0",
"0", "AAGA", "*", "NM:i:1", "MD:Z:2^A2", "jI:B:i,-1", "jM:B:c,-1"
]
genome = Fasta("input_files/hg38_chr1.fa")
maxLen = 0
spliceAnnot = None
variants = {}
logInfo = TC.init_log_info(sam_fields)
# Init transcript object
transcript = t2.Transcript(sam_fields, genome, spliceAnnot)
# Run correction
TE_entries = TC.correctDeletions(transcript, genome, variants, maxLen,
logInfo)
# Check to see if correction was successful
assert transcript.SEQ == "AAGA"
assert transcript.CIGAR == "2M1D2M"
# Check TE log
expected_TE = "\t".join([
"test_read", "chr1_202892095_202892096", "Deletion", "1",
"Uncorrected", "TooLarge"
]) + "\n"
assert TE_entries == expected_TE
def test_variant_deletion(self):
""" Same deletion again, but with a matching variant at the same
location. Correct action is to leave the deletion in place """
sam_fields = [
"test_read", "0", "chr1", "202892094", "255", "2M1D2M", "*", "0",
"0", "AAGA", "*", "NM:i:1", "MD:Z:2^A2", "jI:B:i,-1", "jM:B:c,-1"
]
genome = Fasta("input_files/hg38_chr1.fa")
maxLen = 5
spliceAnnot = None
variants = {"chr1_202892095_202892096": 1}
logInfo = TC.init_log_info(sam_fields)
# Init transcript object
transcript = t2.Transcript(sam_fields, genome, spliceAnnot)
# Run correction
TE_entries = TC.correctDeletions(transcript, genome, variants, maxLen,
logInfo)
# Check to see if deletion is still there as expected
assert transcript.SEQ == "AAGA"
assert transcript.CIGAR == "2M1D2M"
# Check TE log
expected_TE = "\t".join([
"test_read", "chr1_202892095_202892096", "Deletion", "1",
"Uncorrected", "VariantMatch"
]) + "\n"
assert TE_entries == expected_TE
def test_too_far_away(self):
""" A case where the NCSJ should not be corrected because it is too far
away from the closest annotated junction relative to the maxDist
parameter.
Toy transcript with sequence A|GAA, where the splice motif
is noncanonical.
chr1: 23,071,357 - 23,072,126
"""
# Process references
sjFile = "input_files/test_junctions.txt"
tmp_dir = "scratch/test_jns/TC_tmp/"
chroms = set(["chr1"])
donors, acceptors, sjAnnot = TC.processSpliceAnnotation(
sjFile, tmp_dir, chroms)
genome = Fasta("input_files/hg38_chr1.fa")
# Init transcript object
sam_fields = [
"test_read", "0", "chr1", "23071357", "255", "1M766N3M", "*", "0",
"0", "AGAA", "*", "NM:i:0", "MD:Z:6"
]
transcript = t2.Transcript(sam_fields, genome, sjAnnot)
jnNumber = 0
maxDist = 1
correction_status, reason, dist = TC.attempt_jn_correction(
transcript, jnNumber, genome, donors, acceptors, sjAnnot, maxDist)
assert correction_status == False
assert reason == "TooFarFromAnnotJn"
assert dist == 2
def test_wrong_variant_mismatch(self):
""" Toy transcript with sequence AACGA, where the C is a mismatch to the
reference base 'A' in the location, but not matching, a known SNP.
chr1: 202,892,094 - 202,892,098. Mismatch is at 202,892,096 """
sam_fields = [
"test_read", "0", "chr1", "202892094", "255", "5M", "*", "0", "0",
"AACGA", "*", "NM:i:1", "MD:Z:2A2", "jI:B:i,-1", "jM:B:c,-1"
]
genome = Fasta("input_files/hg38_chr1.fa")
spliceAnnot = None
variants = {"chr1_202892096": ["G"]}
logInfo = TC.init_log_info(sam_fields)
# Init transcript object
transcript = t2.Transcript(sam_fields, genome, spliceAnnot)
# Run correction
error_entries = TC.correctMismatches(transcript, genome, variants,
logInfo)
# Check to see if correction was successful
assert transcript.SEQ == "AAAGA"
assert transcript.CIGAR == "5M"
# Check the number and content of the transcript error entries
assert error_entries.count('\n') == 1
assert "Corrected" in error_entries
assert "VariantMatch" not in error_entries
def _get_all_text(self):
if self.text:
return self.text
links = transcript.getLinksForTranscripts(self.series)
transcripts = [transcript.Transcript(link) for link in links]
self.text = ''
for tp in transcripts:
self.text += " ".join([line.text for line in tp.getAllLines()])
return self.text
def test_two_annotated_SJs_without_ref(self):
""" Same example, but no splice annot provided, so no junctions can
show up as annotated
"""
sam = "input_files/sams/perfectReferenceMatch_twoIntrons.sam"
genome = Fasta("input_files/hg38_chr1.fa")
with open(sam, 'r') as f:
