clipkit: clipkit_repo/tests/integration/test_gappy

annotate clipkit_repo/tests/integration/test_gappy_mode.py @ 0:49b058e85902 draft

"planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"

author	padge
date	Fri, 25 Mar 2022 13:04:31 +0000
parents
children

rev	line source
0 49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	1 import pytest
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	2 from pathlib import Path
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	3
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	4 from clipkit.clipkit import execute
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	5 from clipkit.files import FileFormat
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	6 from clipkit.modes import TrimmingMode
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	7
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	8 here = Path(__file__)
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	9
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	10
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	11 @pytest.mark.integration
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	12 class TestGappyMode(object):
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	13 def test_simple_no_change(self):
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	14 """
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	15 test gappy where no changes are expected in the resulting
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	16 output alignment.
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	17 usage: clipkit simple.fa
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	18 """
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	19 input_file = f"{here.parent}/samples/simple.fa"
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	20 output_file = "output/simpla.fa.clipkit"
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	21 kwargs = dict(
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	22 input_file=input_file,
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	23 output_file=output_file,
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	24 input_file_format='fasta',
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	25 output_file_format='fasta',
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	26 complement=False,
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	27 gaps=0.9,
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	28 mode=TrimmingMode.gappy,
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	29 use_log=False,
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	30 )
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	31 execute(**kwargs)
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	32
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	33 with open(input_file, "r") as expected:
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	34 expected_content = expected.read()
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	35
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	36 with open(output_file, "r") as out_file:
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	37 output_content = out_file.read()
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	38
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	39 assert expected_content == output_content
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	40
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	41 def test_simple_no_change_long_description(self):
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	42 """
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	43 test gappy where no changes are expected in the resulting
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	44 output alignment.
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	45 usage: clipkit simple.fa
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	46 """
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	47 input_file = f"{here.parent}/samples/simple_long_description.fa"
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	48 output_file = "output/simple_long_description.fa.clipkit"
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	49 kwargs = dict(
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	50 input_file=input_file,
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	51 output_file=output_file,
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	52 input_file_format='fasta',
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	53 output_file_format='fasta',
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	54 complement=False,
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	55 gaps=0.9,
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	56 mode=TrimmingMode.gappy,
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	57 use_log=False,
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	58 )
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	59 execute(**kwargs)
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	60
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	61 with open(input_file, "r") as expected:
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	62 expected_content = expected.read()
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	63
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	64 with open(output_file, "r") as out_file:
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	65 output_content = out_file.read()
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	66
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	67 assert expected_content == output_content
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	68
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	69 def test_12_YIL115C_Anc_2_253_codon_aln(self):
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	70 """
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	71 test gappy with codon alignment of yeast sequences
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	72 usage: clipkit 12_YIL115C_Anc_2.253_codon_aln.fasta
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	73 """
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	74 input_file = f"{here.parent}/samples/12_YIL115C_Anc_2.253_codon_aln.fasta"
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	75 output_file = "output/12_YIL115C_Anc_2.253_codon_aln.fasta.clipkit"
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	76
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	77 kwargs = dict(
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	78 input_file=input_file,
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	79 output_file=output_file,
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	80 input_file_format='fasta',
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	81 output_file_format='fasta',
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	82 complement=False,
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	83 gaps=0.9,
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	84 mode=TrimmingMode.gappy,
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	85 use_log=False,
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	86 )
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	87 execute(**kwargs)
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	88
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	89 with open(
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	90 f"{here.parent}/expected/12_YIL115C_Anc_2.253_codon_aln.fasta_gappy", "r"
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	91 ) as expected:
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	92 expected_content = expected.read()
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	93
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	94 with open(output_file, "r") as out_file:
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	95 output_content = out_file.read()
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	96
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	97 assert expected_content == output_content
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	98
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	99 def test_12_YIL115C_Anc_2_253_aa_aln(self):
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	100 """
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	101 test gappy with amino acid alignment of yeast sequences
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	102 usage: clipkit 12_YIL115C_Anc_2.253_aa_aln.fasta
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	103 """
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	104 input_file = f"{here.parent}/samples/12_YIL115C_Anc_2.253_aa_aln.fasta"
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	105 output_file = "output/12_YIL115C_Anc_2.253_aa_aln.fasta.clipkit"
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	106
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	107 kwargs = dict(
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	108 input_file=input_file,
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	109 output_file=output_file,
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	110 input_file_format='fasta',
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	111 output_file_format='fasta',
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	112 complement=False,
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	113 gaps=0.9,
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	114 mode=TrimmingMode.gappy,
