Tag Archives: sed

Remove new lines from a text file

I want to copy some text from a PDF file into a word processor. Copying works, but the line breaks from the PDF formatting are also copied. This messes up the text and results in disconnected text with many rows. … Continue reading

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Cleaning up with sed 2

I have a list of nucleotide sequences in fasta format, obtained from NCBI. I want to clean the sequences names, leaving only the accession numbers. Additionally, I want to extract the accession numbers to a separate list. I am not … Continue reading

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Cleaning up with sed

I needed to clean up some plain text files from data and characters I did not want. To be more precise, I have a phylogenetic tree, obtained from the TimeTree web-site. Species presented there are mainly birds, several reptiles and … Continue reading

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Making a patch

I usually fix the SlackBuilds I maintain by sed, as it makes things much more transparent. However, sed is not always an option, especially for some big fixes or fixes that contain “weird” characters, for example something like this: The … Continue reading

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