Update to fpa 0.4

MANIFEST.in

 include *.md
 include knot/*.rules
 include knot/config.yaml
+recursive-include knot/analysis *
+recursive-include knot/extremity_search *
+recursive-include knot/filter_tig *
+recursive-include knot/path_search *
+recursive-include knot/sg_generation *
 recursive-include knot/analysis/template *

conda_env.yml

@@ -6,7 +6,7 @@ channels:
 dependencies:
  - python=3
  - yacrd
- - fpa
+ - fpa=0.4
  - snakemake
  - pip:
    - "git+https://gitlab.inria.fr/pmarijon/knot.git"

knot/AAG.rules

@@ -10,7 +10,7 @@ rule build_AGG:
         "{prefix}_AAG.csv"
 
     shell:
-        "python -m knot.path_search {input.search} {output} {input.ovl_graph} {input.read2asm} {input.asm_graph} {input.tig2tig} --search-mode " + config["search_mode"]
+        "knot.path_search {input.search} {output} {input.ovl_graph} {input.read2asm} {input.asm_graph} {input.tig2tig} --search-mode " + config["search_mode"]
 
 rule filter_contigs:
     input:
@@ -20,7 +20,7 @@ rule filter_contigs:
         "{prefix}_filtred.fasta"
     
     shell:
-        "python -m knot.filter_tig {input} {output} -t " + str(config['min_contig_length'])
+        "knot.filter_tig {input} {output} -t " + str(config['min_contig_length'])
 
 rule map_contigs2contigs:
     input:
@@ -68,6 +68,6 @@ rule find_extremity:
         "{prefix}ext_search.csv"
 
     shell:
-        "python -m knot.extremity_search {input.read2asm} {input.read2read} {output}"
+        "knot.extremity_search {input.read2asm} {input.read2read} {output}"
 
 

knot/SG.rules

@@ -36,4 +36,4 @@ rule overlap2overlapgraph:
         "{path}.gfa"
     
     shell:
-        "fpa -o gfa1 -s -c -i {output} {input}"
+        "fpa -o gfa1 -s -c -i {input} {output}"

knot/filter_tig/__main__.py

@@ -5,7 +5,7 @@ import argparse
 
 from Bio import SeqIO
 
-def main(args):
+def main(args=None):
 
     if args is None:
         args = sys.argv[1:]

setup.py

@@ -41,6 +41,7 @@ setup(
         'console_scripts': [
             'knot = knot.__main__:main',
             'knot.path_search = knot.path_search.__main__:main',
+            'knot.filter_tig = knot.filter_tig.__main__:main',
             'knot.sg_generation = knot.sg_generation.__main__:main',
             'knot.extremity_search = knot.extremity_search.__main__:main',
             'knot.analysis.classifications = knot.analysis.classifications:main',