Scripts

Main scripts

SAM2profilesGenomic.py

usage: Generates genomic profiles from SAM files.

options:

-h, --help: show this help message and exit

Options for input files:

-f FILE: SAM file (default: None)

-u {read,3end,5end} Generate profiles using reads (read) or the 3’ ends (end) (default: 3end) -n Save non-coded polyA ends. Can be used ONLY with: -u 3end (default: False) -c TOCLEAR String of signs to be cleared from the name of SAM file (default: _comp_flexbar_STARAligned.out) –chunks CHUNKS Divide list of genes into a chunks of given size (default: 0)

SAM2profiles.py

usage: Generates profiles from SAM files for a list of given transcripts.

optional arguments:

-h, --help: show this help message and exit

Options for input files:

-f FILE: SAM file (default: None)
-l FILE: list of genes file (default: None)
-d DETAILS_FILE: file with transcriptome details. (default: /homes/tollervey/COVID19/databases/transcriptome_details_biomart_tRNA_rRNA_UPDATEJan2021.tab)
--del: Generate additional profiles for deletions (default: False)
-p: SAve output as pickle DataFrame (default: False)
-e EXPAND: For deletions position can be expanded by the value on each side (e=5 gives 10 nt long) (default: 5)
-c TOCLEAR: String of signs to be cleared from the name of SAM file (default: _comp_flexbar_STARAligned.out)
--chunks CHUNKS: Divide list of genes into a chunks of given size (default: 0)

Supporting scripts

csv2pickle.py

usage: Read CSV file and save as a pickle

optional arguments:

-h, --help: show this help message and exit

Options for input files:

-f FILE: SAM file (default: None)
--gzip: gzip compression (default: False)

mergeSalmon.py

usage: merges Salmon quantification files to one tab file

optional arguments:

-h, --help: show this help message and exit

Options for input files:

-i INPUT: String of signs to be found in Salmon output directory (default: None)
-o OUTPUT: Name of output file (default: merged)
-u USE: column to be used {TPM,NumReads} (default: NumReads)
-f FILTER: String of signs to be found in Salmon output directory. Optional as additional filter (default: None)
-c CLEAR: String of signs to be found in Salmon output directory, will be cleared (default: None)
-a ADD: String of signs to be added to experiment name (default: None)