Commit 21763641 authored by MARIJON Pierre's avatar MARIJON Pierre

Update to fpa 0.4

parent 2ec94158
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 *
......@@ -6,7 +6,7 @@ channels:
dependencies:
- python=3
- yacrd
- fpa
- fpa=0.4
- snakemake
- pip:
- "git+https://gitlab.inria.fr/pmarijon/knot.git"
......@@ -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}"
......@@ -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}"
......@@ -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:]
......
......@@ -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',
......
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