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	115 use_log=False,
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	116 )
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	117 execute(**kwargs)
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	118
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	119 with open(
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	120 f"{here.parent}/expected/12_YIL115C_Anc_2.253_aa_aln.fasta_gappy", "r"
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	121 ) as expected:
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	122 expected_content = expected.read()
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	123
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	124 with open(output_file, "r") as out_file:
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	125 output_content = out_file.read()
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	126
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	127 assert expected_content == output_content
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	128
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	129 def test_24_ENSG00000163519_aa_aln(self):
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	130 """
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	131 test gappy with amino acid alignment of mammalian sequences
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	132 usage: clipkit 24_ENSG00000163519_aa_aln.fasta
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	133 """
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	134 input_file = f"{here.parent}/samples/24_ENSG00000163519_aa_aln.fasta"
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	135 output_file = "output/24_ENSG00000163519_aa_aln.fasta.clipkit"
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	136
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	137 kwargs = dict(
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	138 input_file=input_file,
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	139 output_file=output_file,
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	140 input_file_format='fasta',
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	141 output_file_format='fasta',
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	142 complement=False,
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	143 gaps=0.9,
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	144 mode=TrimmingMode.gappy,
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	145 use_log=False,
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	146 )
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	147 execute(**kwargs)
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	148
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	149 with open(
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	150 f"{here.parent}/expected/24_ENSG00000163519_aa_aln.fasta_gappy", "r"
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	151 ) as expected:
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	152 expected_content = expected.read()
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	153
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	154 with open(output_file, "r") as out_file:
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	155 output_content = out_file.read()
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	156
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	157 assert expected_content == output_content
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	158
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	159 def test_24_ENSG00000163519_codon_aln(self):
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	160 """
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	161 test gappy with codon alignment of mammalian sequences
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	162 usage: clipkit 24_ENSG00000163519_codon_aln.fasta
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	163 """
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	164 input_file = f"{here.parent}/samples/24_ENSG00000163519_codon_aln.fasta"
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	165 output_file = "output/24_ENSG00000163519_codon_aln.fasta.clipkit"
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	166
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	167 kwargs = dict(
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	168 input_file=input_file,
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	169 output_file=output_file,
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	170 input_file_format='fasta',
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	171 output_file_format='fasta',
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	172 complement=False,
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	173 gaps=0.9,
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	174 mode=TrimmingMode.gappy,
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	175 use_log=False,
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	176 )
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	177 execute(**kwargs)
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	178
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	179 with open(
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	180 f"{here.parent}/expected/24_ENSG00000163519_codon_aln.fasta_gappy", "r"
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	181 ) as expected:
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	182 expected_content = expected.read()
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	183
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	184 with open(output_file, "r") as out_file:
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	185 output_content = out_file.read()
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	186
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	187 assert expected_content == output_content
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	188
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	189 def test_EOG091N44M8_aa(self):
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	190 """
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	191 test gappy with amino acid alignment of Penicillium sequences
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	192 usage: clipkit EOG091N44M8_aa.fa
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	193 """
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	194 input_file = f"{here.parent}/samples/EOG091N44M8_aa.fa"
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	195 output_file = "output/EOG091N44M8_aa.fa.clipkit"
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	196
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	197 kwargs = dict(
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	198 input_file=input_file,
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	199 output_file=output_file,
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	200 input_file_format='fasta',
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	201 output_file_format='fasta',
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	202 complement=False,
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	203 gaps=0.9,
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	204 mode=TrimmingMode.gappy,
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	205 use_log=False,
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	206 )
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	207 execute(**kwargs)
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	208
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	209 with open(f"{here.parent}/expected/EOG091N44M8_aa.fa_gappy", "r") as expected:
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	210 expected_content = expected.read()
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	211
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	212 with open(output_file, "r") as out_file:
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	213 output_content = out_file.read()
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	214
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	215 assert expected_content == output_content
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	216
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	217 def test_EOG091N44M8_nt(self):
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	218 """
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	219 test gappy with nucleotide alignment of Penicillium sequences
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	220 usage: clipkit EOG091N44M8_nt.fa
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	221 """
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	222 input_file = f"{here.parent}/samples/EOG091N44M8_nt.fa"
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	223 output_file = "output/EOG091N44M8_nt.fa.clipkit"
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	224
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	225 kwargs = dict(
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	226 input_file=input_file,
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	227 output_file=output_file,
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	228 input_file_format='fasta',
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	229 output_file_format='fasta',