sam_line = f.readline().strip().split('\t')
transcript = t2.Transcript(sam_line, genome, {})
assert transcript.allJnsAnnotated == False
assert transcript.isCanonical == True
def test_no_jns(self):
""" Return transcript.allJnsAnnotated = True for a transcript without
junctions"""
sam = "input_files/sams/perfectReferenceMatch_noIntrons.sam"
genome = Fasta("input_files/hg38_chr1.fa")
with open(sam, 'r') as f:
sam_line = f.readline().strip().split('\t')
transcript = t2.Transcript(sam_line, genome, {})
assert transcript.allJnsAnnotated == True
assert transcript.isCanonical == True
def test_perfect_match(self):
""" Since this read is a perfect match to the reference, its CIGAR and
sequence fields should definitely be the same length """
sam = "input_files/sams/perfectReferenceMatch_noIntrons.sam"
genome = Fasta("input_files/hg38_chr1.fa")
sjDict = set()
with open(sam, 'r') as f:
sam_line = f.readline().strip().split('\t')
transcript = t2.Transcript(sam_line, genome, sjDict)
assert t2.check_seq_and_cigar_length(transcript.SEQ,
transcript.CIGAR) == True
def test_mismatch(self):
""" Compare SEQ and CIGAR for a spliced transcript that contains a
mismatch. """
sam = "input_files/sams/mismatch.sam"
genome = Fasta("input_files/hg38_chr1.fa")
sjDict = set()
with open(sam, 'r') as f:
sam_line = f.readline().strip().split('\t')
transcript = t2.Transcript(sam_line, genome, sjDict)
assert t2.check_seq_and_cigar_length(transcript.SEQ,
transcript.CIGAR) == True
def test_perfect_match_with_introns(self):
""" Compare SEQ and CIGAR for a transcript that is a perfect
reference match containing introns. """
sam = "input_files/sams/perfectReferenceMatch_twoIntrons.sam"
genome = Fasta("input_files/hg38_chr1.fa")
sjDict = set()
with open(sam, 'r') as f:
sam_line = f.readline().strip().split('\t')
transcript = t2.Transcript(sam_line, genome, sjDict)
assert t2.check_seq_and_cigar_length(transcript.SEQ,
transcript.CIGAR) == True
def test_crash_dmel(self):
""" This is a Drosophila junction that borders a small match preceded by
a 7 bp deletion. It is also supposed to crash correction, but did
not in TC v2.0.1."""
# Process references
sjFile = "input_files/drosophila_example/chr3R_SJs.tsv"
tmp_dir = "scratch/dmel/TC"
os.system("mkdir -p %s" % tmp_dir)
refs = dstruct.Struct()
chroms = set(["chr3R"])
refs.donors, refs.acceptors, refs.sjAnnot = TC.processSpliceAnnotation(
sjFile, tmp_dir, chroms)
refs.genome = Fasta("input_files/drosophila_example/chr3R.fa")
sam = "input_files/drosophila_example/no_SJ_corr.sam"
with open(sam, 'r') as f:
for sam_line in f:
if sam_line.startswith("@"):
continue
else:
sam_line = sam_line.strip().split('\t')
# Init transcript object
transcript = t2.Transcript(sam_line, refs.genome, refs.sjAnnot)
maxDist = 5
logInfo = TC.init_log_info(sam_line)
orig_CIGAR = transcript.CIGAR
orig_seq = transcript.SEQ
orig_MD = transcript.MD
expected_TE = "\t".join([
"m160713_133433_42182_c101000162550000001823232709161620_s1_p0/121139/11291_13013",
"chr3R_14890436_14890699", "NC_SJ_boundary", "5", "Uncorrected",
"Other"
]) + "\n"
assert transcript.isCanonical == False
# Attempt to correct the splice junction
new_transcript, TE_entries = TC.cleanNoncanonical(
transcript, refs, maxDist, logInfo)
print(TE_entries)
assert new_transcript.isCanonical == False
assert TE_entries == expected_TE
assert new_transcript.MD == orig_MD
assert logInfo.corrected_NC_SJs == 0
assert logInfo.uncorrected_NC_SJs == 1
assert new_transcript.CIGAR == orig_CIGAR
assert new_transcript.SEQ == orig_seq
def test_insertion(self):
""" Compute the correct MD tag for a spliced transcript that contains an
insertion. """
sam = "input_files/sams/insertion.sam"
genome = Fasta("input_files/hg38_chr1.fa")
with open(sam, 'r') as f:
sam_line = f.readline().strip().split('\t')
transcript = t2.Transcript(sam_line, genome, {})
correct_MD = "MD:Z:3069"
correct_NM = "NM:i:2"
assert transcript.MD == correct_MD
assert transcript.NM == correct_NM
def test_insertion_deletion_mismatch_ncsj(self):
""" Compare SEQ and CIGAR for a transcript that contains an
insertion, deletion, mismatch, and noncanonical splice junction in
it. """
sam = "input_files/sams/deletion_insertion_mismatch_nc.sam"
