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thanhleviet/parse.txt

Last active March 12, 2018 03:16
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Parsing BLAST results
Raw
parse.txt
ClusterBlast scores for /home/wms_joe/PVCs/other_genomes/multigene/operon_genbank/PVCcif_ATCC43949.gbk
Table of genes, locations, strands and annotations of query cluster:
PAU_01961 8 457 + T4-like_virus_tail_tube_protein_gp19 no_locus_tag
PAU_01962 521 1618 + major_tail_sheath_protein no_locus_tag
PAU_01963 1799 3280 + tail_sheath_protein no_locus_tag
PAU_01964 3334 4533 + tail_sheath_protein no_locus_tag
PAU_01965 4547 5005 + T4-like_virus_tail_tube_protein_gp19 no_locus_tag
PAU_01966 5002 5181 + hypothetical_protein no_locus_tag
PAU_01967 5168 5851 + hypothetical_protein no_locus_tag
PAU_01968 5848 7449 + Rhs_element_Vgr_protein no_locus_tag
PAU_01969 7462 7905 + baseplate_wedge_subunit no_locus_tag
PAU_01970 7902 8318 + hypothetical_protein no_locus_tag
PAU_01971 8527 11253 + hypothetical_protein no_locus_tag
PAU_01972 11246 14197 + hypothetical_protein no_locus_tag
PAU_01973 14333 15184 + hypothetical_protein no_locus_tag
PAU_01974 15247 17145 + hypothetical_protein no_locus_tag
PAU_01975 17155 19227 + ATP-dependent_zinc_metalloprotease_FtsH no_locus_tag
PAU_01976 19252 20166 + hypothetical_protein no_locus_tag
PAU_01977 20327 21223 + hypothetical_protein no_locus_tag
PAU_01978 21308 22291 + hypothetical_protein no_locus_tag
PAU_01979 22788 23684 + hypothetical_protein no_locus_tag
PAU_01980 23656 24114 + hypothetical_protein no_locus_tag
Significant hits:
1. PAU_1 Photorhabdus asymbiotica strain ATCC43949.
2. PAB_1 Photorhabdus asymbiotica strain Beaudesert.
3. PAN_5 Photorhabdus asymbiotica strain Nepal.
4. PAT_0 Photorhabdus asymbiotica strain Thai.
Details:
>>
1. PAU_1
Source: Photorhabdus asymbiotica strain ATCC43949.
Number of proteins with BLAST hits to this cluster: 31
MultiGeneBlast score: 31.7
Cumulative Blast bit score: 64022
Table of genes, locations, strands and annotations of subject cluster:
PAU_01961 2233799 2234248 + T4-like_virus_tail_tube_protein_gp19 no_locus_tag
PAU_01962 2234312 2235409 + major_tail_sheath_protein no_locus_tag
PAU_01963 2235590 2237071 + tail_sheath_protein no_locus_tag
PAU_01964 2237125 2238324 + tail_sheath_protein no_locus_tag
PAU_01965 2238338 2238796 + T4-like_virus_tail_tube_protein_gp19 no_locus_tag
PAU_01966 2238793 2238972 + hypothetical_protein no_locus_tag
PAU_01967 2238959 2239642 + hypothetical_protein no_locus_tag
PAU_01968 2239639 2241240 + Rhs_element_Vgr_protein no_locus_tag
PAU_01969 2241253 2241696 + baseplate_wedge_subunit no_locus_tag
PAU_01970 2241693 2242109 + hypothetical_protein no_locus_tag
PAU_01971 2242318 2245044 + hypothetical_protein no_locus_tag
PAU_01972 2245037 2247988 + hypothetical_protein no_locus_tag
PAU_01973 2248124 2248975 + hypothetical_protein no_locus_tag
PAU_01974 2249038 2250936 + hypothetical_protein no_locus_tag
PAU_01976 2253043 2253957 + hypothetical_protein no_locus_tag
PAU_01977 2254118 2255014 + hypothetical_protein no_locus_tag
PAU_01978 2255099 2256082 + hypothetical_protein no_locus_tag
PAU_01979 2256579 2257475 + hypothetical_protein no_locus_tag
PAU_01980 2257447 2257905 + hypothetical_protein no_locus_tag
Table of Blast hits (query gene, subject gene, %identity, blast score, %coverage, e-value):
PAU_01961 PAU_01961 100 309 100.0 2e-108
PAU_01962 PAU_01962 100 749 100.0 0.0
PAU_01963 PAU_01963 100 1015 100.0 0.0
PAU_01964 PAU_01964 100 821 100.0 0.0
PAU_01965 PAU_01965 100 312 100.0 2e-109
PAU_01966 PAU_01966 100 117 100.0 1e-35
PAU_01967 PAU_01967 100 471 100.0 1e-169
PAU_01968 PAU_01968 100 1095 100.0 0.0
PAU_01969 PAU_01969 100 298 100.0 5e-104
PAU_01970 PAU_01970 100 277 100.0 3e-96
PAU_01971 PAU_01971 100 1866 100.0 0.0
PAU_01972 PAU_01972 100 2034 100.0 0.0
PAU_01973 PAU_01973 100 583 100.0 0.0
PAU_01974 PAU_01974 100 1273 100.0 0.0
PAU_01976 PAU_01976 100 614 100.0 0.0
PAU_01977 PAU_01977 100 604 100.0 0.0
PAU_01978 PAU_01978 100 676 100.0 0.0
PAU_01979 PAU_01979 100 608 100.0 0.0
PAU_01980 PAU_01980 100 300 100.0 1e-104
>>
2. PAB_1
Source: Photorhabdus asymbiotica strain Beaudesert.