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	230 complement=False,
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	231 gaps=0.9,
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	232 mode=TrimmingMode.gappy,
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	233 use_log=False,
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	234 )
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	235 execute(**kwargs)
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	236
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	237 with open(f"{here.parent}/expected/EOG091N44M8_nt.fa_gappy", "r") as expected:
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	238 expected_content = expected.read()
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	239
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	240 with open(output_file, "r") as out_file:
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	241 output_content = out_file.read()
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	242
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	243 assert expected_content == output_content
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	244
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	245 @pytest.mark.slow
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	246 def test_EOG092C4VOX_aa(self):
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	247 """
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	248 test gappy with amino alignment of fungal sequences
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	249 usage: clipkit EOG092C4VOX_aa_aln.fasta
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	250 """
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	251 input_file = f"{here.parent}/samples/EOG092C4VOX_aa_aln.fasta"
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	252 output_file = "output/EOG092C4VOX_aa_aln.fasta.clipkit"
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	253
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	254 kwargs = dict(
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	255 input_file=input_file,
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	256 output_file=output_file,
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	257 input_file_format='fasta',
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	258 output_file_format='fasta',
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	259 complement=False,
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	260 gaps=0.9,
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	261 mode=TrimmingMode.gappy,
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	262 use_log=False,
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	263 )
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	264 execute(**kwargs)
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	265
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	266 with open(
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	267 f"{here.parent}/expected/EOG092C4VOX_aa_aln.fasta_gappy", "r"
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	268 ) as expected:
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	269 expected_content = expected.read()
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	270
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	271 with open(output_file, "r") as out_file:
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	272 output_content = out_file.read()
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	273
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	274 assert expected_content == output_content
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	275
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	276
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	277 @pytest.mark.integration
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	278 class TestGappyModeCustomGapsParameter(object):
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	279 def test_simple(self):
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	280 """
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	281 test gappy with a custom gaps parameter
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	282 usage: clipkit simple.fa -g 0.2
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	283 """
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	284 input_file = f"{here.parent}/samples/simple.fa"
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	285 output_file = "output/simpla.fa.clipkit"
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	286
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	287 kwargs = dict(
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	288 input_file=input_file,
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	289 output_file=output_file,
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	290 input_file_format='fasta',
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	291 output_file_format='fasta',
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	292 complement=False,
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	293 gaps=0.2,
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	294 mode=TrimmingMode.gappy,
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	295 use_log=False,
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	296 )
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	297 execute(**kwargs)
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	298
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	299 with open(
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	300 f"{here.parent}/expected/simple.fa_gappy_gaps_set_to_0.2", "r"
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	301 ) as expected:
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	302 expected_content = expected.read()
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	303
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	304 with open(output_file, "r") as out_file:
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	305 output_content = out_file.read()
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	306
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	307 assert expected_content == output_content
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	308
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	309 def test_12_YIL115C_Anc_2_253_codon_aln(self):
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	310 """
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	311 test gappy with codon alignment of yeast sequences
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	312 usage: clipkit 12_YIL115C_Anc_2.253_codon_aln.fasta -g 0.3
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	313 """
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	314 input_file = f"{here.parent}/samples/12_YIL115C_Anc_2.253_codon_aln.fasta"
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	315 output_file = "output/12_YIL115C_Anc_2.253_codon_aln.fasta.clipkit"
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	316
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	317 kwargs = dict(
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	318 input_file=input_file,
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	319 output_file=output_file,
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	320 input_file_format='fasta',
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	321 output_file_format='fasta',
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	322 complement=False,
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	323 gaps=0.3,
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	324 mode=TrimmingMode.gappy,
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	325 use_log=False,
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	326 )
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	327 execute(**kwargs)
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	328
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	329 with open(
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	330 f"{here.parent}/expected/12_YIL115C_Anc_2.253_codon_aln.fasta_gappy_custom_gaps",
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	331 "r",
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	332 ) as expected:
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	333 expected_content = expected.read()
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	334
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	335 with open(output_file, "r") as out_file:
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	336 output_content = out_file.read()
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	337
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	338 assert expected_content == output_content
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	339
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	340 def test_24_ENSG00000163519_codon_aln(self):
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	341 """
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	342 test gappy with codon alignment of mammalian sequences
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	343 usage: clipkit 24_ENSG00000163519_codon_aln.fasta -g .4
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	344 """
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	345 input_file = f"{here.parent}/samples/24_ENSG00000163519_codon_aln.fasta"
