simple-v-microbiome

These are scripts that help make it possible to run an analysis solely from a bash script

1. trim_to_exact_level.py

• use this script with the output from something like qiimeToMaaslin
• this will trim the output to an exact level of your choosing

1. heatmap.R

• use this from the command line to make heatmaps using one category of your choosing
• uses the output from transpose.py as included with Maaslin

1. add_metadata.py

• use this to add metadata to your tsv otu table without modifying the features
• requires a tsv formatted otu table (with the top line as sample ids)

1. fastq_barcode_primer_checker.py

• use this to check if your barcodes and primers look like they match a fastq file
• I use this when I am taking fastq files, barcodes, and primers from SRA, as I am not confident that all was entered correctly
• it will output a new mapping file with the values of proportion exact match for both the barcode and the primer
• it will print a warning if a certain sample matches its barcode under a specified proportion [default: 0.5]

1. fix_after_qiimeToMaaslin.py

• when qiimeToMaalin.py cannot detect the format of a file, it adds a big header
• this will sense that and remove it if necessary

1. get_barcodes_from_extracted_barcodes.py

• use this to help build a mapping file when you are just given fastq files
• it takes a barcodes.fastq file from extract barcodes.py
• extract_barcodes.py -f compiled.fastq -c barcode_single_end --bc1_len 12 -o extracted_barcodes
• it will also print a warning if the best barcode match was below an arbitrary cutoff

1. guess_status_from_otu_table.py

• use this to add a column to a mapping file indicating presence or absence of a feature
• it takes in a mapping file, a tsv otu table, and a feature name in all cases
• optionally, it can take in a category (from the original mapping file) and that category's positive value and will print some standard metrics

1. make_stirrups_otu_table.py

• use this to make an otu table and a rep set from the assignments file that is the output of running stirrups reference

• the reference set is helpful for building a tree so that phylogeny based metrics can be calculated

• Some things to note:

• I will try to get some examples up soon

• I have only tested these with my data - they have worked so far, but if there is an issue, post it

• You can contact me here