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added progress printing for phmmer executions #3

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Aug 26, 2024
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added progress printing for phmmer executions #3

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9 changes: 6 additions & 3 deletions orthohmm/externals.py
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Original file line number Diff line number Diff line change
@@ -1,7 +1,9 @@
import math
import multiprocessing
from multiprocessing.synchronize import Lock
from multiprocessing.sharedctypes import Synchronized
import subprocess
import sys
from typing import List


Expand All @@ -21,11 +23,12 @@ def update_progress(
lock: Lock,
completed_tasks: Synchronized,
total_tasks: int,
) -> None:
) -> None:
with lock:
completed_tasks.value += 1
progress = (completed_tasks.value / total_tasks) * 100
print(f" {progress:.1f}% complete")
sys.stdout.write(f"\r {math.floor(progress)}% complete")
sys.stdout.flush()


def execute_phmmer_search(
Expand All @@ -37,7 +40,7 @@ def execute_phmmer_search(
pool = multiprocessing.Pool(processes=cpu)

# Create a counter and lock for tracking progress
completed_tasks = multiprocessing.Value('i', 0)
completed_tasks = multiprocessing.Value("i", 0)
total_tasks = len(phmmer_cmds)
lock = multiprocessing.Lock()

Expand Down
6 changes: 3 additions & 3 deletions orthohmm/orthohmm.py
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Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,7 @@
import os
import sys
import time
from typing import Union
from typing import Union, List

from .args_processing import process_args
from .externals import (
Expand Down Expand Up @@ -52,7 +52,7 @@ def execute(

# get FASTA files to identify orthologs from
extensions = (".fa", ".faa", ".fas", ".fasta")
files = [file for file in os.listdir(fasta_directory) if os.path.splitext(file)[1].lower() in extensions]
files: List[str] = [file for file in os.listdir(fasta_directory) if os.path.splitext(file)[1].lower() in extensions]

if start != StartStep.search_res:
phmmer_cmds = generate_phmmer_cmds(
Expand Down Expand Up @@ -102,7 +102,7 @@ def execute(
phmmer_cmds,
cpu,
)
print(" Completed!\n")
print("\r Completed! \n")
current_step += 1

