User: Olorin

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Olorin50
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PhD at INRA

Posts by Olorin

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Comment: C: msa alignement: sorted sequences by sequence name
... Good to know. thank you ...
written 2.7 years ago by Olorin50
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Comment: C: msa alignement: sorted sequences by sequence name
... Yes. I know right. But I need to keep the full species names ( Genus species strain ) but my pdf is nice ...
written 2.7 years ago by Olorin50
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Comment: C: msa alignement: sorted sequences by sequence name
... I saw right. you can see msaPrettyPrint help. If you add code arguments, it overrides all other arguments: code this argument can be used to specify the entire LaTeX code in the texshade environment. This overrides all arguments that customize the appearance of the output. Instead, all customi ...
written 2.7 years ago by Olorin50
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Answer: A: msa alignement: sorted sequences by sequence name
... PROBLEM SOLVED ______________________________ for (i in 1:n){ current_seq <- readAAStringSet(myFiles[i]) permutation <- order(names(current_seq ) current_align <- msa(current_seq[permutation],order="input")   #I prefer to make tex file first   msaPrettyPrint(current_align, output=" ...
written 2.7 years ago by Olorin50
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Answer: A: msa alignement: sorted sequences by sequence name
... Thanks for you great help! Your solutions is tricky but I understand how you solve my problem =) Your solution works fine. Sequences in fasta file are sorted by name and in the pdf too. But there are 2 littles issues: -My sequences names are like : Escherichia coli|gene_name|. In the pdf i get on ...
written 2.7 years ago by Olorin50
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msa alignement: sorted sequences by sequence name
... Hello, I wonder if there is a way to use msaPrettyPrint() with sorted alignement by sequence name without rewriting the output fasta file. I know I can read the output fasta file with python, and re-order the sequences by the sequence name, but I'm pretty sure there is a quickest way to achieve tha ...
output msa alignement sorted written 2.7 years ago by Olorin50
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Answer: A: Using msa msaPrettyPrint(): issues with latex
... See my last answer in https://support.bioconductor.org/p/91525/#91528 PROBLEM SOLVED ...
written 2.7 years ago by Olorin50
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Answer: A: Using msa msaPrettyPrint(): saving multiple alignement fasta file
... PROBLEM SOLVED: I have resolved my problems. 1. Save tex file with msaPrettyPrint() 2. Construct pdf with texi2pdf() bdir = "E:/DOCTORAT/workspace/alignement_prot_ribo_all" workdir = file.path(bdir,"one_file_per_ptne/") outdir = file.path(bdir,"alignements") myFiles = list.files(path = workdir ...
written 2.7 years ago by Olorin50
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Answer: A: Using msa msaPrettyPrint(): saving multiple alignement fasta file
... I'm trying this # # bdir = "E:/DOCTORAT/workspace/alignement_prot_ribo_all" workdir = file.path(bdir,"one_file_per_ptne/") outdir = file.path(bdir,"alignements") myFiles = list.files(path = workdir,full.names = TRUE) for (i in 1:66){ newdir = substr(basename(myFiles[i]), start = 1 ,stop = 6) ...
written 2.7 years ago by Olorin50
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Using msa msaPrettyPrint(): saving multiple alignement fasta file
... Hello. I know when I use msaPrettyPrint() function, this write the aligned sequences in fasta file ; C:/Users/SEBASTIEN/AppData/Local/Temp/RtmpMTD00Y/seq21e072f6414e.fasta Is there a way to change the ouput directory? ...
fasta msa msaprettyprint() written 2.7 years ago by Olorin50 • updated 2.4 years ago by tongtong.wang12100

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