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v0.2.0 #39

Merged
merged 120 commits into from
Jan 19, 2024
Merged

v0.2.0 #39

merged 120 commits into from
Jan 19, 2024

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SamBryce-Smith
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@SamBryce-Smith SamBryce-Smith commented Oct 14, 2022 •
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closes #38

14/10/22 - THIS IS UNFINISHED - DO NOT MERGE! Don't know why can't mark as a draft...

@SamBryce-Smith
filter_tx_by_cond - filters individual GTF files. Currently untested
b9847d4
@SamBryce-Smith
initial commit new script to extract candidate novel last exons
1e7a7a7
@SamBryce-Smith
get_novel_last_exons - _df_add not _df_annotate (script still untested
7d71ad0
@SamBryce-Smith
functions to id extension & spliced events (untested)
05ebdb3
@SamBryce-Smith
updates to get script working (internal seem to be missing?)
fe9d09c
@SamBryce-Smith
Fix logic of extract_format_exons_introns. Fix event type classificat…
ded0c43 
…ion (don't add region rank to novel obj)
@SamBryce-Smith
use read_gtf_restricted -saves ~30s reading in ref GTF vs full
e4cca72
@SamBryce-Smith
if tx has multiple event types assigned, collapse to ',' sep string
c5be51a
@SamBryce-Smith
output spliced last exons not last SJs
68f3490
@SamBryce-Smith
output spliced last exons not last SJs
07061a7
@SamBryce-Smith
Merge branch 'v0.2.0' of https://github.com/frattalab/PAPA into v0.2.0
2e32dcf
@SamBryce-Smith
skeleton of merge last exons script
ed72001
@SamBryce-Smith
working script to merge last_exon GTFs, assign sample & last_exon IDs
8736a82
@SamBryce-Smith
Script starts with last exons GTF, remove input match stats TSV. Repo…
cb416da 
…rt motif dist from 3'end. Select 3'end with min deviation from exptd position for motif only. Works at CL
@SamBryce-Smith
select repr atlas site. Update 3'end to nearest atlas. Output updated…
ae1dfd4 
…/selected les to gtf, summary stats are per last exon ID
@SamBryce-Smith
update function name for clarity of task
d9aa346
@SamBryce-Smith
fnc to read gtf with extraction of custom GTF attributes only
b45e56c
@SamBryce-Smith
initial commit get_quant_gtf - getting annoying read_gtf error. _fetc…
c30571f 
…h_attributes regex needs fixing (match space)
@SamBryce-Smith
update conda env
5511cda
@SamBryce-Smith
get le ids for ext & no ext genes. Internal extension unique regions …
2db9a9b 
…be weird...
@SamBryce-Smith
output GTFs and tx2le, le2gene dfs
141ade8
@SamBryce-Smith
fix regex in _fetch_attributes - extracts correctly if has suffixed cols
fbbba3e
@SamBryce-Smith
add command line args
d48cb86
@SamBryce-Smith
add option to not add last exon ID col
efde4eb
@SamBryce-Smith
fixes to filter_tx_by_condition_tpm.py
33461e0
@SamBryce-Smith
I give up
13a8f7e
@SamBryce-Smith
fix check_stranded to ensure outputs stranded gr
5a68f52
@SamBryce-Smith
list of conditions without duplicates
6559888
@SamBryce-Smith
fix check_per_sample_mean_tpm_filtered. Some log name corrections
c0d1a8f
@SamBryce-Smith
output 'not_found' string if no motifs founds - empty str attributes …
3c2e839 
…in GTF cause read error in future step (bug)
SamBryce-Smith and others added 28 commits January 17, 2023 18:08
@SamBryce-Smith
fix gene_id_ref collapsing in case of NaNs
215331c
@SamBryce-Smith
fix reporting count of events with ref_extension_string
8131ad8
@SamBryce-Smith
Add option to use input GTF of last exons to combine with ref GTF. Ex…
7ca5cc0 
…tra checks on boolean flags for pipeline specification. Successful dry run
@SamBryce-Smith
add script to combine & annotate predicted last exons from multiple e…
5005278 
…xperiments into a single gtf
@SamBryce-Smith
Add an explicit check for hyphen characters in sample_name IDs from s…
0c52d38 
…ample_tbl before declaring pipeline run
@SamBryce-Smith
document requirement for no hyphens in sample_name column of sample t…
b6281ea 
…able
@SamBryce-Smith
optionally pass bias/other cl flags to salmon quant
e17dd09
@SamBryce-Smith
dryrun - option to use precomputed salmon index and skip redundant co…
17effde 
…nstruction
@SamBryce-Smith
pass config file as command line arg
7bf8abf
@SamBryce-Smith
provide conda prefix as command line arg
a869bc8
@SamBryce-Smith
correct salmon index path in params if use precomputed index
10a4951
@SamBryce-Smith
example of saturn output
66a77e7
@SamBryce-Smith
Replace SatuRn with DEXSeq (#47)
aa03455 
* switch saturn for dexseq in differential_apa

* remove mentions to saturn and associated scripts

* add dexseq_apa to cluster.yaml
@SamBryce-Smith
Clean up README
ffaf622
@SamBryce-Smith
update readme
668bd2e
@SamBryce-Smith
update docs on quant & differential output files
c405030
@SamBryce-Smith
add note on specifying base condition in sample table
8d9fefd
@SamBryce-Smith
add docs on final combined novel GTF
ec4bd55
@SamBryce-Smith
add docs on combined GTFs
7463d20
@SamBryce-Smith
notes on ID mapping files. Remove redundancy for event_type descriptions
b0d7bcc
@SamBryce-Smith
remove sge profile (not working)
5ee4485
@SamBryce-Smith
minor updates to README
77a073d
@SamBryce-Smith
remove deprecated parameters
75cf329
@SamBryce-Smith
link to example files
41ef470
@SamBryce-Smith
remove empty md
0166248
@SamBryce-Smith
remove deprecated scripts
fc100f2
@SamBryce-Smith
add license information
2eb3976
@SamBryce-Smith
tiny formatting change
5e579e2
@SamBryce-Smith SamBryce-Smith merged commit 04a10a0 into master Jan 19, 2024
@SamBryce-Smith SamBryce-Smith deleted the v0.2.0 branch January 19, 2024 15:55
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[Meta] - v0.2.0
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