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Update length using function #37

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Merged
mohammedkhalfan merged 11 commits into from
May 24, 2025
Merged

Update length using function #37

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edfd89b
addjust script printing
YuWei-CH Jan 29, 2025
ee82a45
add just print statement
YuWei-CH Feb 3, 2025
58058ce
split modify process
YuWei-CH Feb 5, 2025
f1aecaa
add new chrom
YuWei-CH Feb 8, 2025
05a6e15
remove redundancy comments and temp file
YuWei-CH Feb 8, 2025
b2c1bb4
Fix bugs
YuWei-CH Mar 3, 2025
bf158ee
Read meta-data from input gtf/gff
YuWei-CH Mar 14, 2025
d7047cd
feature improvement
YuWei-CH Apr 14, 2025
eccc15c
Resolve comments
YuWei-CH Apr 22, 2025
df04901
use f-string
YuWei-CH Apr 22, 2025
1c263aa
Helper Function for Chromosome Length Calculation
YuWei-CH Apr 25, 2025
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530 changes: 383 additions & 147 deletions reform.py
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4 changes: 4 additions & 0 deletions test_data/17/gold.fa
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@@ -0,0 +1,4 @@
>X
ZZZZABBBBBDDDDDCCCCCIIIIIKKKKK
>Y
AAAATTTTGGGGCCCC
8 changes: 8 additions & 0 deletions test_data/17/gold.gtf
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X ref exon 5 25 . + 0 gene_id "ref_gene"; transcript_id "ref_gene.1";
X ref CDS 8 22 . + 0 gene_id "ref_gene"; transcript_id "ref_gene.1";
X ref start_codon 5 7 . + 0 gene_id "ref_gene"; transcript_id "ref_gene.1";
X ref stop_codon 23 25 . + 0 gene_id "ref_gene"; transcript_id "ref_gene.1";
Y ref exon 1 16 . + 0 gene_id "new_gene"; transcript_id "new_gene.1";
Y ref CDS 4 14 . + 0 gene_id "new_gene"; transcript_id "new_gene.1";
Y ref start_codon 1 3 . + 0 gene_id "new_gene"; transcript_id "new_gene.1";
Y ref stop_codon 14 16 . + 0 gene_id "new_gene"; transcript_id "new_gene.1";
2 changes: 2 additions & 0 deletions test_data/17/in.fa
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>Y
AAAATTTTGGGGCCCC
4 changes: 4 additions & 0 deletions test_data/17/in.gtf
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Y ref exon 1 16 . + 0 gene_id "new_gene"; transcript_id "new_gene.1";
Y ref CDS 4 14 . + 0 gene_id "new_gene"; transcript_id "new_gene.1";
Y ref start_codon 1 3 . + 0 gene_id "new_gene"; transcript_id "new_gene.1";
Y ref stop_codon 14 16 . + 0 gene_id "new_gene"; transcript_id "new_gene.1";
2 changes: 2 additions & 0 deletions test_data/17/ref.fa
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>X
ZZZZABBBBBDDDDDCCCCCIIIIIKKKKK
4 changes: 4 additions & 0 deletions test_data/17/ref.gtf
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X ref exon 5 25 . + 0 gene_id "ref_gene"; transcript_id "ref_gene.1";
X ref CDS 8 22 . + 0 gene_id "ref_gene"; transcript_id "ref_gene.1";
X ref start_codon 5 7 . + 0 gene_id "ref_gene"; transcript_id "ref_gene.1";
X ref stop_codon 23 25 . + 0 gene_id "ref_gene"; transcript_id "ref_gene.1";
8 changes: 8 additions & 0 deletions test_data/18/gold.fa
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Original file line number Diff line number Diff line change
@@ -0,0 +1,8 @@
>X
ZZZZABBBBBDDDDDCCCCCIIIIIKKKKK
>Y
AAAATTTTGGGGCCCC
>H
GGGGAATTCCCCGGGG
>M
CCCCGGGGAAAATTTT
18 changes: 18 additions & 0 deletions test_data/18/gold.gtf
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X ref exon 5 25 . + 0 gene_id "ref_gene"; transcript_id "ref_gene.1";
X ref CDS 8 22 . + 0 gene_id "ref_gene"; transcript_id "ref_gene.1";
X ref start_codon 5 7 . + 0 gene_id "ref_gene"; transcript_id "ref_gene.1";
