Merge pull request #266 from karel-brinda/docs_make_format

Docs make format

.style.yapf

@@ -1,3 +1,4 @@
 [style]
+BASED_ON_STYLE = google
 COLUMN_LIMIT=120
 

Makefile

@@ -1,4 +1,4 @@
-.PHONY: all test help clean cleanall cluster download download_asms download_cobs match map format report config conda
+.PHONY: all test help clean cleanall cluster download download_asms download_cobs match map checkformat report config conda
 
 SHELL=/usr/bin/env bash -eo pipefail
 DATETIME=$(shell date -u +"%Y_%m_%dT%H_%M_%S")
@@ -106,9 +106,9 @@ report: ## Generate Snakemake report
 
 
 
-##########
-## Misc ##
-##########
+#############
+## Cluster ##
+#############
 cluster_slurm: ## Submit to a SLURM cluster
 	sbatch \
         -c 10 \
@@ -124,6 +124,13 @@ cluster_lsf: ## Submit to LSF cluster
 	scripts/check_if_config_is_ok_for_cluster_run.py
 	scripts/submit_lsf.sh
 
+####################
+## For developers ##
+####################
 format: ## Reformat Python and Snakemake files
 	yapf -i */*.py
 	snakefmt Snakefile
+
+checkformat: ## Check source code format
+	snakefmt --check Snakefile
+	yapf --diff */*.py

README.md

@@ -243,6 +243,7 @@ Here's a list of all implemented commands (to be executed as `make {command}`):
 ####################
 # General commands #
 ####################
+
    all                Run everything (the default rule)
    test               Quick test using 3 batches
    help               Print help messages

scripts/batch_align.py

@@ -52,7 +52,8 @@ def readfq(fp):
                 if l[0] in '>@':  # fasta/q header line
                     last = l[:-1]  # save this line
                     break
-        if not last: break
+        if not last:
+            break
 
         ####
         # modified to include comments
@@ -72,7 +73,8 @@ def readfq(fp):
             seqs.append(l[:-1])
         if not last or last[0] != '+':  # this is a fasta record
             yield name, comment, ''.join(seqs), None  # yield a fasta record
-            if not last: break
+            if not last:
+                break
         else:  # this is a fastq record
             seq, leng, seqs = ''.join(seqs), 0, []
             for l in fp:  # read the quality

scripts/filter_queries.py

@@ -75,7 +75,8 @@ def readfq(fp):  # this is a generator function
                 if l[0] in '>@':  # fasta/q header line
                     last = l[:-1]  # save this line
                     break
-        if not last: break
+        if not last:
+            break
         name, seqs, last = last[1:].partition(" ")[0], [], None
         for l in fp:  # read the sequence
             if l[0] in '@+>':
@@ -84,7 +85,8 @@ def readfq(fp):  # this is a generator function
             seqs.append(l[:-1])
         if not last or last[0] != '+':  # this is a fasta record
             yield name, ''.join(seqs), None  # yield a fasta record
-            if not last: break
+            if not last:
+                break
         else:  # this is a fastq record
             seq, leng, seqs = ''.join(seqs), 0, []
             for l in fp:  # read the quality

scripts/filter_queries_2.py

@@ -98,7 +98,8 @@ def fa_iterator(fn):  # this is a generator function
                     if l[0] in '>@':  # fasta/q header line
                         last = l[:-1]  # save this line
                         break
-            if not last: break
+            if not last:
+                break
             name, seqs, last = last[1:].partition(" ")[0], [], None
             for l in fp:  # read the sequence
                 if l[0] in '@+>':
@@ -107,7 +108,8 @@ def fa_iterator(fn):  # this is a generator function
                 seqs.append(l[:-1])
             if not last or last[0] != '+':  # this is a fasta record
                 yield name, ''.join(seqs), None  # yield a fasta record
-                if not last: break
+                if not last:
+                    break
             else:  # this is a fastq record
                 seq, leng, seqs = ''.join(seqs), 0, []
                 for l in fp:  # read the quality

scripts/final_stats.py

@@ -17,7 +17,8 @@ def readfq(fp):
                 if l[0] in '>@':
                     last = l[:-1]
                     break
-        if not last: break
+        if not last:
+            break
         name, seqs, last = last[1:].partition(" ")[0], [], None
         for l in fp:
             if l[0] in '@+>':
@@ -26,7 +27,8 @@ def readfq(fp):
             seqs.append(l[:-1])
         if not last or last[0] != '+':
             yield name, ''.join(seqs), None
-            if not last: break
+            if not last:
+                break
         else:
             seq, leng, seqs = ''.join(seqs), 0, []
             for l in fp: