Shell script that runs the a pipeline for metagenomic abundance estimates against all bacterial genomes

Preps fasta, builds indexes, aligns reads, merges with dataset-specific alignment, and runs express.
Table of expansions of genome name abbreviations from the Martin_etal genome dataset
Script to analyze the pickle created by M_calculate_coverage.py
Now pickles both the raw pileup (for faster re-runs) and the processed coverage data (for further analysis)
Removed conditional check for previously-made _justbody.txt files

If the script was interrupted while making those files, they ended up truncated without warning, causing the resulting merge to be missing parts. Also added print statements to explain what's taking so long.
Added verbose print statements to help figure out why fasta still has duplicates. Turns out it's because the input file needs to be sorted first.
Pickle diffs for later analysis. Also replaced name-cleaning function with library function.
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Uncommented lines; this is the full, runnable version of the version 1.0 script.
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Updated file names for use as testM
Samtools view failed on testE_M probably due to failure of merge; rerunning merge + downstream steps.
Updated paths to point to new ~/tools/ repository
Script that writes a full pipeline shell script, given parameters and existing files. Currently set up to produce version 1.2, for testL_J.
Fixed check for bowtie alignment file
eXpress now outputs to a directory, to avoid conflicts.

eXpress outputs to a directory with the name of the merged alignment file, and the script then renames and moves the results files back to the primary directory. Directory is not currently deleted.