genome = Fasta("input_files/hg38_chr1.fa")
sjDict = set()
with open(sam, 'r') as f:
sam_line = f.readline().strip().split('\t')
transcript = t2.Transcript(sam_line, genome, sjDict)
assert t2.check_seq_and_cigar_length(transcript.SEQ,
transcript.CIGAR) == True
def test_deletion_insertion_mismatch(self):
""" Compute the correct MD tag for a spliced transcript that contains an
insertion, deletion, and mismatch. """
sam = "input_files/sams/deletion_insertion_mismatch.sam"
genome = Fasta("input_files/hg38_chr1.fa")
with open(sam, 'r') as f:
sam_line = f.readline().strip().split('\t')
transcript = t2.Transcript(sam_line, genome, {})
correct_MD = "MD:Z:475C0A0C0C0A1082^C1347G17C205"
correct_NM = "NM:i:9"
assert transcript.MD == correct_MD
assert transcript.NM == correct_NM
def test_perfect_match_with_introns(self):
""" Compute the correct MD tag for a transcript that is a perfect
reference match containing introns. """
sam = "input_files/sams/perfectReferenceMatch_twoIntrons.sam"
genome = Fasta("input_files/hg38_chr1.fa")
with open(sam, 'r') as f:
sam_line = f.readline().strip().split('\t')
transcript = t2.Transcript(sam_line, genome, {})
correct_MD = "MD:Z:3400"
correct_NM = "NM:i:0"
assert transcript.MD == correct_MD
assert transcript.NM == correct_NM
def test_insertion_deletion_mismatch_ncsj(self):
""" Compute the correct MD tag for a transcript that contains an
insertion, deletion, mismatch, and noncanonical splice junction in
it. """
sam = "input_files/sams/deletion_insertion_mismatch_nc.sam"
genome = Fasta("input_files/hg38_chr1.fa")
with open(sam, 'r') as f:
sam_line = f.readline().strip().split('\t')
transcript = t2.Transcript(sam_line, genome, {})
correct_MD = "MD:Z:414G0A450^C405^C2435"
correct_NM = "NM:i:5"
assert transcript.MD == correct_MD
assert transcript.NM == correct_NM
def test_pre_correction_dmel(self):
""" This is a noisy Drosophila read, but prior to correction, the CIGAR
and SEQ strings should definitely match """
sam = "input_files/drosophila_example/input_read.sam"
genome = Fasta("input_files/drosophila_example/chr3R.fa")
sjDict = set()
with open(sam, 'r') as f:
for sam_line in f:
if sam_line.startswith("@"):
continue
else:
sam_line = sam_line.strip().split('\t')
transcript = t2.Transcript(sam_line, genome, sjDict)
assert t2.check_seq_and_cigar_length(transcript.SEQ,
transcript.CIGAR) == True
def test_plus_strand(self):
""" Toy transcript with sequence AAAGA on the plus strand. Sequence
should be output as listed in the SAM fields."""
sam_fields = ["test_read", "0", "chr1", "202892094", "255", "5M", "*",
"0", "0", "AAAGA", "*", "NM:i:0", "MD:Z:5", "jI:B:i,-1",
"jM:B:c,-1" ]
genome = Fasta("input_files/hg38_chr1.fa")
spliceAnnot = None
# Init transcript object
transcript = ts.Transcript(sam_fields, genome, spliceAnnot)
# Output fasta and check against expected
expected_fasta = ">test_read" + "\n" + "AAAGA"
assert transcript.printableFa() == expected_fasta
def test_two_annotated_SJs(self):
""" Transcript with 2 junctions and each match the provided reference
"""
sam = "input_files/sams/perfectReferenceMatch_twoIntrons.sam"
genome = Fasta("input_files/hg38_chr1.fa")
sjFile = "input_files/GM12878_SJs_chr1.tab"
outprefix = "scratch/test"
tmp_dir = "scratch/test_jIjM/TC_tmp/"
chroms = set(["chr1"])
donors, acceptors, sjDict = TC.processSpliceAnnotation(sjFile, tmp_dir,
chroms)
with open(sam, 'r') as f:
sam_line = f.readline().strip().split('\t')
transcript = t2.Transcript(sam_line, genome, sjDict)
assert transcript.allJnsAnnotated == True
assert transcript.isCanonical == True
def get_transcript(sid, pin):
""" get transcript including list of classes taken, grade, and current gpa """
login_number = 2
#If we are not logged in we will loop around again
for i in range(login_number):
#The transcript page url
html = fetch_html.get_transcript()
if parse_html.get_page_title(html) != 'Login':
# We set the transcript variable to a instance of the transcript class
grades = parse_html.get_grades(html)
credits = parse_html.get_credits(html)
gpa = parse_html.get_gpa(html)
return transcript.Transcript(html, grades, credits, gpa)
else:
login(sid, pin)
