Fix copy-pasted UMI help text on paired-guide --pg-* options (#22)

CHANGELOG.md

@@ -35,6 +35,12 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
   Previously the permutation test resampled the same full set, found no
   exceedance of the zero score, and returned `p_permutation=0`; such pathways
   now short-circuit to a p-value of 1.0 so they cannot distort sorting or FDR.
+- Corrected the `count` help text for the paired-guide options `--pg-start`,
+  `--pg-end`, `--pg-start-2`, and `--pg-end-2`, which was accidentally copied from
+  the UMI options (it described the position "of UMI" and referenced `--umi-start`
+  / `--umi-end`). It now describes the second guide and the correct coordinate
+  reference for each `--pairguide` mode. Also fixed the `--pg-min-read` help, which
+  stated "Default 2" while the actual default is 3. See issue #22.
 - `pathway --method gsea` no longer ranks the gene-ranking file's header row as a
   phantom gene. The default input is a `*.gene_summary.txt` whose first row is a
   header; `mageckGSEA` used to parse it as a gene named `id` with score 0,

mageck2/argsParser.py

@@ -71,11 +71,11 @@ def arg_count(subparser):
   cnt_pggroup.add_argument('--pairguide',choices=['none','firstpair','secondpair','auto'],default='none',help='Search for second gRNA, located within the first pair or the second pair of the read, or automatically search for possible guides. If you are aware of the location of the guide, specify the values of --pg-start/--pg-end (if --pairguide firstpair), or --pg-start-2/--pg-end-2 (if --pairguide secondpair). The program will automatically search for locations if --pairguide auto.')
   cnt_pggroup.add_argument('--list-seq-2',required=False,help='A library file for the second sgRNA, containing the list of sgRNA names, their sequences and associated genes. Support file format: csv and txt. ')
   cnt_pggroup.add_argument('--reverse-complement-2',action='store_true',help='Reverse complement the sequences in the second pair guide library for read mapping. Note: for performance considerations, only the guide sequences are reverse complemented, not the read.')
-  cnt_pggroup.add_argument('--pg-start',type=int,default=-1,help='The relative start position of UMI from guides, if UMI is found on the first pair. For example, for a read NNNNAATACGNNNCGACNNNN with guide AATACG and UMI CGAC, set --umi-start to 4 and --umi-end to 8.')
-  cnt_pggroup.add_argument('--pg-end',type=int,default=-1,help='The relative end position of UMI from guides, if UMI is found on the first pair.')
-  cnt_pggroup.add_argument('--pg-start-2',type=int,default=-1,help='The relative start position of UMI (from the first nucleotide of the read), if UMI is found on the second pair. For example, for a read NNNNCGAC with UMI CGAC, set --umi-start-2 to 4 and --umi-end-2 to 8.')
-  cnt_pggroup.add_argument('--pg-end-2',type=int,default=-1,help='The relative end position of UMI (from the first nucleotide of the read), if UMI is found on the second pair.')
-  cnt_pggroup.add_argument('--pg-min-read',type=int,default=3,help='Only report paired-guides whose total reads in all samples no less than this number. Setting to higher numbers to avoid reporting a large number of records with very few reads. Default 2.')
+  cnt_pggroup.add_argument('--pg-start',type=int,default=-1,help='The relative start position of the second guide, measured from the end of the first guide, when the second guide is on the first read (--pairguide firstpair). For a second guide immediately following the first guide, set --pg-start to 0.')
+  cnt_pggroup.add_argument('--pg-end',type=int,default=-1,help='The relative end position of the second guide, measured from the end of the first guide, when the second guide is on the first read (--pairguide firstpair).')
+  cnt_pggroup.add_argument('--pg-start-2',type=int,default=-1,help='The relative start position of the second guide, measured from the first nucleotide of the second read, when the second guide is on the second read (--pairguide secondpair). For example, for a 20bp second guide at the very start of read 2, set --pg-start-2 to 0 and --pg-end-2 to 20.')
+  cnt_pggroup.add_argument('--pg-end-2',type=int,default=-1,help='The relative end position of the second guide, measured from the first nucleotide of the second read, when the second guide is on the second read (--pairguide secondpair).')
+  cnt_pggroup.add_argument('--pg-min-read',type=int,default=3,help='Only report paired-guides whose total reads in all samples no less than this number. Setting to higher numbers to avoid reporting a large number of records with very few reads. Default 3.')
   cnt_pggroup.add_argument('--pg-pair-only',help='Only report paired-guides whose combination is listed in the file designated by --pg-pair-only. Each line in this file should has the format "sgid_1 sgid_2", where sgid_1 and sgid_2 are sgRNA IDs from --list-seq and --list-seq-2, respectively.')
 
 def arg_test(subparser):