Skip to content
GitLab
Menu
Projects
Groups
Snippets
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in
Toggle navigation
Menu
Open sidebar
Blaise LI
bioinfo_utils
Commits
7a5d7c85
Commit
7a5d7c85
authored
Jan 22, 2020
by
Blaise Li
Browse files
Update mCherry transgene.
parent
822f1a47
Changes
1
Hide whitespace changes
Inline
Side-by-side
make_mCherry_transgene.py
View file @
7a5d7c85
...
...
@@ -10,11 +10,59 @@ from mappy import fastx_read
from
fs.osfs
import
OSFS
as
FS
#from fs.tempfs import TempFS as FS
# Older version
#fasta_transgene = """\
#>mex5_promoter
#ATATCAGTTTTTAAAAAATTAAACCATAAAACAAATAATATAACCCAATTTTTACATCAAACCACAAGAAAAAAATACATTTGGGCCCACGGATAAAGAAATTAAAAAAATACATTTTTTAAAGGCGCACCGAATTAAAATTCATTTGGGTCTTACCGCGTATACCGTACTCCGTTTGTTTGATCATTTTTGTCAGCGCTGGCGGTTGTTTTTTCATTTCATTTCTGCTTCAAAGACGTTTTCTCGAATAATTTTTCGTTTATTCTCTTTTTTAAAATTAATTTCTAGCCGTAAATGTTATAAATTCACCCATTTAACGCAAATTTCATGGTAATCTCATGGAAAAATGCAGTTTCTTTGTTAAAGAAAGCTTAAATAGCAAAAATTCCCCGACTTTCCCCAAAATCCTGCTCGATTTTCCGTTTTCTCATTGTATTCTCTCTTAATTAATTTTATCGATAATCAATTGAATGTTTCAGACAGAGA
#>exon_1
#ATGGTCTCAAAGGGTGAAGAAGATAACATGGCAATTATTAAAGAGTTTATGCGTTTCAAGGTGCATATGGAGGGATCTGTCAATGGGCATGAGTTTGAAATTGAAGGTGAAGGAGAAGGCCGACCATATGAGGGAACACAAACCGCAAAACTAAAG
#>intron_1
#GTAAGTTTAAACATATATATACTAACTAACCCTGATTATTTAAATTTTCAG
#>exon_2
#GTAACTAAAGGCGGACCATTACCATTCGCCTGGGACATCCTCTCTCCACAGTTCATGTATGGAAGTAAAGCTTATGTTAAACATCCGGCAGATATACCAGATTATTTGAAACTTTCATTCCCGGAGGGTTTTAAGTGGGAACGCGTAATGAATTTTGAAGACGGAGGAGTTGTTACAGTGACGCAAGACTCAAG
#>intron_2
#GTAAGTTTAAACAGTTCGGTACTAACTAACCATACATATTTAAATTTTCAG
#>exon_3
#CCTCCAAGATGGAGAATTTATTTATAAAGTCAAACTTCGAGGAACGAATTTCCCCTCGGATGGACCTGTTATGCAGAAGAAGACTATGGGATGGGAAGCTTCAAGTGAAAGAATGTACCCTGAAGACGGTGCTCTTAAGGGAGAGATTAAACAACGTCTTAAATTGAAAGATGGAGGACATTACGATGCTGAG
#>intron_3
#GTAAGTTTAAACATGATTTTACTAACTAACTAATCTGATTTAAATTTTCAG
#>exon_4
#GTGAAGACAACTTACAAAGCCAAAAAACCAGTTCAGCTGCCAGGAGCGTACAATGTTAATATTAAACTGGATATCACCTCCCACAACGAGGATTACACTATCGTTGAGCAATATGAAAGAGCTGAAGGGCGGCACTCGACAGGTGGCATGGATGAATTGTATAAGG
#>his11