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	346 output_file = "output/24_ENSG00000163519_codon_aln.fasta.clipkit"
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	347
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	348 kwargs = dict(
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	349 input_file=input_file,
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	350 output_file=output_file,
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	351 input_file_format='fasta',
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	352 output_file_format='fasta',
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	353 complement=False,
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	354 gaps=0.4,
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	355 mode=TrimmingMode.gappy,
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	356 use_log=False,
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	357 )
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	358 execute(**kwargs)
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	359
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	360 with open(
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	361 f"{here.parent}/expected/24_ENSG00000163519_codon_aln.fasta_gappy_custom_gaps",
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	362 "r",
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	363 ) as expected:
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	364 expected_content = expected.read()
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	365
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	366 with open(output_file, "r") as out_file:
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	367 output_content = out_file.read()
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	368
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	369 assert expected_content == output_content
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	370
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	371 def test_EOG091N44M8_nt(self):
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	372 """
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	373 test gappy with nucleotide alignment of Penicillium sequences
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	374 usage: clipkit EOG091N44M8_nt.fa -g .1
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	375 """
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	376 input_file = f"{here.parent}/samples/EOG091N44M8_nt.fa"
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	377 output_file = "output/EOG091N44M8_nt.fa.clipkit"
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	378
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	379 kwargs = dict(
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	380 input_file=input_file,
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	381 output_file=output_file,
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	382 input_file_format='fasta',
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	383 output_file_format='fasta',
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	384 complement=False,
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	385 gaps=0.1,
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	386 mode=TrimmingMode.gappy,
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	387 use_log=False,
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	388 )
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	389 execute(**kwargs)
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	390
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	391 with open(
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	392 f"{here.parent}/expected/EOG091N44M8_nt.fa_gappy_custom_gaps", "r"
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	393 ) as expected:
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	394 expected_content = expected.read()
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	395
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	396 with open(output_file, "r") as out_file:
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	397 output_content = out_file.read()
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	398
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	399 assert expected_content == output_content
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	400
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	401 @pytest.mark.slow
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	402 def test_EOG092C0CZK_aa(self):
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	403 """
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	404 test gappy with amino alignment of fungal sequences
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	405 usage: clipkit EOG092C0CZK_aa_aln.fasta -g .5
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	406 """
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	407 input_file = f"{here.parent}/samples/EOG092C0CZK_aa_aln.fasta"
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	408 output_file = "output/EOG092C0CZK_aa_aln.fasta.clipkit"
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	409
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	410 kwargs = dict(
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	411 input_file=input_file,
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	412 output_file=output_file,
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	413 input_file_format='fasta',
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	414 output_file_format='fasta',
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	415 complement=False,
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	416 gaps=0.5,
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	417 mode=TrimmingMode.gappy,
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	418 use_log=False,
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	419 )
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	420 execute(**kwargs)
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	421
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	422 with open(
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	423 f"{here.parent}/expected/EOG092C0CZK_aa_aln.fasta_gappy_custom_gaps", "r"
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	424 ) as expected:
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	425 expected_content = expected.read()
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	426
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	427 with open(output_file, "r") as out_file:
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	428 output_content = out_file.read()
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	429
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	430 assert expected_content == output_content
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	431
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	432 @pytest.mark.slow
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	433 def test_EOG092C4VOX_aa(self):
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	434 """
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	435 test gappy with amino alignment of fungal sequences
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	436 usage: clipkit EOG092C4VOX_aa_aln.fasta -g .25
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	437 """
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	438 input_file = f"{here.parent}/samples/EOG092C4VOX_aa_aln.fasta"
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	439 output_file = "output/EOG092C4VOX_aa_aln.fasta.clipkit"
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	440
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	441 kwargs = dict(
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	442 input_file=input_file,
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	443 output_file=output_file,
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	444 input_file_format='fasta',
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	445 output_file_format='fasta',
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	446 complement=False,
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	447 gaps=0.25,
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	448 mode=TrimmingMode.gappy,
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	449 use_log=False,
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	450 )
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	451 execute(**kwargs)
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	452
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	453 with open(
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	454 f"{here.parent}/expected/EOG092C4VOX_aa_aln.fasta_gappy_custom_gaps", "r"
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	455 ) as expected:
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	456 expected_content = expected.read()
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	457
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	458 with open(output_file, "r") as out_file:
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	459 output_content = out_file.read()
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	460
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty" padge parents: diff changeset	461 assert expected_content == output_content

Mercurial > repos > padge > clipkit

annotate clipkit_repo/tests/integration/test_gappy_mode.py @ 0:49b058e85902 draft