Some scripts for daily research in the Aquatic Plant Lab of CNBG.
Author: Linhe Sun
duncan.test.aqua.r and duncan.test.aqua.withoutrep.r are duncan test scripts for our lab.They can arrange ANOVA and Duncan test then draw barplots with error bar and significance. They depend two packages in R: agricolae and ggplot2.
Data sample: (Use '\t' as space)
Group Temp mmHg DO%L DO.mg/L C-uS/cm SAL.ppt pH ORP.mV TN(mg/L) NH4+(mg/L) NO2-(mg/L) NO3-(mg/L) TP(mg/L) Cu2+(ppb) Zn2+(ppb) Cd2+(ppb)
CK 29.6 748.2 3.4 0.26 498.4 0.22 9.02 58.6 6.08 0.54 0.081 1 0.138 356.20 666.2 1020.80
CK 29 748.2 3.1 0.24 482.7 0.21 8.98 62.2 6.36 0.52 0.057 0.1 0.134 302.20 572.6 1062.20
CK 29.2 748.4 2.9 0.22 489.6 0.22 8.89 70 5.24 0.8 0.051 0.1 0.141 387.00 725 1050.60
ZDQ 29.9 748.3 4.4 0.33 390.1 0.17 7.97 8.3 2.02 0 0.058 0 0.028 61.2 2.6669 25.559
ZDQ 29.8 748.3 4.2 0.31 428 0.19 7.86 94.8 4.47 0 0.157 0 0.088 464.2 3275.2 2150.2
ZDQ 29.1 748.3 3.2 0.24 437.4 0.19 8.47 102.4 7.42 1.11 0.092 1.3 0.092 435.4 2484.8 2245.4
ZSQ 29.8 748.3 4.3 0.32 429.8 0.19 8.13 43.4 6.80 0.23 0 1.2 0.092 340.8 1814.8 1870.4
ZSQ 29.1 748.2 3.5 0.26 377.7 0.17 8.39 94.4 2.41 0 0 0 0.028 70.8 206.4 278.8
ZSQ 29.2 748.3 3.2 0.24 425.1 0.19 8.56 92.1 7.15 0.95 0.134 0.8 0.092 375.6 1605.2 1775.2
YSQ 29.8 748.3 4.2 0.31 427.3 0.19 8.17 79.3 6.11 0.29 0.2 1.2 0.100 539.4 1877.4 1829.6
YSQ 29.3 748.3 4 0.3 425.3 0.19 8.09 99.9 4.87 0 0 0.1 0.088 358.2 2159.6 1880.6
YSQ 29.2 748.3 3.1 0.23 423.9 0.19 8.83 79.1 6.70 0.54 0.085 0.7 0.107 506.6 1404.8 1557.2
duncan.test.aqua.r will read multiple data files. But the each files should have the same tests.
duncan.test.aqua.withoutrep.r will read only one data file. You need to give a name for the plot.
Use transcripts like this:
Rscripts duncan.test.aqua.r data1.txt data2.txt ...
Rscripts duncan.test.aqua.withoutrep.r data1.txt data1.pdf
get_func_in_gtf is a python script for you to get all the gene ids and their locs and functions from the lotus gtf fileGCF_000365185.1_Chinese_Lotus_1.1_genomic.gtf.
python get_func_in_gtf <GCF_000365185.1_Chinese_Lotus_1.1_genomic.gtf> <output_file_name>
It's output file format is:
LOC104600515 NW_010729074.1 144306 147149 receptor protein kinase-like protein ZAR1
LOC104594717 NW_010729074.1 1090747 1178857 uncharacterized LOC104594717, transcript variant X4
LOC104603444 NW_010729074.1 3471500 3476022 aldose 1-epimerase-like
LOC104607325 NW_010729074.1 4470407 4471690 probable calcium-binding protein CML25
LOC104608648 NW_010729074.1 4717595 4720129 putative pentatricopeptide repeat-containing protein At1g09680
LOC104594711 NW_010729074.1 5222130 5226266 MDIS1-interacting receptor like kinase 2-like
TRNAD-GUC_2 NW_010729074.1 8604646 8604717 tRNA-Asp
LOC104592301 NW_010729074.1 9471781 9475961 pentatricopeptide repeat-containing protein At1g60770-like
LOC104593369 NW_010729074.1 12171307 12184718 two-component response regulator-like PRR95
readfa.py is a script read fasta file and it can extract the sequence with index and range.
python readfa.py -d <database> -i <index> -f <startnum> -t <endnum> -o <outputfile> -l <indexlistoutput>
-d & --data Data file in fasta format.
-i & --index The index of the sequence you want to extract. If you do not know, you can get the index list with -l & --list.
-f and -t The range of the sequence you want to extract. -f must be less than -t. If you ignore this two parameter you will get the full length.
-o & --out The output file name. If you ignaore this parameter. The seq you want will be printed on the screen.
-l & --list If you want a list of the index of your fasta file, please add this parameter with a filename followed.
-h & --help Show this information.
For multiple sequences extraction. You can use the script get_gene_seq.py.It depends readfa.py.
First you shoud prepare a sort file with format like this:
<seqname> <index> <from> <to>
LOC104600243 NW_010729075.1 9052416 9058589
LOC104606401 NW_010729076.1 5694797 5697430
Then use the scripts: python ger_gene_seq.py <fasta file name> <sort file name>