How to write multi-sequence alignment data frame as a fasta format fast

Question

I have a data frame where the row names are the species names, and each column can either be an Amino-Acid character or "-".

I wish to write it in a fasta format. Simple example of the format is:

>UniRef90_A0A1V4QIJ3
------------------------------------------------------------
--------------------------MDISTFSP-----PVAG-----------VE----
------ITAF-------------V------------------------------------
LN--------G-------------------------------------------------
----EKIPA-----------------------------------------IVLSKD----
---LNPFL------------------Q-ELLDQEPAC-----------------------
------------EHDIGTCYG------------------------DA-------------
--------------------------------------------------PC-----IS-
-----------------------GPDAWNHSGFQC----Q---------VC---------
------------GLVKSWNL-------------------VGDFVVYRQE-----------
>UniRef90_A0A0L9V5F8
------------------------------------------------------------
RFHTLFRNEYGHLRVLQRFDQRSKQIQNLENYRLVEFKSKPNTLLLPHHADADFLLVVLN
GRALLTLVNP-------------D---------------------------------G--
RDSYILEQGHA-------------------------------------------------
----QKIPAGTIFFLVNPNDNENLRI------------------------IKIATPINNP
HRFQDFFL-------------SSTEAQQSYLQG--FS-----------------------
----------------KNVLEASFDSEFKEINRVLFGEEGQQQQGEESQQEGVIVELERE
QIRELIKHA-----------------------------------------KSSSRRSLS-
-----------------------SQ-----DEPFNLRNRKP--------IY--SN-----
------------KF-GRWYEITPEKNP------------Q--------------------

I can do it using the following for loop:

for (n in row.names(df)){
    ss = do.call(paste, c(as.list(mu_df[1, ]), sep = ""))
    write.fasta(ss,
                  names=n,
                  as.string=TRUE,
                  open="a",
                  new_file_path)
}

Is there a faster way of writing it? I have to write millions of those files and I wish to optimize it.

In order to create the data frame:

