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Merged
mohammedkhalfan merged 13 commits into from
May 24, 2025
Merged

Printing&logic improve #38

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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
ad7d6a4
Improve printing in Reform and Test
YuWei-CH May 9, 2025
6a27a58
Addauto correction for wrong input GTF/GFF length
YuWei-CH May 9, 2025
f0aa0c0
Remove Mismatch WARNING in editing existed sequence
YuWei-CH May 9, 2025
9ee72e3
Improved logging
mohammedkhalfan May 24, 2025
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622 changes: 438 additions & 184 deletions reform.py
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4 changes: 4 additions & 0 deletions test_data/17/gold.fa
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>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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>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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>X
ZZZZABBBBBDDDDDCCCCCIIIIIKKKKK
4 changes: 4 additions & 0 deletions test_data/18/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/19/gold.fa
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@@ -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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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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>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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>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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>X
ZZZZABBBBBDDDDDCCCCCIIIIIKKKKK
4 changes: 4 additions & 0 deletions test_data/19/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";
4 changes: 4 additions & 0 deletions test_data/20/gold.fa
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>X
XZZZABBBBBDDDDDCCCCCIIIIIKKKKK
>Y
----------
5 changes: 5 additions & 0 deletions test_data/20/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 new exon 1 10 . + 0 gene_id "new"; transcript_id "new.1";
2 changes: 2 additions & 0 deletions test_data/20/in.fa
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>test 1
----------
1 change: 1 addition & 0 deletions test_data/20/in.gtf
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X new exon 1 3 . + 0 gene_id "new"; transcript_id "new.1";
2 changes: 2 additions & 0 deletions test_data/20/ref.fa
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>X
XZZZABBBBBDDDDDCCCCCIIIIIKKKKK
4 changes: 4 additions & 0 deletions test_data/20/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";
14 changes: 14 additions & 0 deletions test_order_explanation.py
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import unittest

class TestOrderExample(unittest.TestCase):
def test_z_third(self):
print("This runs third despite being defined first")

def test_a_first(self):
print("This runs first despite being defined second")

def test_b_second(self):
print("This runs second despite being defined third")

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