Python-Scripts

Several python scripts that perfrom various tasks such as:

• Sequence parsing (seqtools)
• Phylogeny manipulation (treetools)
• Machine Learning (sklearn_dbscan)
• Heat map generation via seaborn (seq_pheno_clustering)
• Protein homology modeling via modeller (homology_prediction)
• Flow cytometry (flow_analysis)

Sequence parsing and analysis (seqtools.py)

Dependencies:

seqtools.py uses progressbar.py which is included in this repo.

Usage:

Prepare your workspace.

>>> import seqtools as st
>>> reader = st.ReadSequenceFile()
>>> writer = st.WriteSequenceFile()
>>> parser = st.ParseSequences()

Read in a fasta file:

>>> data = reader.fasta("test.fasta")

Parse the data (for example remove sequences that contain 'X'):

>>> data_clean = parser.remove_bad_seqs_protein(data)
Enter characters to remove: X
---
1030 protein sequences remove
Sequences in dataset:  5166

Parsing functions available:

Name	Description
remove_bad_seqs_DNA	Remove user defined bad sequences from DNA data.
remove_bad_seqs_protein	Remove user defined bad seuences from protein data.
site_count_DNA	Calculates the percentage of A/G/T/C at a user defined site.

• remove_duplicates: Removes duplicate sequences.
• sort_seqs: Sorts sequences based on the user defined site and character. Outputs a list containing the sequences meeting the defined criteria and sequences that do not.
• pattern_match: Returns a list that match a specific user defined pattern.

Write output files:

writer.fasta("output.fasta", data)
Done.

Features coming soon:

• NEXUS file format support
• site_count for protein
• Dictionary iteration instead of list iterations
• Consensus sequence generation (user defined percentage)

Flow Cytometry Cell Cycle Analysis

FlowCytometryTools (latest version) matplotlib (>1.13.1) scipy (latest version) ipython

Installation - Seq_pheno_clustering

$ sudo apt-get install python3-pyqt4
$ pip3 install -U --user ete3

Credit

Credit should be given to user 'themantalope' for explaining and providing code for converting a newick format tree to a scipy.cluster.hierachy linkage matrix: https://stackoverflow.com/questions/31033835/newick-tree-representation-to-scipy-cluster-hierarchy-linkage-matrix-format

*Note dbscan_lev_distance does not work as intended