E. coli is a model organism. The strain E. coli K-12 was isolated from the stool of a convalescent diphtheria patient in 1922, and it has been used in the lab for nearly 100 years. (The first 1⁄2 is documented in an interesting paper – Bachmann 1972 (PMID: 4568763)). It was one of the first organisms to have its whole genome sequenced. It was such a big deal it was published in 1997 in Science! Most researchers either buy their strain from a stock collection or know the history of their strain (i.e., who gave it to them, who gave it them, etc.). These strains are going to inevitably evolve over time. Recently, researchers have returned back to these K-12 strains to resequence them and ones that were derived (evolved) from the original K-12 strain. The goal is to develop a Python wrapper to automate the execution of software tools that analyze genomic data.
Clone repository into personal directory using this command,
git clone https://github.com/ssohail1/compbio-PyWrap-miniproject.git
To move into compbio-PyWrap-miniproject directory use cd,
cd compbio-PyWrap-miniproject
To run the program for test data SRR8185310 and SRR1411276:
python miniproj_runall.py
This program will only work for single-end reads.
If you will implement this program for a different SRR file, simply change the 'SRR8185310' in the miniproj_runall.py file to your SRR file of interest
Move the SRR file to the compbio-PyWrap-miniproject folder:
mv SRRfile compbio-PyWrap-miniproject
- miniproject.log: log file with commands, number of contigs greater than 1000 in length, bp in assembly of contigs greater than 1000 in length.
- miniproj_runall.py: python script to run analyses using the tools described. It includes functions that download SRA files, pulls fasta files, run SPades, assembles the reads, counts the number of contigs and number of base pairs in the assembly, runs GeneMark to output the predicted protein sequences for the identified genes, runs BLAST with the GeneMark protein output against the protein database, calculate difference between the RefSeq for E. coli K-12 (NC_000913) and BLAST output. Additionally, run TopHat with fastq file of E. coli transcriptome project of a K-12 derivative BW38028, fasta file of complete annotated genome NC_000913, and GFF file from GeneMark annotation, and then run Cufflinks and parse through output to create the Fragments Per Kb of transcript per Million mapped reads (fpkm) file
All output will be in results folder.
| File | Description |
|---|---|
| contigs.fasta | Output from SPAdes: these are the resulting contigs after reads assembly is completed |
| contigsthousand.fasta | Modified contigs.fasta file: This is the contig file that only has contigs that are greater than 1000 bp in length |
| predictseqs.fasta | Output from GeneMark: This fasta file has the predicted protein sequences for the identified genes |
| predict_functionality.csv | Output from BLAST: This is a CSV file that identifies the predicted function of each coding region |
| accepted_hits.bam | Output from TopHat: A list of read alignments in SAM format |
| fpkm file | Output from Cufflinks: Is the counts of mapped fragments over total mapped fragments which is multiplied by exon length of transcript |