print(f"Step {current_step}/{total_steps}: Determining edge thresholds")
Expand Down
8 changes: 4 additions & 4 deletions ...is_elegans.WBcel235.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt
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Expand Up @@ -7,9 +7,9 @@ WBGene00013724.1 - WBGene00013724.1 - 9.1e-152 489.8
# Program: phmmer
# Version: 3.3.1 (Jul 2020)
# Pipeline mode: SEARCH
# Query file: tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa
# Target file: tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa
# Option settings: phmmer --tblout tests/samples//orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa
# Query file: ./tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa
# Target file: ./tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa
# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa ./tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa
# Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli
# Date: Mon Aug 26 08:38:17 2024
# Date: Mon Aug 26 16:30:23 2024
# [ok]
8 changes: 4 additions & 4 deletions ...abditis_elegans.WBcel235.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt
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Expand Up @@ -7,9 +7,9 @@ ENSCAFP00000048558 - WBGene00013724.1 - 4.3e-60 190.9
# Program: phmmer
# Version: 3.3.1 (Jul 2020)
# Pipeline mode: SEARCH
# Query file: tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa
# Target file: tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa
# Option settings: phmmer --tblout tests/samples//orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa
# Query file: ./tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa
# Target file: ./tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa
# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa ./tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa
# Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli
# Date: Mon Aug 26 08:38:17 2024
# Date: Mon Aug 26 16:30:23 2024
# [ok]
8 changes: 4 additions & 4 deletions ...enorhabditis_elegans.WBcel235.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt
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Expand Up @@ -7,9 +7,9 @@ ENSCINP00000010262 - WBGene00013724.1 - 4.1e-65 207.3
# Program: phmmer
# Version: 3.3.1 (Jul 2020)
# Pipeline mode: SEARCH
# Query file: tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa
# Target file: tests/samples//Ciona_intestinalis.KH.pep.all.fa
# Option settings: phmmer --tblout tests/samples//orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa tests/samples//Ciona_intestinalis.KH.pep.all.fa
# Query file: ./tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa
# Target file: ./tests/samples//Ciona_intestinalis.KH.pep.all.fa
# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa ./tests/samples//Ciona_intestinalis.KH.pep.all.fa
# Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli
# Date: Mon Aug 26 08:38:18 2024
# Date: Mon Aug 26 16:30:23 2024
# [ok]
8 changes: 4 additions & 4 deletions .../Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt
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Expand Up @@ -10,9 +10,9 @@ ENSDARP00000149121 - WBGene00013724.1 - 4e-50 159.3
# Program: phmmer
# Version: 3.3.1 (Jul 2020)
# Pipeline mode: SEARCH
# Query file: tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa
# Target file: tests/samples//Danio_rerio.GRCz11.pep.all.fa
# Option settings: phmmer --tblout tests/samples//orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa tests/samples//Danio_rerio.GRCz11.pep.all.fa
# Query file: ./tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa
# Target file: ./tests/samples//Danio_rerio.GRCz11.pep.all.fa
# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Danio_rerio.GRCz11.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa ./tests/samples//Danio_rerio.GRCz11.pep.all.fa
# Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli
# Date: Mon Aug 26 08:38:17 2024
# Date: Mon Aug 26 16:30:23 2024
# [ok]
8 changes: 4 additions & 4 deletions ...aenorhabditis_elegans.WBcel235.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt
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Expand Up @@ -7,9 +7,9 @@ ENSGALP00000028084 - WBGene00013724.1 - 1.8e-65 208.5
# Program: phmmer
# Version: 3.3.1 (Jul 2020)
# Pipeline mode: SEARCH
# Query file: tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa
# Target file: tests/samples//Gallus_gallus.GRCg6a.pep.all.fa
# Option settings: phmmer --tblout tests/samples//orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa tests/samples//Gallus_gallus.GRCg6a.pep.all.fa
# Query file: ./tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa
# Target file: ./tests/samples//Gallus_gallus.GRCg6a.pep.all.fa
# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Gallus_gallus.GRCg6a.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa ./tests/samples//Gallus_gallus.GRCg6a.pep.all.fa
# Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli
# Date: Mon Aug 26 08:38:18 2024
# Date: Mon Aug 26 16:30:23 2024
# [ok]
8 changes: 4 additions & 4 deletions ...Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt
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Expand Up @@ -7,9 +7,9 @@ ENSP00000340836 - WBGene00013724.1 - 4.7e-68 216.9
# Program: phmmer
# Version: 3.3.1 (Jul 2020)
# Pipeline mode: SEARCH
# Query file: tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa
# Target file: tests/samples//Homo_sapiens.GRCh38.pep.all.fa
# Option settings: phmmer --tblout tests/samples//orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa tests/samples//Homo_sapiens.GRCh38.pep.all.fa
# Query file: ./tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa
# Target file: ./tests/samples//Homo_sapiens.GRCh38.pep.all.fa
# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Homo_sapiens.GRCh38.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa ./tests/samples//Homo_sapiens.GRCh38.pep.all.fa
# Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli
# Date: Mon Aug 26 08:38:17 2024
# Date: Mon Aug 26 16:30:23 2024
# [ok]
8 changes: 4 additions & 4 deletions ...tis_elegans.WBcel235.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt
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Expand Up @@ -7,9 +7,9 @@ ENSMODP00000002384 - WBGene00013724.1 - 1.8e-68 218.2
# Program: phmmer
# Version: 3.3.1 (Jul 2020)
# Pipeline mode: SEARCH
# Query file: tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa
# Target file: tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa
# Option settings: phmmer --tblout tests/samples//orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa
# Query file: ./tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa
# Target file: ./tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa
# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Monodelphis_domestica.ASM229v1.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa ./tests/samples//Monodelphis_domestica.ASM229v1.pep.all.fa
# Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli
# Date: Mon Aug 26 08:38:18 2024
# Date: Mon Aug 26 16:30:23 2024
# [ok]
8 changes: 4 additions & 4 deletions ...Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt
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Expand Up @@ -7,9 +7,9 @@ ENSMUSP00000025631 - WBGene00013724.1 - 3.7e-67 214.7