X ref stop_codon 23 25 . + 0 gene_id "ref_gene"; transcript_id "ref_gene.1";
##sequence-region Y 1 16
Y ref exon 1 16 . + 0 gene_id "new_gene"; transcript_id "new_gene.1";
Y ref CDS 4 14 . + 0 gene_id "new_gene"; transcript_id "new_gene.1";
Y ref start_codon 1 3 . + 0 gene_id "new_gene"; transcript_id "new_gene.1";
Y ref stop_codon 14 16 . + 0 gene_id "new_gene"; transcript_id "new_gene.1";
##sequence-region H 1 16
H ref exon 1 16 . + 0 gene_id "gene2"; transcript_id "gene2.1";
H ref CDS 4 14 . + 0 gene_id "gene2"; transcript_id "gene2.1";
H ref start_codon 1 3 . + 0 gene_id "gene2"; transcript_id "gene2.1";
H ref stop_codon 14 16 . + 0 gene_id "gene2"; transcript_id "gene2.1";
M ref exon 1 16 . + 0 gene_id "gene4"; transcript_id "gene4.1";
M ref CDS 4 14 . + 0 gene_id "gene4"; transcript_id "gene4.1";
M ref start_codon 1 3 . + 0 gene_id "gene4"; transcript_id "gene4.1";
M ref stop_codon 14 16 . + 0 gene_id "gene4"; transcript_id "gene4.1";
2 changes: 2 additions & 0 deletions test_data/18/in1.fa
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>Y
AAAATTTTGGGGCCCC
5 changes: 5 additions & 0 deletions test_data/18/in1.gtf
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##sequence-region Y.11 1 16
Y ref exon 1 16 . + 0 gene_id "new_gene"; transcript_id "new_gene.1";
Y ref CDS 4 14 . + 0 gene_id "new_gene"; transcript_id "new_gene.1";
Y ref start_codon 1 3 . + 0 gene_id "new_gene"; transcript_id "new_gene.1";
Y ref stop_codon 14 16 . + 0 gene_id "new_gene"; transcript_id "new_gene.1";
2 changes: 2 additions & 0 deletions test_data/18/in2.fa
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>H
GGGGAATTCCCCGGGG
5 changes: 5 additions & 0 deletions test_data/18/in2.gtf
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##sequence-region F.11 3 27
H ref exon 1 16 . + 0 gene_id "gene2"; transcript_id "gene2.1";
H ref CDS 4 14 . + 0 gene_id "gene2"; transcript_id "gene2.1";
H ref start_codon 1 3 . + 0 gene_id "gene2"; transcript_id "gene2.1";
H ref stop_codon 14 16 . + 0 gene_id "gene2"; transcript_id "gene2.1";
2 changes: 2 additions & 0 deletions test_data/18/in3.fa
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>M
CCCCGGGGAAAATTTT
4 changes: 4 additions & 0 deletions test_data/18/in3.gtf
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M ref exon 1 16 . + 0 gene_id "gene4"; transcript_id "gene4.1";
M ref CDS 4 14 . + 0 gene_id "gene4"; transcript_id "gene4.1";
M ref start_codon 1 3 . + 0 gene_id "gene4"; transcript_id "gene4.1";
M ref stop_codon 14 16 . + 0 gene_id "gene4"; transcript_id "gene4.1";
2 changes: 2 additions & 0 deletions test_data/18/ref.fa
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@@ -0,0 +1,2 @@
>X
ZZZZABBBBBDDDDDCCCCCIIIIIKKKKK
4 changes: 4 additions & 0 deletions test_data/18/ref.gtf
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@@ -0,0 +1,4 @@
X ref exon 5 25 . + 0 gene_id "ref_gene"; transcript_id "ref_gene.1";
X ref CDS 8 22 . + 0 gene_id "ref_gene"; transcript_id "ref_gene.1";
X ref start_codon 5 7 . + 0 gene_id "ref_gene"; transcript_id "ref_gene.1";
X ref stop_codon 23 25 . + 0 gene_id "ref_gene"; transcript_id "ref_gene.1";
8 changes: 8 additions & 0 deletions test_data/19/gold.fa
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Original file line number Diff line number Diff line change
@@ -0,0 +1,8 @@
>X
ZZZZABBBBBDDDDDCCCCCIIIIIKKKKK
>Y
AAAATTTTGGGGCCCC
>H
GGGGAATTCCCCGGGG
>M
CCCCGGGGAAAATTTT
18 changes: 18 additions & 0 deletions test_data/19/gold.gtf
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Original file line number Diff line number Diff line change
@@ -0,0 +1,18 @@
X ref exon 5 25 . + 0 gene_id "ref_gene"; transcript_id "ref_gene.1";
