This is a collection of command-line tools I wrote to make various repetitive tasks more convenient. They will typically take input from standard input and will output to standard output. I make an effort to not use external libraries so that compilation requires the least possible dependencies. Note that some other tools/scripts I write for other projects use these tools and assume they can be found in your PATH.

ambiguity2gap.py: Convert ambiguous characters to gaps

For help message: python ambiguity2gap.py -h

barplot.py: Create a barplot from a list of labels

Reads the list of labels from standard input by default, or a file can be passed vi -i
- Only include labels, no counts! The script will count them for you! Niema Niema Niema Moshiri Moshiri
The order of the x-axis will be the order in which each label first appeared in the input
- From left to right, the above example will plot "Niema" (with a count of 3) followed by "Moshiri" (with a count of 2)
For help message: python barplot.py -h

boxplots.py: Create box plots from data

Reads the data from standard input by default, or a file can be passed via -i
- The data must be in the JSON (or Python dictionary) format
For help message: python boxplots.py -h

convert_trees.py: Convert input tree(s) to different formats

Can convert branch support values from decimal to percentage (and vice-versa)
Can convert tree schema between formats: {'newick','nexus','phyloxml','nexml'}
For branches without support values, can give them a default value (e.g. 100), or keep them empty by default
For help message: python convert_trees.py

download_m3u8.py: Download an m3u8 video stream

For help message: python download_m3u8.py -h

fasta1ln.py: Convert a multiline FASTA file to one-line

For help message: python fasta1ln.py -h

fasta2json.py: Convert a FASTA file to JSON

For help message: python fasta2json.py -h

fasta2phylip.py: Convert a FASTA multiple sequence alignment to Phylip

For help message: python fasta2phylip.py -h

fasta_cut_seqs.py: Cut the sequences of a given FASTA file to be a given length

For help message: python fasta_cut_seqs.py -h

fasta_subsample.py: Subsample a given FASTA file

For help message: python fasta_subsample.py -h

fastq_header_rename_illumina.py: Rename the read identifiers of a FASTQ file to follow the Illumina standard

For help message: python fastq_header_rename_illumina.py -h

fastq_merge.py: Merge multiple FASTQ files

Usage: fastq_merge.py <fastq_files>

fastq2fasta.py: Convert a FASTQ file to FASTA

For help message: python fastq2fasta.py -h

hamming.py: Compute all pairwise Hamming distances from a given multiple sequence alignment

For help message: python hamming.py -h

histogram.py: Create a histogram from a list of numbers

Reads the list of numbers from standard input by default, or a file can be passed via -i
- The numbers in the list must be whitespace-delimited
For help message: python histogram.py -h

hmmer_to_pomegranate.py: Convert a profile HMM from the HMMER-3 format to the pomegranate serialized JSON format

For help message: python hmmer_to_pomegranate.py -h

mergebib.py: Merge multiple BibTeX files into a single file named `merged.bib`

Usage: python mergebib.py <file1.bib> <file2.bib> ...
Verbose messages are output to standard error, and the merged file is output to standard output

numlist: Perform various basic tasks on a list of numbers

The list of numbers must be passed in via standard input
Run it without arguments to see the usage message, which contains a list of functions
The list of numbers can be integers or decimals: the tool handles both
The numbers must be delimited by whitespace
If your numbers are not delimited by whitespace, you can use tr to fix your list. For example:
```
echo "1,2,3,4,5" | tr ',' ' ' | numlist -sum
```

You can compile it using make or as follows:

g++ -Wall -pedantic -O3 -o numlist numlist.cpp

nw_error: Compute various error metrics on Newick trees

Usage: nw_error metric tree1 tree2

patristic_distances.py: Compute all patristic distances from the given tree

For help message: python patristic_distances.py -h

ranDNA.py: Generate random DNA sequences

For help message: python ranDNA.py -h

resolve_random.py: Randomly resolve a multifurcating tree

Reads multifurcating tree from STDIN and writes resolved tree to STDOUT
Usage: resolve_random.py < UNRESOLVED.tre > RESOLVED.tre

rmdup.sh: Remove consecutive identical files (keep first instance)

Usage: rmdup.sh

safenames.py: Convert the identifiers of a FASTA file to random safe names

Safename FASTA is output to STDOUT
Dictionary of name mappings is output to STDERR
For help message: python safenames.py -h

samstats: Compute basic statistics on a SAM file passed in via STDIN

Statistics are printed to STDERR
Also useful for converting from SAM to FASTQ/FASTA extremely quickly
Usage: samstats [output_format]
Valid output formats:
- none: Don't output the SAM file's contents
- fasta: Output a FASTA file to STDOUT
- fastq: Output a FASTQ file to STDOUT
- sam: Output the same exact SAM file to STDOUT