Number of proteins with BLAST hits to this cluster: 31
MultiGeneBlast score: 31.7
Cumulative Blast bit score: 62512
Table of genes, locations, strands and annotations of subject cluster:
cmlA 528550 528990 + Chloramphenicol_acetyltransferase_2 no_locus_tag
PAB_00496 530556 531005 + T4-like_virus_tail_tube_protein_gp19 no_locus_tag
PAB_00497 531069 532169 + major_tail_sheath_protein no_locus_tag
PAB_00498 532217 533698 + tail_sheath_protein no_locus_tag
PAB_00499 533752 534951 + tail_sheath_protein no_locus_tag
PAB_00500 534965 535423 + T4-like_virus_tail_tube_protein_gp19 no_locus_tag
PAB_00501 535420 535599 + hypothetical_protein no_locus_tag
PAB_00502 535586 536269 + hypothetical_protein no_locus_tag
PAB_00503 536266 537867 + Rhs_element_Vgr_protein no_locus_tag
PAB_00504 537880 538323 + baseplate_wedge_subunit no_locus_tag
PAB_00505 538320 538733 + hypothetical_protein no_locus_tag
PAB_00506 538802 541537 + hypothetical_protein no_locus_tag
PAB_00507 541530 544499 + hypothetical_protein no_locus_tag
PAB_00508 544638 545486 + hypothetical_protein no_locus_tag
PAB_00509 545549 547444 + hypothetical_protein no_locus_tag
ftsH_1 547454 549538 + ATP-dependent_zinc_metalloprotease_FtsH no_locus_tag
PAB_00511 549563 550462 + hypothetical_protein no_locus_tag
PAB_00512 550627 551526 + hypothetical_protein no_locus_tag
PAB_00516 554417 555034 + hypothetical_protein no_locus_tag
PAB_00517 555006 555464 + hypothetical_protein no_locus_tag
dsdX_1 555806 557191 - DsdX_permease no_locus_tag
srlR_1 558367 559143 - Glucitol_operon_repressor no_locus_tag
ygbM 559155 559934 - Putative_hydroxypyruvate_isomerase_YgbM no_locus_tag
fucA_1 560079 560714 - L-fuculose_phosphate_aldolase no_locus_tag
Table of Blast hits (query gene, subject gene, %identity, blast score, %coverage, e-value):
PAU_01961 PAB_00496 99 308 100.0 5e-108
PAU_01962 PAB_00497 91 692 100.273972603 0.0
PAU_01963 PAB_00498 84 803 101.419878296 0.0
PAU_01964 PAB_00499 92 770 100.0 0.0
PAU_01965 PAB_00500 96 302 99.3421052632 2e-105
PAU_01966 PAB_00501 98 115 100.0 6e-35
PAU_01967 PAB_00502 95 453 100.0 2e-162
PAU_01968 PAB_00503 94 1039 100.0 0.0
PAU_01969 PAB_00504 93 280 100.0 1e-96
PAU_01970 PAB_00505 89 248 100.0 2e-84
PAU_01971 PAB_00506 84 1572 100.330396476 0.0
PAU_01972 PAB_00507 84 1706 100.915564598 0.0
PAU_01973 PAB_00508 72 410 100.706713781 9e-144
PAU_01974 PAB_00509 79 992 100.316455696 0.0
PAU_01975 ftsH_1 77 1095 100.579710145 0.0
PAU_01976 PAB_00511 83 507 98.6842105263 0.0
PAU_01977 PAB_00512 87 533 100.0 0.0
PAU_01979 PAB_00516 95 396 68.7919463087 3e-139
PAU_01980 PAB_00517 96 291 100.0 4e-101
>>
3. PAN_5
Source: Photorhabdus asymbiotica strain Nepal.
