documentation update

jaredgk · Sep 17, 2019 · 0631083 · 0631083
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diff --git a/pgpipe/admixture.py b/pgpipe/admixture.py
@@ -12,7 +12,7 @@
 
     .. code-block:: bash
         
-        python admixture.py
+        admixture.py
 
     *************
     Example usage
@@ -22,7 +22,7 @@
 
     .. code-block:: bash
         
-        python admixture.py --binary-ped-prefix hapmap3 --pop 3
+        admixture.py --binary-ped-prefix hapmap3 --pop 3
 
     ############
     Dependencies 

diff --git a/pgpipe/bed_tasks.py → pgpipe/bed_utilities.py b/pgpipe/bed_tasks.py → pgpipe/bed_utilities.py
@@ -1,9 +1,38 @@
 #!/usr/bin/env python
 '''
-    Utilites for BED-formatted files
+    Automates various utilites for BED-formatted files. This currently includes: i) 
+    subtract from a BED that overlap with a second BED file; ii) extend a BED upstream, 
+    downstream, or both upstream and downstream; iii) sort a single BED; iv) merge 
+    features within one or more BED files; v) create a BED of complementary features.
 
-    Automates various utilites for BED-formatted files. This currently includes:
-    MORE INFO.
+    ##################
+    Command-line Usage
+    ##################
+    The BED utilites function may be called using the following command:
+
+    .. code-block:: bash
+        
+        bed_utilites.py
+
+    *************
+    Example usage
+    *************
+    Extend flanks (i.e. both upstream and downstream) by 10kb:
+
+    .. code-block:: bash
+        
+        bed_utilites.py --bed input.bed chr22.vcf.gz --utility extend --extend-flanks 10000
+
+    Merge multiple BED files:
+
+    .. code-block:: bash
+        
+        bed_utilites.py --beds Input_BEDs --utility merge
+    
+    ############
+    Dependencies 
+    ############
+    * `BEDtools <https://bedtools.readthedocs.io/en/latest/>`_
     
     ############################
     Input Command-line Arguments

diff --git a/pgpipe/eigenstrat_fstats.py b/pgpipe/eigenstrat_fstats.py
@@ -3,6 +3,37 @@
     Automates the calculation of multiple admixture statistics, including: Patterson's D, 
     F4 statistic, F4-ratio statistic, and F3 statistic.
 
+    ##################
+    Command-line Usage
+    ##################
+    The admixture statistics automater may be called using the following command:
+
+    .. code-block:: bash
+        
+        eigenstrat_fstats.py
+
+    *************
+    Example usage
+    *************
+    Command-line to calculate Patterson's D:
+
+    .. code-block:: bash
+        
+        eigenstrat_fstats.py --eigenstrat-prefix snps --calc-admix-statistic D --admix-w-pop French --admix-x-pop Yoruba --admix-y-pop Vindija --admix-z-pop Chimp 
+    
+    Command-line to calculate the F4-ratio: 
+
+    .. code-block:: bash
+        
+        eigenstrat_fstats.py --eigenstrat-prefix snps --calc-admix-statistic F4-ratio --admix-a-pop Altai --admix-b-pop Vindija --admix-c-pop Yoruba --admix-x-pop French --admix-o-pop Chimp  
+    
+    ############
+    Dependencies 
+    ############
+    * `AdmixTools <https://github.com/DReichLab/AdmixTools>`_
+    * `admixr <https://github.com/bodkan/admixr>`_
+
+
     ############################
     Input Command-line Arguments
     ############################
@@ -139,21 +170,6 @@
         Argument used to define a file of population(s) to represent C in the supported 
         admixure statistic. If multiple populations the statistic will be repeated until each 
         population has represented C.
-    
-    ##########################
-    Example Command-line Usage
-    ##########################
-    Command-line to calculate Patterson's D:
-
-    .. code-block:: bash
-        
-        python eigenstrat_fstats.py --eigenstrat-prefix snps --calc-admix-statistic D --admix-w-pop French --admix-x-pop Yoruba --admix-y-pop Vindija --admix-z-pop Chimp 
-    
-    Command-line to calculate the F4-ratio: 
-
-    .. code-block:: bash
-        
-        python eigenstrat_fstats.py --eigenstrat-prefix snps --calc-admix-statistic F4-ratio --admix-a-pop Altai --admix-b-pop Vindija --admix-c-pop Yoruba --admix-x-pop French --admix-o-pop Chimp  
 '''
 