X ref CDS 8 22 . + 0 gene_id "ref_gene"; transcript_id "ref_gene.1";
X ref start_codon 5 7 . + 0 gene_id "ref_gene"; transcript_id "ref_gene.1";
X ref stop_codon 23 25 . + 0 gene_id "ref_gene"; transcript_id "ref_gene.1";
##sequence-region Y 1 16
Y ref exon 1 16 . + 0 gene_id "new_gene"; transcript_id "new_gene.1";
Y ref CDS 4 14 . + 0 gene_id "new_gene"; transcript_id "new_gene.1";
Y ref start_codon 1 3 . + 0 gene_id "new_gene"; transcript_id "new_gene.1";
Y ref stop_codon 14 16 . + 0 gene_id "new_gene"; transcript_id "new_gene.1";
##sequence-region H 1 16
H ref exon 1 16 . + 0 gene_id "gene2"; transcript_id "gene2.1";
H ref CDS 4 14 . + 0 gene_id "gene2"; transcript_id "gene2.1";
H ref start_codon 1 3 . + 0 gene_id "gene2"; transcript_id "gene2.1";
H ref stop_codon 14 16 . + 0 gene_id "gene2"; transcript_id "gene2.1";
M ref exon 1 16 . + 0 gene_id "gene4"; transcript_id "gene4.1";
M ref CDS 4 14 . + 0 gene_id "gene4"; transcript_id "gene4.1";
M ref start_codon 1 3 . + 0 gene_id "gene4"; transcript_id "gene4.1";
M ref stop_codon 14 16 . + 0 gene_id "gene4"; transcript_id "gene4.1";
2 changes: 2 additions & 0 deletions test_data/19/in1.fa
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@@ -0,0 +1,2 @@
>Z
AAAATTTTGGGGCCCC
5 changes: 5 additions & 0 deletions test_data/19/in1.gtf
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##sequence-region Y.11 1 16
Z ref exon 1 16 . + 0 gene_id "new_gene"; transcript_id "new_gene.1";
Z ref CDS 4 14 . + 0 gene_id "new_gene"; transcript_id "new_gene.1";
Z ref start_codon 1 3 . + 0 gene_id "new_gene"; transcript_id "new_gene.1";
Z ref stop_codon 14 16 . + 0 gene_id "new_gene"; transcript_id "new_gene.1";
2 changes: 2 additions & 0 deletions test_data/19/in2.fa
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@@ -0,0 +1,2 @@
>Y
GGGGAATTCCCCGGGG
5 changes: 5 additions & 0 deletions test_data/19/in2.gtf
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##sequence-region F.11 3 27
H ref exon 1 16 . + 0 gene_id "gene2"; transcript_id "gene2.1";
H ref CDS 4 14 . + 0 gene_id "gene2"; transcript_id "gene2.1";
H ref start_codon 1 3 . + 0 gene_id "gene2"; transcript_id "gene2.1";
H ref stop_codon 14 16 . + 0 gene_id "gene2"; transcript_id "gene2.1";
2 changes: 2 additions & 0 deletions test_data/19/in3.fa
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>M
CCCCGGGGAAAATTTT
5 changes: 5 additions & 0 deletions test_data/19/in3.gtf
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##Test Data
M ref exon 1 16 . + 0 gene_id "gene4"; transcript_id "gene4.1";
K ref CDS 4 14 . + 0 gene_id "gene4"; transcript_id "gene4.1";
Z ref start_codon 1 3 . + 0 gene_id "gene4"; transcript_id "gene4.1";
M ref stop_codon 14 16 . + 0 gene_id "gene4"; transcript_id "gene4.1";
2 changes: 2 additions & 0 deletions test_data/19/ref.fa
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Original file line number Diff line number Diff line change
@@ -0,0 +1,2 @@
>X
ZZZZABBBBBDDDDDCCCCCIIIIIKKKKK
4 changes: 4 additions & 0 deletions test_data/19/ref.gtf
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Original file line number Diff line number Diff line change
@@ -0,0 +1,4 @@
X ref exon 5 25 . + 0 gene_id "ref_gene"; transcript_id "ref_gene.1";
X ref CDS 8 22 . + 0 gene_id "ref_gene"; transcript_id "ref_gene.1";
X ref start_codon 5 7 . + 0 gene_id "ref_gene"; transcript_id "ref_gene.1";
X ref stop_codon 23 25 . + 0 gene_id "ref_gene"; transcript_id "ref_gene.1";
118 changes: 118 additions & 0 deletions test_reform.py
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Expand Up @@ -684,5 +684,123 @@ def test_case_16(self):

