User: erick_rc93

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erick_rc9310
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Posts by erick_rc93

<prev • 11 results • page 1 of 2 • next >
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Parsing gbk file
... I have multiples genbak (.gbk) files, and each file is a concatenated file with multiple chromosomes and plasmids and I would like to split in single files, I'm trying with the next code in awk awk -v n=1 '/^\/\//{close("out"n);n++;next} {print > "out"n}' filename.gbk I'd like to get the ...
shell written 16 months ago by erick_rc9310 • updated 16 months ago by Pierre Lindenbaum131k
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parse of file multifasta in python
... I'm trying to parse a multifasta file with python with the next script import re def loadFasta(filename): if (filename.endswith(".gz")): fp = gzip.open(filename, 'rb') else: fp = open(filename, 'rb') # split at headers data = fp.r ...
sequence written 21 months ago by erick_rc9310 • updated 21 months ago by finswimmer14k
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merge two multifasta files
... I have two multifasta files that have almost the same headers, for example file1.fasta >header_1 dnasequenceoffastafile1 >header_2 dnasequenceoffastafile1 >header_3 dnasequenceoffastafile1 file2.fasta >header_1_f ...
sequence written 21 months ago by erick_rc9310 • updated 21 months ago by Brice Sarver3.5k
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Use the Pfam database and a local database together to find protein domains
... I have downloaded the Pfam-A database to find protein domains, but I'd like to add new domains that I have build with HMMER, but I don't know how to use both database together. For the new database, I have download the protein sequences in amino acids in a single fasta file, then I aligned the sequ ...
genome gene alignment written 24 months ago by erick_rc9310
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(Closed) merging data frames in r
... I want to merge two data.frames in R, the first one is a data frame with 50,000 rows and 95 columns and the second one has only 1 row and 95 columns, I'm using the rbind function, but I'm not sure how this function works, for example, Is necessary that both colnames in data frames are sorted or it d ...
R written 2.0 years ago by erick_rc9310
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plot with ggplot2
... I have merged two data.frames with the same column names but different number and name of rownames in R, and I have made a scatter plot in ggplot, but I'd like two have two different colour of dots in the plot model_3 <- rbind(df_1,df_2) plot <- ggplot(data=model_3, aes(x= ...
R written 2.1 years ago by erick_rc9310
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taxa names in phylogenetic tree
... I have a phylogenetic tree in newick format, and I would like to remove some fragments of the name of the taxa, 1_[genus_specie_1]_characters:0.2654682758,(((((((((((((((2_[genus_specie_2]_characters:0.0379334280,54_[genus_specie_2]_characters:0.0605802067)/1/100:0.0121248674,(3_[genus_specie_ ...
perl phylogenetics newick shell written 2.1 years ago by erick_rc9310 • updated 2.1 years ago by Pierre Lindenbaum131k
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(Closed) for loop to subset data.frame in R
... I have two data frames one with 94 rows and 167 columns (df_1) and the other one with 94 rows and 1 column (df_2) and I would like to do 167 different data frames with each column of the first data frame and the same column of the second data frame for (i in seq_len(ncol(df_1))){ df_[[i]] ...
R written 2.2 years ago by erick_rc9310
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codon alignment with pal2nal
... I'm trying to do multiple alignment with pal2nal, which requires two input files, I have a folder with multiple files whose extensions are **-e1-e2_aa_aln.faa** and **-e1-e2.fasta**, for a single alignment the command would be pal2nal.pl file_one-e1-e2_aa_aln.faa file_one-e1-e2.fasta> ...
alignment written 2.2 years ago by erick_rc9310 • updated 2.2 years ago by h.mon31k
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edit headers of fasta files
... I have a directory with fasta files and these files have headers like this \> ID:WP_070393975.1 | [Moorea producens PAL-8-15-08-1] | PAL-8-15-08-1 | hypothetical protein | 351 | NZ_CP017599(9673108):5662931-5663281:-1 ^^ Moorea producens PAL-8-15-08-1 chromosome, complete genome. First I wante ...
sequence written 2.2 years ago by erick_rc9310 • updated 2.2 years ago by sacha2.0k

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Popular Question 21 months ago, created a question with more than 1,000 views. For for loop to subset data.frame in R

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