Entering edit mode
8.4 years ago
mforthman
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50
I've posted this question before without any success in resolving my issue; one answer was provided and did not work. Rather than entirely redoing the old thread, I'm creating a new one. I performed pairwise RBH with transcriptomes against a reference. I pooled the individual outputs into one:
query id query length subject id subject length qframe qstart qend sframe sstart send evalue bitscore pident nident length qframe qstart qend sframe sstart send evalue bitscore pident nident length
Apil_comp27594_c0_seq1 274 OFAS000003-RA-EXON01 483 1 140 269 1 3 133 2.00E-37 152 87.79 115 131 1 3 133 1 140 269 1.00E-36 152 87.79 115 131
Btri_comp28710_c0_seq1 495 OFAS000003-RA-EXON01 483 1 43 170 1 130 3 3.00E-39 159 89.06 114 128 1 3 130 1 170 43 9.00E-39 159 89.06 114 128
Apil_comp19172_c0_seq1 2893 OFAS000101-RA-EXON03 229 1 306 532 1 1 227 7.00E-52 204 82.89 189 228 1 1 227 1 306 532 1.00E-52 204 82.89 189 228
Ctom_512426543_01008091.1 743 OFAS000115-RA-EXON01 531 1 14 188 1 357 531 1.00E-33 141 81.14 142 175 1 357 531 1 14 188 8.00E-34 141 81.14 142 175
Apil_comp16418_c0_seq1 2079 OFAS000119-RA-EXON01 1584 1 414 2001 1 1 1584 0 963 77.85 1248 1603 1 1 1584 1 414 2001 0 963 77.85 1248 1603
Atri_comp13712_c0_seq1 1938 OFAS000119-RA-EXON01 1584 1 199 1640 1 1455 14 0 913 78.21 1134 1450 1 14 1455 1 1640 199 0 913 78.21 1134 1450
Ctom_512431611_01003023.1 2162 OFAS000119-RA-EXON01 1584 1 104 1393 1 1304 13 0 861 78.78 1021 1296 1 13 1304 1 1393 104 0 861 78.78 1021 1296
Atri_comp37099_c0_seq1 568 OFAS000126-RA-EXON01 219 1 7 217 1 219 9 1.00E-58 224 85.78 181 211 1 9 219 1 217 7 1.00E-58 224 85.78 181 211
Apil_comp19291_c1_seq1 7078 OFAS000131-RA-EXON13 286 1 6308 6602 1 1 286 4.00E-73 276 84.12 249 296 1 1 286 1 6308 6602 4.00E-74 276 84.12 249 296
Atri_comp13247_c0_seq1 4998 OFAS000131-RA-EXON13 286 1 438 732 1 286 1 1.00E-66 254 82.71 244 295 1 1 286 1 732 438 2.00E-67 254 82.71 244 295
Btri_comp25977_c0_seq1 450 OFAS000146-RA-EXON01 514 1 196 341 1 514 368 2.00E-34 143 84.35 124 147 1 368 514 1 341 196 9.00E-34 143 84.35 124 147
Btri_comp11536_c0_seq1 1754 OFAS000161-RA-EXON02 225 1 348 565 1 8 225 4.00E-52 204 83.49 182 218 1 8 225 1 348 565 2.00E-52 204 83.49 182 218
Atri_comp27210_c0_seq1 613 OFAS000167-RA-EXON01 2433 1 10 603 1 2052 1456 1.00E-103 374 78.2 470 601 1 1456 2052 1 603 10 1.00E-102 374 78.2 470 601
Ctom_512426598_01008036.1 1040 OFAS000206-RA-EXON01 1897 1 4 806 1 1203 376 1.00E-115 414 76.29 634 831 1 376 1203 1 806 4 2.00E-115 414 76.29 634 831
Btri_comp20624_c0_seq1 1763 OFAS000234-RA-EXON01 6339 1 1201 1721 1 534 14 9.00E-44 176 73.31 390 532 1 14 534 1 1721 1201 1.00E-42 176 73.26 389 531
