Update README.md

Utilities/README.md

@@ -2,7 +2,7 @@
 # Utilities
 > This folder contains many useful tools for analyzing sequence data.
 
-## For taxonomy dir:
+## For Taxonomies dir:
 ### Query_SRA_egs.py:
 
 **Purpose** Gives a spreadsheet of all SRA codes or GCA codes from Genbank associated with taxonomic terms in an input csv file
@@ -19,13 +19,57 @@ Written by Elinor 1/26, updated 2/12
 
 **Purpose** make lists of unique taxonomy from phylotol master taxonomy column (genbank taxonomy for each taxa in the pipeline). These lists are the intended input for Query_SRA_egs.py. This cuts off the genus (and species if there is one), uniquifies the list and writes them out to files by the first word of the taxonomy
 
-**Input** text file of taxonomies. make sure each taxonomic level is separated with '; ' (semicolon space) or the script will not parse the names right
+**Input** text file of taxonomies called `all_taxa.txt`. make sure each taxonomic level is separated with `; ` (semicolon space) or the script will not parse the names right
 
+**Output** txt file of _all_ unique names found, and a directory of txt files of unique names sorted by major clade (the first word in the line of input taxonomy
+
+**Usage**
+>`python get_unique_taxa.py`
 
 WARNING: if you run the script multiple times, DELETE THE PREVIOUS OUTPUT. this is because it appends lines to the 
 end of files so you will have many duplicates
 
->  Example command line: `python get_unique_taxa.py`
+### get_taxonomy.py:
+
+**Purpose** 
+
+Queries Entrez Search with the genus and species name associated with 10 digit codes and returns the taxonomy for each name if available.
+
+**Input**
+
+Spreadsheet with ten digit codes in the first column and the genus and species names in the second column (csv).
+
+**Output**
+
+CSV file called `output_taxonomies.csv` with 10 digit codes and genbank taxonomy.
+
+**Usage**
+Input a spreadsheet with ten digit codes in the first column and the genus and species names in the second column. Preferably, the genus and species name will be separated by a space and there will be no extraneous characters in the second column.
+
+>`python get_taxonomy.py --input_file <path to .csv file>`
+
+
+## For Assemblies dir:
+### assess_transcriptomes.py:
+Written March 2023 by Elinor (esterner27@gmail.com) to plot length, coverage and GC of assembled transcripts
+
+**Purpose** Rename rnaSpades output to new names in the txt file, then iterate through them all and gather GC, length and coverage. With that data, it plots R scripts
+
+**Input**
+	Directory of directories output by rnaSpades OR folder called Renamed_assembled_files of previously renamed files (if this is the case, put `-r` or --renamed in the command line)
+	txt file of LKH number and new names formatted like this: LKHxxx\tLKHxxx-10_digit_code-descriptor_of_taxon
+  R script plot_assemblies.R, which is called from within this python script
+
+**Usage**
+
+To run if your rnaSpades output is **not** renamed yet:
+>`python assess_transcriptomes.py --raw <pathway to directory of spades output>`
+
+To run if your files are already renamed:
+>`python assess_transcriptomes.py --renamed  <pathway to directory of renamed assemblies>`
+
+**Output** csv file of length, GC, coverage of each transcript, and multiple R plots, faceted by taxon and a csv file of data. It plots GC by length, and distributions of coverage, length and GC content across the whole transcript
+
 
 ### Katz lab
 >[About Katz Lab](https://www.science.smith.edu/katz-lab/)  &nbsp; \| &nbsp;