Number of proteins with BLAST hits to this cluster: 29
MultiGeneBlast score: 29.2
Cumulative Blast bit score: 61588
Table of genes, locations, strands and annotations of subject cluster:
tdiR 3118573 3119202 + Transcriptional_regulatory_protein_TdiR no_locus_tag
xerD_3 3123014 3123238 - Tyrosine_recombinase_XerD no_locus_tag
PAN_02769 3124026 3124475 + T4-like_virus_tail_tube_protein_gp19 no_locus_tag
PAN_02770 3124539 3125639 + major_tail_sheath_protein no_locus_tag
PAN_02771 3125687 3127156 + tail_sheath_protein no_locus_tag
PAN_02772 3127210 3128409 + tail_sheath_protein no_locus_tag
PAN_02773 3128423 3128881 + T4-like_virus_tail_tube_protein_gp19 no_locus_tag
PAN_02774 3128878 3129057 + hypothetical_protein no_locus_tag
PAN_02775 3129044 3129727 + hypothetical_protein no_locus_tag
PAN_02776 3129724 3131325 + Rhs_element_Vgr_protein no_locus_tag
PAN_02777 3131338 3131781 + baseplate_wedge_subunit no_locus_tag
PAN_02778 3131778 3132191 + hypothetical_protein no_locus_tag
PAN_02779 3132260 3134998 + hypothetical_protein no_locus_tag
PAN_02780 3134991 3137954 + hypothetical_protein no_locus_tag
PAN_02781 3138093 3138938 + hypothetical_protein no_locus_tag
PAN_02782 3139001 3140908 + hypothetical_protein no_locus_tag
PAN_02784 3143027 3143926 + hypothetical_protein no_locus_tag
PAN_02785 3144090 3144989 + hypothetical_protein no_locus_tag
PAN_02789 3146760 3147656 + hypothetical_protein no_locus_tag
PAN_02790 3147628 3148086 + hypothetical_protein no_locus_tag
hcpA_11 3148136 3148615 - Secreted_protein_hcp no_locus_tag
ygbN 3148802 3150187 - Inner_membrane_permease_YgbN no_locus_tag
Table of Blast hits (query gene, subject gene, %identity, blast score, %coverage, e-value):
PAU_01961 PAN_02769 99 308 100.0 5e-108
PAU_01962 PAN_02770 91 691 100.273972603 0.0
PAU_01963 PAN_02771 85 810 100.60851927 0.0
PAU_01964 PAN_02772 92 769 100.0 0.0
PAU_01965 PAN_02773 97 305 99.3421052632 1e-106
PAU_01966 PAN_02774 98 115 100.0 6e-35
PAU_01967 PAN_02775 95 452 100.0 3e-162
PAU_01968 PAN_02776 94 1040 100.0 0.0
PAU_01969 PAN_02777 93 280 100.0 1e-96
PAU_01970 PAN_02778 90 251 100.0 9e-86
PAU_01971 PAN_02779 84 1571 100.660792952 0.0
PAU_01972 PAN_02780 84 1701 100.915564598 0.0
PAU_01973 PAN_02781 70 407 100.706713781 1e-142
PAU_01974 PAN_02782 79 981 100.949367089 0.0
PAU_01976 PAN_02784 82 503 98.6842105263 1e-179
PAU_01977 PAN_02785 87 536 100.0 0.0
PAU_01979 PAN_02789 94 572 100.0 0.0
PAU_01980 PAN_02790 97 296 100.0 5e-103
>>
4. PAT_0
Source: Photorhabdus asymbiotica strain Thai.