 import os

diff --git a/pgpipe/plink_ld.py b/pgpipe/plink_ld.py
@@ -2,6 +2,30 @@
 '''
     Automates the calculation of multiple LD statistics using Plink.
 
+    ##################
+    Command-line Usage
+    ##################
+    The LD statistics automater may be called using the following command:
+
+    .. code-block:: bash
+        
+        plink_ld.py
+
+    *************
+    Example usage
+    *************
+    Command-line to calculate Lewontin's D-prime statistic
+
+    .. code-block:: bash
+        
+        plink_ld.py --ped-prefix hapmap1 --ld-format table --ld-statistic r2 --table-d-statistic dprime
+
+    ############
+    Dependencies 
+    ############
+    * `plink 1.9 <https://www.cog-genomics.org/plink2/>`_
+    * `plink 2.0 <https://www.cog-genomics.org/plink/2.0/>`
+
     ############################
     Input Command-line Arguments
     ############################
@@ -89,15 +113,6 @@
         multiple times if desired.
     **--table-snps** *<snp_filename>*
 		Argument used to define a file with one or more SNP(s) for LD analysis.
-    
-    ##########################
-    Example Command-line Usage
-    ##########################
-    Command-line to calculate Lewontin's D-prime statistic
-
-    .. code-block:: bash
-        
-        python plink_ld.py --ped-prefix hapmap1 --ld-format table --ld-statistic r2 --table-d-statistic dprime
 '''
 
 import os

diff --git a/pgpipe/stat_sampler.py b/pgpipe/stat_sampler.py
@@ -12,7 +12,7 @@
 
     .. code-block:: bash
         
-        python stat_sampler.py
+        stat_sampler.py
 
     *************
     Example usage
@@ -22,7 +22,7 @@
 
     .. code-block:: bash
         
-        python admixture.py --statistic-file merged_chr1_10000.windowed.weir.fst 
+        stat_sampler.py --statistic-file merged_chr1_10000.windowed.weir.fst 
         --calc-statistic windowed-weir-fst --sampling-scheme random --sample-size 20
 
     ############################

diff --git a/pgpipe/vcf_calc.py b/pgpipe/vcf_calc.py
@@ -11,7 +11,7 @@
 
     .. code-block:: bash
         
-        python vcf_calc.py
+        vcf_calc.py
 
     *************
     Example usage
@@ -20,13 +20,13 @@
 
     .. code-block:: bash
         
-        python vcf_calc.py --vcf input.vcf --calc-statistic TajimaD --statistic-window-size 10000
+        vcf_calc.py --vcf input.vcf --calc-statistic TajimaD --statistic-window-size 10000
 
     Command-line to calculate windowed Fst on the two populations within the model *2Pop*: 
 
     .. code-block:: bash
         
-        python vcf_calc.py --vcf input.vcf.gz --model-file input.model --model 2Pop --calc-statistic windowed-weir-fst --statistic-window-size 10000 --statistic-window-step 10000
+        vcf_calc.py --vcf input.vcf.gz --model-file input.model --model 2Pop --calc-statistic windowed-weir-fst --statistic-window-size 10000 --statistic-window-step 10000
     
     ############
     Dependencies 

diff --git a/pgpipe/vcf_filter.py b/pgpipe/vcf_filter.py
@@ -10,7 +10,7 @@
 
     .. code-block:: bash
         
-        python vcf_filter.py
+        vcf_filter.py
 
     *************
     Example usage
@@ -19,19 +19,19 @@
 
     .. code-block:: bash
         
-        python vcf_filter.py --vcf input.bcf --filter-min-alleles 2 --filter-max-alleles 2
+        vcf_filter.py --vcf input.bcf --filter-min-alleles 2 --filter-max-alleles 2
 
