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TODO
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TODO
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#1. integrate gb2fasta
#2. integrate batch_query
#3. integrate uniq
#4. integrate remove-long
#5. use Shannon Index
#6. pick primer pair
#7. too few primer found!!!!!!!!!!!!!
#8. some primers do not have info (test2,156989)
#9. 30min for a cp genome, too slow
#10. try to replace Bio.SearchIO (10 second+, 50% of runtime)
#11. +1 or not
#12. use tree_value or not, mafft seems give 1.0 always
#13. too slow for chloroplast genome, 10 samples, 6 hours
#14. difflib
#15. log
#16. give fragment name by gb file
#17. use time.test2 to profile
#18. too much primer candidate
#19. update_id for Pair
#20. Fabaceae got zero primer, does length have to larger than 0?
#21. use fragments to test
22. 3' 3-5 base must match
23. GC content
24. delta G
#25. integrate mafft
#26. matK.aln use 89 seconds, need profiling (now 7s)
#27. clean output file
#28. print hint
#29. reorder functions
#30. package
#31. update to pip
#32. requirement
#33. readme
#34. figure title as gene name
#35. rps12
#36. output path
#37. utf-8
#38. use namedtuple
39. BiopythonParserWarning: Expected sequence length 491, found 1083 (U58558.1).
#40. add animal order
#41. use avg to calc tm
#42. stop 1 for divide, 2 for analyze, 3 for primer design
#43. TypeError: unique() got an unexpected keyword argument 'axis'
#44. time usage, memory usage
45. >CBS|Primates|Hominidae|Homo|sapiens|X87816|
#46. primer3-py is hard to install
#47. merge primers result
#48. test aln output path
#49. windows blast, macos
#50. test large data
#51. test quick example
#52. check memory usage of pick_pair
#53. no_gap.fasta should not be put on current workdir
#54. Pair's init seems slow
55. score #and sample number
#56. genaf for genome?
#57. trnK_matK?(get_spacer())
#58. do not check dependency if stop 1
#59. use set to speedup order_exceptions
#60. figure axis
#61. test install
#62. iqtree to IQ-TREE
63. max_hsp, filter
#64. data missing at head/tail
65. blast score/penalty
#66. use requests instead of biopython to solve timeout
#67. add note for fake class/kingdom
#68. rewrite uniq
#69. fix no_divide
70. NC_ repeat with other accession
#71. plastid or chloroplast
#72. expand 0 if stop 1
#73. intron
#74. gene CDS tRNA rRNA spacer
75. upstream/downstream gene
76. No. of gene
#77. isotype or specimen
78. strand
#79. consider to use primer3 rather than primer3-py
#80. A_B or B_A
#81. use pathlib
#82. readme for gb.plus, spacer options
#83. expand create new feature instead of change old
#84. repeat option apply on gene
#85. repeat rrna
#86. indent for log
#87. intron for trna and rrna that missed in gene
#88. exist intron may me repeat
#89. primer3-py 0.5.7 for python3.6: macosx windows /python3.7:macosx
#90. docker or exe
#91. GUI
92. all DNASP method
93. option for gap, another kind of base/ignore/penalty
94. simple or full lineage
#95. few dependency
96. remove short seq
97. recognize weird seq
98. simple readme
99. readme for chinese
100. genaf for spacer
101. gooey is too big, use tkinter?
#102. lineage exception sperated from source code (use pkg_resource?)
#103. remove temp log
#104. filter length
105. filter sequences with too much gap
106. conda
107. clean comment
#108. type.name.fasta
#109. remove tmp files
110. intron_intronIndex
111. user-defined id format string
112, rename trn, gene name list
#113. shannon index may be negative
#114. digit 4
115. gap in head and tail
116. better uniq
#117. x axis of figure
118. analyse distribution of data on Genbank
#119. write name.type.fasta?
#120. remove by-name
121. AH009860 have clear annotation of every part in ITS, but MN528716 only use "contains ITS, 5.8s, etc"
122. HC476670 have CDS but not gene
123. check genbank file to remove empty record is too slow, how to directly exclude them when querying in Genbank
#124. option for long/short sequence id
#125. integrate rename
#126. regular expression for rename gene is not good
127. Z00028 has bad annotation of introns
128. check genbank file is too slow
129. cannot extract X68919,X68889,X68921
#130. ITS too much is Unknown
#131. spacer misc_feature, intergenic_spacer_region/intergenic_spacer
#132. split to 3 modules
#133. trnH-psbA or psbA-trnH
#134. copy user's input to output folder to make working folder clean
135. filename may be duplicate in Windows
136. abnormal length in divide_gene
137. continue to download if break
#138. skip tree in Pair if arg.fast
#139. remove clean_path
#140. remove Temp.log
141. clean empty fasta record
142. trnfM, trnM, trnF
143. test init in linux and mac
144. atpB-rbcL and rbcL-atpB
145. tRNA His (GUG)
146. annotation across tail and head will be misextracted
# 147. add web interface
# 148. ImportError: cannot import name 'Iterable' from 'collections'
# 2022.4.14
# 149. remove primer3-py or restrict python version in windows
150. Invalid alignment file E:\Linux\barcodefinder\Result\Alignment\CDS-atpB-consensus.fastq
# 151. blastn/makeblastdb only requires nghttp2.dll, consider to rewrite get_software
152. compared with phylosuite https://blog.csdn.net/qazplm12_3/article/details/129434310