- Is there a way to convert a hmmer output to a pandas dataframe?
- I am also unsure how to load a hmmer tblout table into python via the Bio module.
I believe you can call a hmmer format with SeqIO.parse or SeqIO.search.The format of the table appears tab separated however it seems to be a collection of random spaces meaning if I remove the headers and # leaving only the table information there is not easy way to split the table using a tab separator.
A small example of a hmmer --tblout file is below:
# --- full sequence ---- --- best 1 domain ---- --- domain number estimation ----
# target name accession query name accession E-value score bias E-value score bias exp reg clu ov env dom rep inc description of target
#------------------- ---------- -------------------- ---------- --------- ------ ----- --------- ------ ----- --- --- --- --- --- --- --- --- ---------------------
3300000568@Draft_10015026@Draft_1001502652 - Bacteria_NODE_1_length_628658_cov_8.291329_24 - 7.1e-07 29.3 0.0 1.9e-05 24.6 0.0 2.0 1 1 1 2 2 2 2 -
7000000546@SRS019910_WUGC_scaffold_3948@SRS019910_WUGC_scaffold_3948_gene_2890 - Bacteria_NODE_1_length_628658_cov_8.291329_53 - 1.6e-07 31.7 0.0 0.00051 20.3 0.0 2.2 2 0 0 2 2 2 2 -
#
# Program: hmmscan
# Version: 3.1b2 (February 2015)
# Pipeline mode: SCAN
# Query file: ../Exponential_High_Complexity_Simulation.faa
# Target file: final_list.hmm
# Option settings: hmmscan --tblout Exponential_Earth.txt -E 1e-5 --cpu 8 final_list.hmm ../Exponential_High_Complexity_Simulation.faa
# Current dir: /Strong/home/glickmanc/Programs/EarthVirome
# Date: Mon Feb 24 10:47:51 2020
# [ok]