# Program: phmmer
# Version: 3.3.1 (Jul 2020)
# Pipeline mode: SEARCH
# Query file: tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa
# Target file: tests/samples//Mus_musculus.GRCm38.pep.all.fa
# Option settings: phmmer --tblout tests/samples//orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa tests/samples//Mus_musculus.GRCm38.pep.all.fa
# Query file: ./tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa
# Target file: ./tests/samples//Mus_musculus.GRCm38.pep.all.fa
# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Mus_musculus.GRCm38.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa ./tests/samples//Mus_musculus.GRCm38.pep.all.fa
# Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli
# Date: Mon Aug 26 08:38:17 2024
# Date: Mon Aug 26 16:30:23 2024
# [ok]
8 changes: 4 additions & 4 deletions ...bditis_elegans.WBcel235.pep.all.fa_2_Pan_troglodytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt
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Expand Up @@ -7,9 +7,9 @@ ENSPTRP00000079818 - WBGene00013724.1 - 4.7e-68 216.9
# Program: phmmer
# Version: 3.3.1 (Jul 2020)
# Pipeline mode: SEARCH
# Query file: tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa
# Target file: tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa
# Option settings: phmmer --tblout tests/samples//orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Pan_troglodytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa
# Query file: ./tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa
# Target file: ./tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa
# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Pan_troglodytes.Pan_tro_3.0.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa ./tests/samples//Pan_troglodytes.Pan_tro_3.0.pep.all.fa
# Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli
# Date: Mon Aug 26 08:38:17 2024
# Date: Mon Aug 26 16:30:23 2024
# [ok]
8 changes: 4 additions & 4 deletions ...abditis_elegans.WBcel235.pep.all.fa_2_Rattus_norvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt
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Expand Up @@ -8,9 +8,9 @@ ENSRNOP00000016871 - WBGene00013724.1 - 4e-68 217.5
# Program: phmmer
# Version: 3.3.1 (Jul 2020)
# Pipeline mode: SEARCH
# Query file: tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa
# Target file: tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa
# Option settings: phmmer --tblout tests/samples//orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Rattus_norvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa
# Query file: ./tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa
# Target file: ./tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa
# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Rattus_norvegicus.Rnor_6.0.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa ./tests/samples//Rattus_norvegicus.Rnor_6.0.pep.all.fa
# Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli
# Date: Mon Aug 26 08:38:18 2024
# Date: Mon Aug 26 16:30:23 2024
# [ok]
8 changes: 4 additions & 4 deletions ..._elegans.WBcel235.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt
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Expand Up @@ -7,9 +7,9 @@ ENSTNIP00000019800 - WBGene00013724.1 - 2.2e-65 208.2
# Program: phmmer
# Version: 3.3.1 (Jul 2020)
# Pipeline mode: SEARCH
# Query file: tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa
# Target file: tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa
# Option settings: phmmer --tblout tests/samples//orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa
# Query file: ./tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa
# Target file: ./tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa
# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Caenorhabditis_elegans.WBcel235.pep.all.fa_2_Tetraodon_nigroviridis.TETRAODON8.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa ./tests/samples//Tetraodon_nigroviridis.TETRAODON8.pep.all.fa
# Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli
# Date: Mon Aug 26 08:38:17 2024
# Date: Mon Aug 26 16:30:23 2024
# [ok]
8 changes: 4 additions & 4 deletions ...amiliaris.CanFam3.1.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt
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Expand Up @@ -7,9 +7,9 @@ WBGene00013724.1 - ENSCAFP00000048558 - 1.3e-60 192.3
# Program: phmmer
# Version: 3.3.1 (Jul 2020)
# Pipeline mode: SEARCH
# Query file: tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa
# Target file: tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa
# Option settings: phmmer --tblout tests/samples//orthohmm_working_res/Canis_familiaris.CanFam3.1.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa
# Query file: ./tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa
# Target file: ./tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa
# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Canis_familiaris.CanFam3.1.pep.all.fa_2_Caenorhabditis_elegans.WBcel235.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa ./tests/samples//Caenorhabditis_elegans.WBcel235.pep.all.fa
# Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli
# Date: Mon Aug 26 08:38:06 2024
# Date: Mon Aug 26 16:30:21 2024
# [ok]
8 changes: 4 additions & 4 deletions ...nis_familiaris.CanFam3.1.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt
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Expand Up @@ -8,9 +8,9 @@ ENSCAFP00000017344 - ENSCAFP00000017344 - 0 5307.6
# Program: phmmer
# Version: 3.3.1 (Jul 2020)
# Pipeline mode: SEARCH
# Query file: tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa
# Target file: tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa
# Option settings: phmmer --tblout tests/samples//orthohmm_working_res/Canis_familiaris.CanFam3.1.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa
# Query file: ./tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa
# Target file: ./tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa
# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Canis_familiaris.CanFam3.1.pep.all.fa_2_Canis_familiaris.CanFam3.1.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa ./tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa
# Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli
# Date: Mon Aug 26 08:38:04 2024
# Date: Mon Aug 26 16:30:20 2024
# [ok]
8 changes: 4 additions & 4 deletions ...es/Canis_familiaris.CanFam3.1.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -8,9 +8,9 @@ ENSCINP00000024362 - ENSCAFP00000017344 - 1.3e-291 958.0
# Program: phmmer
# Version: 3.3.1 (Jul 2020)
# Pipeline mode: SEARCH
# Query file: tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa
# Target file: tests/samples//Ciona_intestinalis.KH.pep.all.fa
# Option settings: phmmer --tblout tests/samples//orthohmm_working_res/Canis_familiaris.CanFam3.1.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa tests/samples//Ciona_intestinalis.KH.pep.all.fa
# Query file: ./tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa
# Target file: ./tests/samples//Ciona_intestinalis.KH.pep.all.fa
# Option settings: phmmer --tblout ./tests/samples//orthohmm_working_res/Canis_familiaris.CanFam3.1.pep.all.fa_2_Ciona_intestinalis.KH.pep.all.fa.phmmerout.txt --noali --notextw --mx BLOSUM62 ./tests/samples//Canis_familiaris.CanFam3.1.pep.all.fa ./tests/samples//Ciona_intestinalis.KH.pep.all.fa
# Current dir: /Users/jacoblsteenwyk/Desktop/BERKELEY/ORTHOHMM/orthohmm/orthohmm_cli
# Date: Mon Aug 26 08:38:06 2024
# Date: Mon Aug 26 16:30:21 2024
# [ok]
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