os.chdir(wd)

def test_case_17(self):
"""
Case 17:
Testing Reform which adding new chrom
"""

wd = os.getcwd()
os.chdir('test_data/17/')

command = """
python3 ../../reform.py \
--new_chrom="Y" \
--in_fasta=in.fa \
--in_gff=in.gtf \
--ref_fasta=ref.fa \
--ref_gff=ref.gtf
"""

response = subprocess.getoutput(command)
print(response)

with open('gold.gtf', 'r') as f:
gold_gff = f.read()
with open('ref_reformed.gtf', 'r') as f:
new_gff = f.read()
print("Testing gtf")
self.assertListEqual(list(gold_gff), list(new_gff))
print("Done")

with open('gold.fa', 'r') as f:
gold_fa = f.read()
with open('ref_reformed.fa', 'r') as f:
new_fa = f.read()
print("Testing Fasta")
self.assertListEqual(list(gold_fa), list(new_fa))
print("Done")

os.chdir(wd)

def test_case_18(self):
"""
Case 18:
Testing Reform which adding multiple new chroms
"""

wd = os.getcwd()
os.chdir('test_data/18/')

command = """
python3 ../../reform.py \
--new_chrom="Y,H,M" \
--in_fasta=in1.fa,in2.fa,in3.fa \
--in_gff=in1.gtf,in2.gtf,in3.gtf \
--ref_fasta=ref.fa \
--ref_gff=ref.gtf
"""

response = subprocess.getoutput(command)
print(response)

with open('gold.gtf', 'r') as f:
gold_gff = f.read()
with open('ref_reformed.gtf', 'r') as f:
new_gff = f.read()
print("Testing gtf")
self.assertListEqual(list(gold_gff), list(new_gff))
print("Done")

with open('gold.fa', 'r') as f:
gold_fa = f.read()
with open('ref_reformed.fa', 'r') as f:
new_fa = f.read()
print("Testing Fasta")
self.assertListEqual(list(gold_fa), list(new_fa))
print("Done")

os.chdir(wd)

def test_case_19(self):
"""
Case 19:
Testing Reform with incorrect new chrom and comments in input FASTA
and annotation files. Also, testing reform with more formal printing
"""

wd = os.getcwd()
os.chdir('test_data/19/')

command = """
python3 ../../reform.py \
--new_chrom="Y,H,M" \
--in_fasta=in1.fa,in2.fa,in3.fa \
--in_gff=in1.gtf,in2.gtf,in3.gtf \
--ref_fasta=ref.fa \
--ref_gff=ref.gtf
"""

response = subprocess.getoutput(command)
print(response)

with open('gold.gtf', 'r') as f:
gold_gff = f.read()
with open('ref_reformed.gtf', 'r') as f:
new_gff = f.read()
print("Testing gtf")
self.assertListEqual(list(gold_gff), list(new_gff))
print("Done")

with open('gold.fa', 'r') as f:
gold_fa = f.read()
with open('ref_reformed.fa', 'r') as f:
new_fa = f.read()
print("Testing Fasta")
self.assertListEqual(list(gold_fa), list(new_fa))
print("Done")

os.chdir(wd)

if __name__ == '__main__':
unittest.main()