Skip to content
Snippets Groups Projects

updated frag files and test

Closed Tanya Santosh Nandan requested to merge tanya5 into main
6 files
+ 105
36
Compare changes
  • Side-by-side
  • Inline
Files
6
+ 3
3
@@ -7,7 +7,7 @@ import numpy as np
@@ -7,7 +7,7 @@ import numpy as np
import pandas as pd # type: ignore
import pandas as pd # type: ignore
from term_frag_sel.fragmentation import fragmentation
from term_frag_sel.fragmentation import fragmentation
from term_frag_sel.utils import check_positive, check_prob
from term_frag_sel.utils import check_positive, check_prob
@@ -97,11 +97,11 @@ def parse_arguments() -> argparse.Namespace:
@@ -97,11 +97,11 @@ def parse_arguments() -> argparse.Namespace:
help="output file path")
help="output file path")
parser.add_argument('--mean', required=False, default=300,
parser.add_argument('--mean', required=False, default=300,
type=check_positive,
type=check_positive,
help="Mean fragment length (default: 10)")
help="Mean fragment length (default: 300)")
parser.add_argument('--std', required=False, default=60,
parser.add_argument('--std', required=False, default=60,
type=check_positive,
type=check_positive,
help="Standard deviation fragment length \
help="Standard deviation fragment length \
(defafult: 1)")
(defafult: 60)")
parser.add_argument('-a', '--A_prob', required=False, default=0.22,
parser.add_argument('-a', '--A_prob', required=False, default=0.22,
type=check_prob,
type=check_prob,
help="Probability cut happens after nucleotide A")
help="Probability cut happens after nucleotide A")
Loading