Number of proteins with BLAST hits to this cluster: 29
MultiGeneBlast score: 29.2
Cumulative Blast bit score: 61577
Table of genes, locations, strands and annotations of subject cluster:
PAT_00132 127877 128326 + T4-like_virus_tail_tube_protein_gp19 no_locus_tag
PAT_00133 128390 129490 + major_tail_sheath_protein no_locus_tag
PAT_00134 129538 131007 + tail_sheath_protein no_locus_tag
PAT_00135 131061 132260 + tail_sheath_protein no_locus_tag
PAT_00136 132274 132732 + T4-like_virus_tail_tube_protein_gp19 no_locus_tag
PAT_00137 132729 132908 + hypothetical_protein no_locus_tag
PAT_00138 132895 133578 + hypothetical_protein no_locus_tag
PAT_00139 133575 135176 + Rhs_element_Vgr_protein no_locus_tag
PAT_00140 135189 135632 + baseplate_wedge_subunit no_locus_tag
PAT_00141 135629 136042 + hypothetical_protein no_locus_tag
PAT_00142 136111 138885 + hypothetical_protein no_locus_tag
PAT_00143 138878 141841 + hypothetical_protein no_locus_tag
PAT_00144 141980 142825 + hypothetical_protein no_locus_tag
PAT_00145 142888 144795 + hypothetical_protein no_locus_tag
PAT_00147 146914 147813 + hypothetical_protein no_locus_tag
PAT_00148 147977 148876 + hypothetical_protein no_locus_tag
PAT_00152 150647 151543 + hypothetical_protein no_locus_tag
PAT_00153 151515 151973 + hypothetical_protein no_locus_tag
hcpA_1 152023 152502 - Secreted_protein_hcp no_locus_tag
Table of Blast hits (query gene, subject gene, %identity, blast score, %coverage, e-value):
PAU_01961 PAT_00132 99 308 100.0 5e-108
PAU_01962 PAT_00133 91 693 100.273972603 0.0
PAU_01963 PAT_00134 85 810 100.60851927 0.0
PAU_01964 PAT_00135 92 769 100.0 0.0
PAU_01965 PAT_00136 97 305 99.3421052632 1e-106
PAU_01966 PAT_00137 98 115 100.0 6e-35
PAU_01967 PAT_00138 95 452 100.0 3e-162
PAU_01968 PAT_00139 94 1039 100.0 0.0
PAU_01969 PAT_00140 93 280 100.0 1e-96
PAU_01970 PAT_00141 89 249 100.0 5e-85
PAU_01971 PAT_00142 83 1568 101.982378855 0.0
PAU_01972 PAT_00143 84 1701 100.915564598 0.0
PAU_01973 PAT_00144 70 407 100.706713781 1e-142
PAU_01974 PAT_00145 78 974 100.949367089 0.0
PAU_01976 PAT_00147 82 503 98.6842105263 1e-179
PAU_01977 PAT_00148 87 536 100.0 0.0
PAU_01979 PAT_00152 94 572 100.0 0.0
PAU_01980 PAT_00153 97 296 100.0 5e-103
Raw
parse_blast.r
library(dplyr)
library(stringr)
text <- readLines("parse.txt")
#Function to split the text into sections based on >> indicator
f_section <- function(text, pattern = "^>>"){
.ind <- grep("^>>", text) %>%
c(1,.)
.result <- lapply(seq(.ind),function(i) text[.ind[i]:c(.ind[-1]-1,length(text))[i]])
return(.result)
}
#Function to find the significant hits
f_significance <- function(vec, cut_off = 30){
.ind <- vec %>% grep("^Significant",.)
.rs <- sapply(vec[.ind:length(vec)], function (x) str_length(x) > cut_off) %>%
vec[.ind:length(vec)][.] %>%
str_split(.,"\\s{4}") %>%
do.call(rbind, .) %>%
as_data_frame()
return(.rs)
}
# Function to find table by its name, i.e. Table of genes; Table of Blast hits
f_table <- function(vec, pattern = "^Table of genes"){
.ind <- grep(pattern, vec) #Find index of the Table name
.end_table_index <- sapply(vec[.ind: length(vec)], function(x) x=="") %>%
which %>% #Find index of x==""
head(.,1) #End of each table is an empty line ""
if (length(.end_table_index) == 0) {
.end_table_index = length(vec)
}
.new_table <- vec[(.ind+1):(.ind +.end_table_index-2)] %>% #Create new table from index of table name to the first empty line
str_trim() %>% #Clean 'invisible' space
str_split(.,"\\s{1,}") %>% #Split text by space into new vector
do.call(rbind, .) %>% #Combine all splitted vecto to a array
as_data_frame() #Format as a data frame
return(.new_table)
}
#Function to extract hit scores
f_score <- function(vec, pattern){
.result <- vec %>%
grep(pattern,., value = TRUE) %>%
gsub("[A-Za-z:\\s]","",., perl = TRUE)
return(.result)
}
f_details <- function(vec){
BLAST_cluster <- f_score(vec, "Number of proteins with BLAST hits to this cluster")
MultiGeneBlast <- f_score(vec, "MultiGeneBlast")
BLAST_bit_score <- f_score(vec, "Cumulative Blast bit score")
table_genes <- f_table(vec, pattern = "^Table of genes")
table_blast_hits <- f_table(vec, pattern = "^Table of Blast hits")
return(list(BLAST_cluster = BLAST_cluster,
MultiGeneBlast = MultiGeneBlast,
BLAST_bit_score = BLAST_bit_score,
table_genes = table_genes,
table_blast_hits = table_blast_hits))
}
sections <- f_section(text)
section_1 <- f_table(sections[[1]])
section_2 <- f_significance(sections[[1]])
section_3 <- lapply(sections[-1], function(x) f_details(x))
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