Apil_comp19456_c0_seq1 3549 OFAS000248-RA-EXON07 4189 1 759 3223 1 1 2465 0 1511 77.84 1928 2477 1 1 2465 1 759 3223 0 1511 77.84 1928 2477
Btri_comp15171_c0_seq1 3766 OFAS000248-RA-EXON07 4189 1 591 3048 1 2458 1 0 1736 79.48 1960 2466 1 1 2458 1 3048 591 0 1736 79.48 1960 2466
Atri_comp2678_c0_seq1 578 OFAS000260-RA-EXON01 1044 1 19 548 1 499 1028 3.00E-84 309 77.21 410 531 1 499 1028 1 19 548 2.00E-83 309 77.21 410 531
Btri_comp13833_c0_seq1 1368 OFAS000260-RA-EXON01 1044 1 278 1282 1 1005 1 0 732 79.88 806 1009 1 1 1005 1 1282 278 0 732 79.88 806 1009
Btri_comp12981_c0_seq1 1656 OFAS000280-RA-EXON05 266 1 596 831 1 239 4 2.00E-60 231 84.32 199 236 1 4 239 1 831 596 1.00E-60 231 84.32 199 236
Atri_comp11944_c0_seq1 603 OFAS000313-RA-EXON22 300 1 89 182 1 1 95 2.00E-25 113 88.42 84 95 1 1 95 1 89 182 4.00E-25 113 88.42 84 95
Btri_comp21809_c0_seq1 1434 OFAS000322-RA-EXON01 235 1 890 988 1 227 129 1.00E-17 89.8 82.83 82 99 1 129 227 1 988 890 5.00E-18 89.8 82.83 82 99
Apil_comp22429_c0_seq1 1431 OFAS000357-RA-EXON13 200 1 1070 1269 1 200 1 3.00E-42 171 82.18 166 202 1 1 200 1 1269 1070 1.00E-42 171 82.18 166 202
Apil_comp12506_c0_seq1 1808 OFAS000367-RA-EXON01 1605 1 120 1724 1 1605 1 0 1020 78.17 1257 1608 1 1 1605 1 1724 120 0 1020 78.23 1261 1612
Atri_comp19469_c0_seq1 1743 OFAS000386-RA-EXON06 262 1 961 1222 1 1 262 2.00E-36 152 77.27 204 264 1 1 262 1 961 1222 7.00E-37 152 77.27 204 264
Ctom_512432154_01002480.1 684 OFAS000386-RA-EXON06 262 1 369 624 1 256 1 6.00E-37 152 77.61 201 259 1 1 256 1 624 369 2.00E-37 152 77.52 200 258
Acur_512410417_01005903.1 1021 OFAS000453-RA-EXON04 210 1 923 1021 1 9 107 3.00E-36 150 93.94 93 99 1 9 107 1 923 1021 5.00E-37 150 93.94 93 99
Apil_comp9637_c0_seq1 1465 OFAS000453-RA-EXON04 210 1 1235 1437 1 1 205 4.00E-66 250 88.78 182 205 1 1 205 1 1235 1437 2.00E-66 250 88.78 182 205
Btri_comp5378_c0_seq1 1334 OFAS000453-RA-EXON04 210 1 1160 1332 1 1 173 1.00E-60 231 90.75 157 173 1 1 173 1 1160 1332 7.00E-61 231 90.75 157 173
I need to process this file so that I can create fasta files containing query sequences that hit to a given reference sequence. The query sequences should span the qstart and qend ranges within the fasta files. I would prefer fasta files that did not include the reference sequence, but would like the reference ID to be used for the fasta file name.
I have searched all over for a script or some insight on how to do this. People have used RBH for multispecies comparisons, beyond two species, and used these results to generate gene datasets. It's easy to get a script to perform RBH, but I cannot find anything that will let me process the output to generate gene datasets. Any advice would be most appreciated.
