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change-log.txt
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change-log.txt
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0.4.4 -- July 24, 2015
Updated:
- fragsummary:
--> reports on molecules >50kb and >100kb now (in addition to >10kb)
--> some print out variables needed to be fixed
- g4/regex
--> g4/regex call on a lot of the same code. some updates to g4 broke the more general usage of regex. now fixed.
Other notes:
- since last version updates to fragstats, fragsummary, info, and main were made
- a license was added
- a citation was added to be used when citing poreminion
0.4.3 -- May 5, 2015
Updated:
- g4: now can count number of g-tracts inside identified g4 motif
0.4.2 -- April 28, 2015
Added subcommand:
- seqlen: print seqname,seqlen for chosen read types in set of fast5 files.
0.4.1 -- April 27, 2015
Added subcommands:
- staypos: BED file type output of where stays (move = 0) are in template and complement sequences (by mapping moves to appropriate sequence index)
Updated:
- some of the under-the-hood: e.g. a lot of functions moved to info.py from other files to help avoid import conflicts
0.4.0
Added subcommands:
- regex: look for regular expressions in minION reads
- g4: look for g4 motifs in minION reads
Updated:
- fragstats now allows collection of g4 counts in rast5 read types
0.3.2
- fragsummary
- performs more summarizing now (more to come)
0.3.1
Added:
- fragsummary -- summarizes a fragstats table file -- lots of useful info. 0.3.2 will have even more info from fragstats summarized.
- fragrobust -- robust calculation -- caution: this is somewhat useless (see message that comes with it) and may be removed in next bump.
- info -- gathers a bunch of info from a given fast5 file
Updated:
- fragstats
--> has2d and hascomp fields are now 1 and 0 instead of "True" and "False"
--> no longer computes "robustness" as this metric is somewhat useless. For now, I kept it as its own subcommand "fragrobust". Be sure to see the message there.
--> computes a bunch of new stuff even in non-extensive mode that do not much affect the speed (columns and metrics below):
--> 15 = channel number molecule traversed
--> 16 = heat sink temperature while molecule traversed
--> 17 = num called template events (after events pruned during base-calling)
--> 18 = num called complement events (after events pruned during base-calling)
--> 19 = num skips in template
--> 20 = num skips in complement
--> 21 = num stays in template
--> 22 = num stays in complement
--> 23 = strand score template
--> 24 = strand score complement
--> 25 = num stutters in template
--> 26 = num stutters in complement
What I know is coming in 0.3.2:
- fragsummary will be more fully fleshed out, summarizing pieces of fragstats tables that the current version does not do yet
0.3.0
More subtools added such as:
- nx (example use: calculate n50 on file column)
- events (example use: print events from a fast5)
- has2D (example use: get True/False 2D info on each file in set of basecalled fast5 files in 2 column output)
- timetest (example use: after filtering base-called files for those that weren't base-called, further filter for files with the known time error (rare and will soon be fixed).)
Updated:
- frastats
--> has an extensive option that gives much more info, but takes longer
--> has a timetest option
Unfinished subtools (that appeared by name only in previous versions although they did not do anything) have been removed (at least for now).
What I know is upcoming in 0.3.1
- update dataconc to be faster -- no need for pandas
- summarizing fragstats files
- plotting fragstats files
0.2.0
More subtools added such as:
qualdist,winner,pct2d,uncalled
-- winner is from poretools, but I enabled a type called "each" to give winners for each read type and an option called --details to only give lengths, not sequence.
-- pct2d goes through all reads in a dir and returns % that have 2D sequences
-- uncalled goes through a dir, finds files that are not base-called and either reports them or moves them to a different dir
Warning: I only work on poreminion every once in a while and some tools are un-finished and/or broken.
Current tools I know to work are:
- data_conc
- qualpos
- qualdist
- kmer
- kmerplot
- kmerdiff
- winner
- pct2d
- uncalled
- numevents
The 'align' subtool is something I tooled with, which was just going to be a wrapper over various aligners. I believe it is not in working order.
Others such as events_stats, get_events, get_model, get_metadata are also un-finished. I have similar functions in another suite that I will make available soon.