#ATGCCACCAAAGCCATCTGCCAAGGGAGCCAAGAAGGCCGCCAAGACCGTTACGAAGCCAAAGGACGGAAAGAAGAGACGTCATGCCCGTAAGGAATCATACTCCGTCTACATCTACCGTGTCCTCAAGCAAGTTCATCCAGACACTGGAGTTTCCTCCAAAGCCATGTCTATCATGAACTCTTTTGTCAACGATGTCTTCGAGCGTATTGCTGCTGAAGCATCCCGTCTTGCTCACTACAACAAGCGTTCCACAATCTCATCCCGCGAAATTCAGACCGCTGTCCGTCTGATCCTTCCAGGAGAGCTTGCCAAGCACGCCGTGTCTGAGGGAACCAAGGCCGTTACCAAGTACACTTCCAGCAAGTAA
#>tbb2_3UTR
#ATGCAAAATCCTTTCAAGCATTCCCTTCTTCTCTATCACTCTTCTTTCTTTTTGTCAAAAAATTCTCTCGCTAATTTATTTGCTTTTTTAATGTTATTATTTTATGACTTTTTATAGTCACTGAAAAGTTTGCATCTGAGTGAAGTGAATGCTATCAAAATGTGATTCTGTCTGATGTACTTTCACAATCTCTCTTCAATTCCATTTTGAAGTGCTTTAAACCCGAAAGGTTGAGAAAAATGCGAGCGCTCAAATATTTGTATTGTGTTCGTTGAGTGACCCAACAAAAAGAGGAAACTTTATTGTGCCGCCAAGAAAAAAGTC
#"""
# New version (19/12/2019)
fasta_transgene_caps
=
"""
\
>mex5_promoter
atctgcaagaaaatacattttcgactgattttacggttttcacaacggcaaaatatcagtttttaaaaaattaaaccataaaacaaataatataacccaatttttacatcaaaccacaagaaaaaaatacatttgggcccacggataaagaaattaaaaaaatacattttttaaaggcgcaccgaattaaaattcatttgggtcttaccgcgtataccgtactccgtttgtttgatcatttttgtcagcgctggcggttgttttttcatttcatttctgcttcaaagacgttttctcgaataatttttcgtttattctcttttttaaaattaatttctagccgtaaatgttataaattcacccatttaacgcaaatttcatggtaatctcatggaaaaatgcagtttctttgttaaagaaagcttaaatagcaaaaattccccgactttccccaaaatcctgctcgattttccgttttctcattgtattctctcttaattaattttatcgataatcaattgaatgtttcagacagaga
>exon_1
atgGGAGGTAGGGCCGGCTCTGTCTCAAAGGGTGAAGAAGATAACATGGCAATTATTAAAGAGTTTATGCGTTTCAAGGTGCATATGGAGGGATCTGTCAATGGGCATGAGTTTGAAATTGAAGGTGAAGGAGAAGGCCGACCATATGAGGGAACACAAACCGCAAAACTAAAG
>intron_1
GTAAGTTTAAACATATATATACTAACTAACCCTGATTATTTAAATTTTCAG
>exon_2
GTAACTAAAGGCGGACCATTACCATTCGCCTGGGACATCCTCTCTCCACAGTTCATGTATGGAAGTAAAGCTTATGTTAAACATCCGGCAGATATACCAGATTATTTGAAACTTTCATTCCCGGAGGGTTTTAAGTGGGAACGCGTAATGAATTTTGAAGACGGAGGAGTTGTTACAGTGACGCAAGACTCAAG
>intron_2
GTAAGTTTAAACAGTTCGGTACTAACTAACCATACATATTTAAATTTTCAG
>exon_3
CCTCCAAGATGGAGAATTTATTTATAAAGTCAAACTTCGAGGAACGAATTTCCCCTCGGATGGACCTGTTATGCAGAAGAAGACTATGGGATGGGAAGCTTCAAGTGAAAGAATGTACCCTGAAGACGGTGCTCTTAAGGGAGAGATTAAACAACGTCTTAAATTGAAAGATGGAGGACATTACGATGCTGAG
>intron_3
GTAAGTTTAAACATGATTTTACTAACTAACTAATCTGATTTAAATTTTCAG
>exon_4
GTGAAGACAACTTACAAAGCCAAAAAACCAGTTCAGCTGCCAGGAGCGTACAATGTTAATATTAAACTGGATATCACCTCCCACAACGAGGATTACACTATCGTTGAGCAATATGAAAGAGCTGAAGGGCGGCACTCGACAGGTGGCATGGATGAATTGTATAAGGGAGGAGGAGGAGGTGGA
>his11
