biobash

A collection of bash scripts for bioinformatics.

• cleannames.sh : Takes NCBI formatted FASTA file and generates a new FASTA file with only the accessions.
• countntbl.sh : Generates a table with sequence names and the number of 'N's in the sequence.
• countseq.sh : Counts sequences in a FASTA file.
• dedup.sh : Removes exact duplicates from a FASTA file. From a tip by Pierre Lindenbaum (see https://www.biostars.org/p/3003/).
• degap.sh : Degaps a FASTA file (see https://www.biostars.org/p/302104/).
• extractacc.sh : Takes NCBI formatted FASTA file and generates a text file with the accessions.
• extractseq.sh : Takes FASTA file and extracts only the sequence.
• fas2csv.sh : Converts FASTA into tab-separated file.
• fas2phylip.sh : Converts FASTA to phylip format, useful for phyml.
• lenseq.sh : Returns length of all sequences in a FASTA file.
• linfasta.sh : Converts a FASTA file into linearized sequences (i.e. alternating titles and sequences). Taken from a hint by Frederic Mahe (see http://www.biostars.org/p/17680).
• longorf.sh : Extracts the longest open reading frame. Requires getorf from EMBOSS.
• numbersequences.sh : Renames sequences with 'X' followed by a number. Use in conjunction with seqnametable.sh.
• relabel.sh: Relabels sequences using a stub concatenated with a numeric index.
• removesmalls.sh : Removes sequences shorter than a given threshold. Taken from a hint by Frederic Mahe (see http://www.biostars.org/p/79202/).
• seqnametable.sh : Generates a tab-separated file of new names generated by numbersequences.sh and the original name.
• sortfasta.sh : Sorts a FASTA file into sequences of decreasing length.
• startatname.sh : Prints a FASTA file beginning at a given sequence name.
• stopatname.sh : Prints a FASTA file until (and including) a given sequence name.
• translate.sh: Uses transeq from EMBOSS to translate sequences, but removes the additional numbering introduced by transeq.
• trimorf.sh: Trims non-coding regions from the beginning and end of a sequence. Requires getorf from EMBOSS.
• tsv2fas.sh: Converts a tab-delimited file (name,sequence with no header to FASTA.