###tcrBiter Usage and Output###
###Author: Lara McGrath
###Date: 8/29/2017

tcrBiter is a python script that can be run from anywhere but must be in the same folder as the included bed files (bed/TRB-hg38.bed) and myFields.alignmentExport.txt
Additional Requirements: Python, mixcr, BLAST and bedtools must be installed and in the path correctly.
Additional Requirements: must have BLAST database of hg38 or create one using makeblastdb.
Usage: python /path/to/runTCRbiter.py /path/to/some_R1.fastq.gz /path/to/some_R2.fastq.gz /path/to/BLAST/db/for/hg38

tcrBiter creates two directories: tcrError/ tcrOutput/

The following files are made in tcrError/

bedtoolsintersect.read1.error.txt   blastcleanread1.error.txt   blastread1.error.txt   intersectBlastMerge.error.txt   MixcrExport.error.txt
bedtoolsintersect.read1.stdout.txt  blastcleanread1.stdout.txt  blastread1.stdout.txt  intersectBlastMerge.stdout.txt  MixcrExport.stdout.txt
bedtoolsintersect.read2.error.txt   blastcleanread2.error.txt   blastread2.error.txt   MixcrAlign.error.txt            MixcrFiltering.error.txt
bedtoolsintersect.read2.stdout.txt  blastcleanread2.stdout.txt  blastread2.stdout.txt  MixcrAlign.stdout.txt           MixcrFiltering.stdout.txt

The following files are made in tcrOutput/

filename.alignmentReport.log        filename.filteredStats.pdf     filename.read1.filtered.fasta    filename.results.csv
filename.description.txt            filename.intersectMerged.txt   filename.read1.intersectBed.txt  filename.results.curated.csv
filename.filteredread1.readkey.txt  filename.intersectStats.txt    filename.read2.bed               filename.results.txt
filename.filteredread1.txt          filename.intersectVDJ.txt      filename.read2.blastClean.txt    filename.statsFiltered.csv
filename.filteredread2.readkey.txt  filename.read1.bed             filename.read2.blast.txt         filename.vdjca
filename.filteredread2.txt          filename.read1.blastClean.txt  filename.read2.filtered.fasta    tcrCommands.txt
filename.filteredResults.csv        filename.read1.blast.txt       filename.read2.intersectBed.txt

Important results files are:

filename.intersectStats.txt		#Defines number of read pairs in: (1) total, (2) with VDJ rearrangment, (3) with only V genes, (4) with only J genes, (5) with one V gene, (6) with one J gene, (7) rearrangement found in single read, (8) rearrangement split across pair

filename.intersectVDJ.txt 		#Breaks down features of each rearranged read

Other results files include:

filename.alignmentReport.log	#MiXCR alignment output report

filename.description.txt		#Information on how many reads were aligned, filtered, and had defined CDR3 regions

filename.filteredStats.pdf		#Displays histograms of features of aligned reads