ATGCCACCAAAGCCATCTGCCAAGGGAGCCAAGAAGGCCGCCAAGACCGTTACGAAGCCAAAGGACGGAAAGAAGAGACGTCATGCCCGTAAGGAATCATACTCCGTCTACATCTACCGTGTCCTCAAGCAAGTTCATCCAGACACTGGAGTTTCCTCCAAAGCCATGTCTATCATGAACTCTTTTGTCAACGATGTCTTCGAGCGTATTGCTGCTGAAGCATCCCGTCTTGCTCACTACAACAAGCGTTCCACAATCTCATCCCGCGAAATTCAGACCGCTGTCCGTCTGATCCTTCCAGGAGAGCTTGCCAAGCACGCCGTGTCTGAGGGAACCAAGGCCGTTACCAAGTACACTTCCAGCAAGTAA
>tbb2_3UTR
atgcaagatcctttcaagcattcccttcttctctatcactcttctttctttttgtcaaaaaattctctcgctaatttatttgcttttttaatgttattattttatgactttttatagtcactgaaaagtttgcatctgagtgaagtgaatgctatcaaaatgtgattctgtctgatgtactttcacaatctctcttcaattccattttgaagtgctttaaacccgaaaggttgagaaaaatgcgagcgctcaaatatttgtattgtgttcgttgagtgacccaacaaaaagaggaaa
"""
fasta_transgene
=
"""
\
>mex5_promoter
ATATCAGTTTTTAAAAAATTAAACCATAAAACAAATAATATAACCCAATTTTTACATCAAACCACAAGAAAAAAATACATTTGGGCCCACGGATAAAGAAATTAAAAAAATACATTTTTTAAAGGCGCACCGAATTAAAATTCATTTGGGTCTTACCGCGTATACCGTACTCCGTTTGTTTGATCATTTTTGTCAGCGCTGGCGGTTGTTTTTTCATTTCATTTCTGCTTCAAAGACGTTTTCTCGAATAATTTTTCGTTTATTCTCTTTTTTAAAATTAATTTCTAGCCGTAAATGTTATAAATTCACCCATTTAACGCAAATTTCATGGTAATCTCATGGAAAAATGCAGTTTCTTTGTTAAAGAAAGCTTAAATAGCAAAAATTCCCCGACTTTCCCCAAAATCCTGCTCGATTTTCCGTTTTCTCATTGTATTCTCTCTTAATTAATTTTATCGATAATCAATTGAATGTTTCAGACAGAGA
ATCTGCAAGAAAATACATTTTCGACTGATTTTACGGTTTTCACAACGGCAAA
ATATCAGTTTTTAAAAAATTAAACCATAAAACAAATAATATAACCCAATTTTTACATCAAACCACAAGAAAAAAATACATTTGGGCCCACGGATAAAGAAATTAAAAAAATACATTTTTTAAAGGCGCACCGAATTAAAATTCATTTGGGTCTTACCGCGTATACCGTACTCCGTTTGTTTGATCATTTTTGTCAGCGCTGGCGGTTGTTTTTTCATTTCATTTCTGCTTCAAAGACGTTTTCTCGAATAATTTTTCGTTTATTCTCTTTTTTAAAATTAATTTCTAGCCGTAAATGTTATAAATTCACCCATTTAACGCAAATTTCATGGTAATCTCATGGAAAAATGCAGTTTCTTTGTTAAAGAAAGCTTAAATAGCAAAAATTCCCCGACTTTCCCCAAAATCCTGCTCGATTTTCCGTTTTCTCATTGTATTCTCTCTTAATTAATTTTATCGATAATCAATTGAATGTTTCAGACAGAGA
>exon_1
ATGGTCTCAAAGGGTGAAGAAGATAACATGGCAATTATTAAAGAGTTTATGCGTTTCAAGGTGCATATGGAGGGATCTGTCAATGGGCATGAGTTTGAAATTGAAGGTGAAGGAGAAGGCCGACCATATGAGGGAACACAAACCGCAAAACTAAAG
ATGG
GAGGTAGGGCCGGCTCTG
TCTCAAAGGGTGAAGAAGATAACATGGCAATTATTAAAGAGTTTATGCGTTTCAAGGTGCATATGGAGGGATCTGTCAATGGGCATGAGTTTGAAATTGAAGGTGAAGGAGAAGGCCGACCATATGAGGGAACACAAACCGCAAAACTAAAG
>intron_1
GTAAGTTTAAACATATATATACTAACTAACCCTGATTATTTAAATTTTCAG
>exon_2
...