     Command-line to only include chromosome chr1:
 
     .. code-block:: bash
         
-        python vcf_filter.py --vcf input.vcf.gz --filter-include-chr chr1
+        vcf_filter.py --vcf input.vcf.gz --filter-include-chr chr1
 
     Command-line to remove indels and ouput a BCF file:
 
     .. code-block:: bash
         
-        python vcf_filter.py --vcf input.vcf --filter-exclude-indels --out-format bcf
+        vcf_filter.py --vcf input.vcf --filter-exclude-indels --out-format bcf
 
     ############
     Dependencies 

diff --git a/pgpipe/vcf_liftover.py b/pgpipe/vcf_liftover.py
@@ -9,7 +9,7 @@
 
     .. code-block:: bash
         
-        python vcf_liftover.py
+        vcf_liftover.py
 
     *************
     Example usage
@@ -18,7 +18,7 @@
 
     .. code-block:: bash
         
-        python vcf_liftover.py --vcf chr22.vcf.gz --chain hg19ToHg38.over.chain
+        vcf_liftover.py --vcf chr22.vcf.gz --chain hg19ToHg38.over.chain
 
     ############
     Dependencies 

diff --git a/pgpipe/vcf_phase.py b/pgpipe/vcf_phase.py
@@ -11,7 +11,7 @@
 
     .. code-block:: bash
         
-        python vcf_phase.py
+        vcf_phase.py
 
     *************
     Example usage
@@ -20,13 +20,13 @@
 
     .. code-block:: bash
         
-        python vcf_phase.py --vcf input.vcf --phase-algorithm beagle --phase-chr chr1
+        vcf_phase.py --vcf input.vcf --phase-algorithm beagle --phase-chr chr1
 
     Command-line to phase using SHAPEIT with 100 burn-in iterations:
 
     .. code-block:: bash
         
-        python vcf_phase.py --vcf input.vcf.gz --phase-algorithm shapeit --shapeit-burn-iter 100
+        vcf_phase.py --vcf input.vcf.gz --phase-algorithm shapeit --shapeit-burn-iter 100
 
     ############
     Dependencies 

diff --git a/pgpipe/vcf_split.py b/pgpipe/vcf_split.py
@@ -5,6 +5,29 @@
     data for the function to operate. If the specified statistic file does not
     contain a BIN_END column, the --statistic-window-size argument may be used.
 
+    ##################
+    Command-line Usage
+    ##################
+    The VCF splitter may be called using the following command:
+
+    .. code-block:: bash
+        
+        vcf_split.py
+
+    *************
+    Example usage
+    *************
+    Command-line to split using a statistic file:
+
+    .. code-block:: bash
+        
+        vcf_split.py --vcf input.vcf --split-file input.windowed.weir.fst --split-method statistic-file
+
+    ############
+    Dependencies 
+    ############
+    * `BCFtools <https://samtools.github.io/bcftools/bcftools.html>`_    
+
     ############################
     Input Command-line Arguments
     ############################
@@ -85,15 +108,6 @@
         Argument used to define a BED file of positions to include.
     **--filter-exclude-bed** *<position_bed_filename>*
         Argument used to define a BED file of positions to exclude.
-
-    ##########################
-    Example Command-line Usage
-    ##########################
-    Command-line to split using a statistic file:
-
-    .. code-block:: bash
-        
-        python vcf_split.py --vcf input.vcf --split-file input.windowed.weir.fst --split-method statistic-file
 '''
 
 import os

diff --git a/setup.py b/setup.py
@@ -19,7 +19,7 @@
                'pgpipe/vcf_phase.py',
                'pgpipe/four_gamete.py',
                'pgpipe/stat_sampler.py',
-               'pgpipe/bed_tasks.py',
+               'pgpipe/bed_utilities.py',
                'pgpipe/informative_loci_filter.py',
                'pgpipe/convert.py',
                'pgpipe/vcf_to_ima.py',