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Issue27 fix#28

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AlaaALatif wants to merge 144 commits into
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issue27_fix
Open

Issue27 fix#28
AlaaALatif wants to merge 144 commits into
masterfrom
issue27_fix

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@AlaaALatif

@AlaaALatif AlaaALatif commented Aug 1, 2021 •
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Fixes #27
Implement a corrected and more intuitive way of numbering deletion mutations, which allows us to:

  1. fix the simplified deletion names displayed on outbreak.info after changes made in PR #24 (fixes issue #411 on outbreak)
  2. facilitate a more intuitive way of generating complete deletion names e.g. ORF1a:DEL3675.1/3677.3 represents a 9-nucleotide deletion in the ORF1a gene that starts at the 1st nucleotide of codon 3675 and ends at the 3rd nucleotide of codon 3677. Similarly, S:DEL68.2/70.1 represents a 6-nucleotide deletion in the S gene that starts at the 2nd nucleotide of codon 68 and ends at the 1st nucleotide of codon 70.

@AlaaALatif
script for downloading GISAID API feed, generating fasta file and pro…
832fc8d 
…cessed metadata
@AlaaALatif
separate env for api data processing, due to issues installing geopan…
caa3064 
…das in the original env
@AlaaALatif
fix strain processing in metadata, require username as input arg
bfa480b
@AlaaALatif
modify aggregate_replacements() and aggregate_deletions() to avoid pa…
9c3d6d0 
…ndas copy warnings
@AlaaALatif
always add ref seq to input fasta to avoid downstream failures, teste…
713703e 
…d with new GISAID API data
@AlaaALatif
fix aggregate funcs to convert date to str to prevent NaN issues
a61afa2
@AlaaALatif
minor formatting fixes
d7b2a70
@AlaaALatif
dev nb, transfer to local machine
a91940d
@AlaaALatif
generate lowercased versions of location info
2a0df49
@AlaaALatif
handle exceptions with mutation aggregation
75a1bdf
@AlaaALatif
fix mutation aggregation funcs
fd5365a
@AlaaALatif
fix field names of normalized locations
d085e0a
@AlaaALatif
migrate to local machine
7fe5cdf
@AlaaALatif
fix bjorn.py to adapt to breaking changes made for outbreak, allowing…
29ca63c 
… it to be used for internal sequence submissions
@AlaaALatif
updated script to tabulate mutations seen in A-lab sequences, excludi…
09e0605 
…ng insertions :(
@AlaaALatif
bash scripts used for sequencing and submission pipelines
1d0bb65
@AlaaALatif
not now...
6bea875
@AlaaALatif
added batch_iterator() function for chunking big fasta files into sma…
b8bd0fe 
…ller ones
@AlaaALatif
script for splitting input fasta into smaller chunks with a user-spec…
5da440b 
…ified maximum number of sequences in each
@AlaaALatif
baseline rules, still need to add chunk_fasta rule and run tests
82aa1c3
@AlaaALatif
tested successfully, takes ~5mins to split file containing ~600K seqs…
30fea4b 
… into 60 files
@AlaaALatif
move current codebase to separate module
65f5b68
@AlaaALatif
tested successfully, still need to add API pull (rule_0) and gcloud u…
100eaaf 
…pload (rule_n)
@AlaaALatif
initial readme for pipeline
f486717
@AlaaALatif
replace hard-coded numbers with dynamic ones, which was used for rapi…
09cb203 
…d testing
@AlaaALatif
fixed chunk_fasta to use single core only, fixed msa_2_mutations to a…
fa171cd 
…void error due to NaN dates
@AlaaALatif
python scripts for pulling API data and merging final results
8dcafcf
@AlaaALatif
added rule_0 and rule_n for pulling API data and generating json for …
9a83c7c 
…upload, still need to test on outbreak.info
@AlaaALatif
changed json2fasta to function def to run inline within pipeline (fas…
0bc1894 
…ter)
@AlaaALatif
add minimap2 to the env, which was the source of most cron errors...
1321ada
AlaaALatif and others added 25 commits May 5, 2021 12:54
@AlaaALatif
code cleanup, removing old commented statements
2ee4941
@flaneuse
Create LICENSE
24629b5
@gkarthik
Pass config file as parameter to scripts
2a47468
@gkarthik
Accept config file. Dynamically accept region split
2f01a29
@gkarthik
Accept config file
1cbac8a
@gkarthik
Set config file
e02697a
@gkarthik
Reset current_datetime
e376bd7
@gkarthik
Restructured to only operate on chunk
ee3b8f6
@gkarthik
Change extenson to tsv
843fb5e
@gkarthik
Check for number of columns
5a4ab5d
@gkarthik
Removed tariling spaces
96eab6e
@gkarthik
Remove config and decouple upload to google cloud
5159555
@gkarthik
Restructured entirely to only process in chunks.
391bc34
@gkarthik
Added datetime back
63f6d06
@gkarthik
Added temp to remove temporary files
11453d0
@gkarthik
Removed print
58f0500
@gkarthik
Added upload script
a925609
@mindoftea
decouple config from msa2mutations
c84860c
@mindoftea
snakefile refactor
7be7d05
@mindoftea
cleanup and usage
633edd8
@gkarthik
Merge pull request #18 from andersen-lab/emory-cleanup
3625a92 
Maintenance I
@AlaaALatif
Issues 21 + 22 fix (#24)
08f2620 
* import GENE2POS directly from data.py, allows for easy exploratorive work in notebooks

* import GENE2POS correctly

* fixes #22, computing point mutations resultant from out-of-frame deletions

* fix indent in line 415

* add docstring to identifying out-of-frame substitutions

* fixes #21

* lab notebook for solving issues 22 and 21, regarding point mutations resultant from out-of-frame deletions

* update deletion naming convention based on corrected numbering system

* add comments

* more docstrings

* import submodules so they can be used in notebooks

* clean up and update
@AlaaALatif
implement improved numbering system for deletions, in order to fix si…
b4598cb 
…mplified deletion naming
@AlaaALatif
implement improved numbering system for deletions, in order to fix si…
fb8cf6f 
…mplified deletion naming
@AlaaALatif
indicate which functions are depracated in docstrings
565c683
@AlaaALatif
AlaaALatif requested review from flaneuse and gkarthik August 1, 2021 17:08
@gkarthik gkarthik mentioned this pull request Aug 4, 2021
Open
@gkarthik
gkarthik force-pushed the master branch 2 times, most recently from af33f06 to 2cb3655 Compare October 18, 2021 21:30
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@flaneuse flaneuse Awaiting requested review from flaneuse
@gkarthik gkarthik Awaiting requested review from gkarthik

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Characteristic mutations display "ORF1a" wrongly Implement corrected Deletion naming after PR #24

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@AlaaALatif @corneliusroemer @gkarthik @flaneuse @mindoftea