...
@@ -26,11 +74,11 @@ CCTCCAAGATGGAGAATTTATTTATAAAGTCAAACTTCGAGGAACGAATTTCCCCTCGGATGGACCTGTTATGCAGAAGA
>intron_3
GTAAGTTTAAACATGATTTTACTAACTAACTAATCTGATTTAAATTTTCAG
>exon_4
GTGAAGACAACTTACAAAGCCAAAAAACCAGTTCAGCTGCCAGGAGCGTACAATGTTAATATTAAACTGGATATCACCTCCCACAACGAGGATTACACTATCGTTGAGCAATATGAAAGAGCTGAAGGGCGGCACTCGACAGGTGGCATGGATGAATTGTATAAGG
GTGAAGACAACTTACAAAGCCAAAAAACCAGTTCAGCTGCCAGGAGCGTACAATGTTAATATTAAACTGGATATCACCTCCCACAACGAGGATTACACTATCGTTGAGCAATATGAAAGAGCTGAAGGGCGGCACTCGACAGGTGGCATGGATGAATTGTATAAGG
GAGGAGGAGGAGGTGGA
>his11
ATGCCACCAAAGCCATCTGCCAAGGGAGCCAAGAAGGCCGCCAAGACCGTTACGAAGCCAAAGGACGGAAAGAAGAGACGTCATGCCCGTAAGGAATCATACTCCGTCTACATCTACCGTGTCCTCAAGCAAGTTCATCCAGACACTGGAGTTTCCTCCAAAGCCATGTCTATCATGAACTCTTTTGTCAACGATGTCTTCGAGCGTATTGCTGCTGAAGCATCCCGTCTTGCTCACTACAACAAGCGTTCCACAATCTCATCCCGCGAAATTCAGACCGCTGTCCGTCTGATCCTTCCAGGAGAGCTTGCCAAGCACGCCGTGTCTGAGGGAACCAAGGCCGTTACCAAGTACACTTCCAGCAAGTAA
>tbb2_3UTR
ATGCAA
A
ATCCTTTCAAGCATTCCCTTCTTCTCTATCACTCTTCTTTCTTTTTGTCAAAAAATTCTCTCGCTAATTTATTTGCTTTTTTAATGTTATTATTTTATGACTTTTTATAGTCACTGAAAAGTTTGCATCTGAGTGAAGTGAATGCTATCAAAATGTGATTCTGTCTGATGTACTTTCACAATCTCTCTTCAATTCCATTTTGAAGTGCTTTAAACCCGAAAGGTTGAGAAAAATGCGAGCGCTCAAATATTTGTATTGTGTTCGTTGAGTGACCCAACAAAAAGAGGAAA
CTTTATTGTGCCGCCAAGAAAAAAGTC
ATGCAA
G
ATCCTTTCAAGCATTCCCTTCTTCTCTATCACTCTTCTTTCTTTTTGTCAAAAAATTCTCTCGCTAATTTATTTGCTTTTTTAATGTTATTATTTTATGACTTTTTATAGTCACTGAAAAGTTTGCATCTGAGTGAAGTGAATGCTATCAAAATGTGATTCTGTCTGATGTACTTTCACAATCTCTCTTCAATTCCATTTTGAAGTGCTTTAAACCCGAAAGGTTGAGAAAAATGCGAGCGCTCAAATATTTGTATTGTGTTCGTTGAGTGACCCAACAAAAAGAGGAAA
"""
mCherry_transcript_parts
=
[
"exon_1"
,
"intron_1"
,
"exon_2"
,
"intron_2"
,
"exon_3"
,
"intron_3"
,
"exon_4"
]
...
...
Write
Preview
Markdown
is supported
0%
Try again
or
attach a new file
.
Attach a file
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Cancel
Please
register
or
sign in
to comment