structure(list(V1 = c("-", "-"), V2 = c("-", "-"), V3 = c("-", 
"-"), V4 = c("-", "-"), V5 = c("-", "-"), V6 = c("-", "-"), V7 = c("-", 
"-"), V8 = c("-", "-"), V9 = c("-", "-"), V10 = c("-", "-"), 
    V11 = c("-", "-"), V12 = c("-", "-"), V13 = c("-", "-"), 
    V14 = c("-", "-"), V15 = c("-", "-"), V16 = c("-", "-"), 
    V17 = c("-", "-"), V18 = c("-", "-"), V19 = c("-", "-"), 
    V20 = c("-", "-"), V21 = c("-", "-"), V22 = c("-", "-"), 
    V23 = c("-", "-"), V24 = c("-", "-"), V25 = c("-", "-"), 
    V26 = c("-", "-"), V27 = c("-", "-"), V28 = c("-", "-"), 
    V29 = c("-", "-"), V30 = c("-", "-"), V31 = c("-", "-"), 
    V32 = c("-", "-"), V33 = c("-", "-"), V34 = c("-", "-"), 
    V35 = c("-", "-"), V36 = c("-", "-"), V37 = c("-", "-"), 
    V38 = c("-", "-"), V39 = c("-", "-"), V40 = c("-", "-"), 
    V41 = c("-", "-"), V42 = c("-", "-"), V43 = c("-", "-"), 
    V44 = c("-", "-"), V45 = c("-", "-"), V46 = c("-", "-"), 
    V47 = c("-", "-"), V48 = c("-", "-"), V49 = c("-", "-"), 
    V50 = c("-", "-"), V51 = c("-", "-"), V52 = c("-", "-"), 
    V53 = c("-", "-"), V54 = c("-", "-"), V55 = c("-", "-"), 
    V56 = c("-", "-"), V57 = c("-", "-"), V58 = c("-", "-"), 
    V59 = c("-", "-"), V60 = c("-", "-"), V61 = c("-", "R"), 
    V62 = c("-", "F"), V63 = c("-", "H"), V64 = c("-", "T"), 
    V65 = c("-", "L"), V66 = c("-", "F"), V67 = c("-", "R"), 
    V68 = c("-", "N"), V69 = c("-", "E"), V70 = c("-", "Y"), 
    V71 = c("-", "G"), V72 = c("-", "H"), V73 = c("-", "L"), 
    V74 = c("-", "R"), V75 = c("-", "V"), V76 = c("-", "L"), 
    V77 = c("-", "Q"), V78 = c("-", "R"), V79 = c("-", "F"), 
    V80 = c("-", "D"), V81 = c("-", "Q"), V82 = c("-", "R"), 
    V83 = c("-", "S"), V84 = c("-", "K"), V85 = c("-", "Q"), 
    V86 = c("-", "I"), V87 = c("M", "Q"), V88 = c("D", "N"), 
    V89 = c("I", "L"), V90 = c("S", "E"), V91 = c("T", "N"), 
    V92 = c("F", "Y"), V93 = c("S", "R"), V94 = c("P", "L"), 
    V95 = c("-", "V"), V96 = c("-", "E"), V97 = c("-", "F"), 
    V98 = c("-", "K"), V99 = c("-", "S"), V100 = c("P", "K"), 
    V101 = c("V", "P"), V102 = c("A", "N"), V103 = c("G", "T"
    ), V104 = c("-", "L"), V105 = c("-", "L"), V106 = c("-", 
    "L"), V107 = c("-", "P"), V108 = c("-", "H"), V109 = c("-", 
    "H"), V110 = c("-", "A"), V111 = c("-", "D"), V112 = c("-", 
    "A"), V113 = c("-", "D"), V114 = c("-", "F"), V115 = c("V", 
    "L"), V116 = c("E", "L"), V117 = c("-", "V"), V118 = c("-", 
    "V"), V119 = c("-", "L"), V120 = c("-", "N"), V121 = c("-", 
    "G"), V122 = c("-", "R"), V123 = c("-", "A"), V124 = c("-", 
    "L"), V125 = c("-", "L"), V126 = c("-", "T"), V127 = c("I", 
    "L"), V128 = c("T", "V"), V129 = c("A", "N"), V130 = c("F", 
    "P"), V131 = c("-", "-"), V132 = c("-", "-"), V133 = c("-", 
    "-"), V134 = c("-", "-"), V135 = c("-", "-"), V136 = c("-", 
    "-"), V137 = c("-", "-"), V138 = c("-", "-"), V139 = c("-", 
    "-"), V140 = c("-", "-"), V141 = c("-", "-"), V142 = c("-", 
    "-"), V143 = c("-", "-"), V144 = c("V", "D"), V145 = c("-", 
    "-"), V146 = c("-", "-"), V147 = c("-", "-"), V148 = c("-", 
    "-"), V149 = c("-", "-"), V150 = c("-", "-"), V151 = c("-", 
    "-"), V152 = c("-", "-"), V153 = c("-", "-"), V154 = c("-", 
    "-"), V155 = c("-", "-"), V156 = c("-", "-"), V157 = c("-", 
    "-"), V158 = c("-", "-"), V159 = c("-", "-"), V160 = c("-", 
    "-"), V161 = c("-", "-"), V162 = c("-", "-"), V163 = c("-", 
    "-"), V164 = c("-", "-"), V165 = c("-", "-"), V166 = c("-", 
    "-"), V167 = c("-", "-"), V168 = c("-", "-"), V169 = c("-", 
    "-"), V170 = c("-", "-"), V171 = c("-", "-"), V172 = c("-", 
    "-"), V173 = c("-", "-"), V174 = c("-", "-"), V175 = c("-", 
    "-"), V176 = c("-", "-"), V177 = c("-", "-"), V178 = c("-", 
    "G"), V179 = c("-", "-"), V180 = c("-", "-"), V181 = c("L", 
    "R"), V182 = c("N", "D"), V183 = c("-", "S"), V184 = c("-", 
    "Y"), V185 = c("-", "I"), V186 = c("-", "L"), V187 = c("-", 
    "E"), V188 = c("-", "Q"), V189 = c("-", "G"), V190 = c("-", 
    "H"), V191 = c("G", "A"), V192 = c("-", "-"), V193 = c("-", 
    "-"), V194 = c("-", "-"), V195 = c("-", "-"), V196 = c("-", 
    "-"), V197 = c("-", "-"), V198 = c("-", "-"), V199 = c("-", 
    "-"), V200 = c("-", "-"), V201 = c("-", "-"), V202 = c("-", 
    "-"), V203 = c("-", "-"), V204 = c("-", "-"), V205 = c("-", 
    "-"), V206 = c("-", "-"), V207 = c("-", "-"), V208 = c("-", 
    "-"), V209 = c("-", "-"), V210 = c("-", "-"), V211 = c("-", 
    "-"), V212 = c("-", "-"), V213 = c("-", "-"), V214 = c("-", 
    "-"), V215 = c("-", "-"), V216 = c("-", "-"), V217 = c("-", 
    "-"), V218 = c("-", "-"), V219 = c("-", "-"), V220 = c("-", 
    "-"), V221 = c("-", "-"), V222 = c("-", "-"), V223 = c("-", 
    "-"), V224 = c("-", "-"), V225 = c("-", "-"), V226 = c("-", 
    "-"), V227 = c("-", "-"), V228 = c("-", "-"), V229 = c("-", 
    "-"), V230 = c("-", "-"), V231 = c("-", "-"), V232 = c("-", 
    "-"), V233 = c("-", "-"), V234 = c("-", "-"), V235 = c("-", 
    "-"), V236 = c("-", "-"), V237 = c("-", "-"), V238 = c("-", 
    "-"), V239 = c("-", "-"), V240 = c("-", "-"), V241 = c("-", 
    "-"), V242 = c("-", "-"), V243 = c("-", "-"), V244 = c("-", 
    "-"), V245 = c("E", "Q"), V246 = c("K", "K"), V247 = c("I", 
    "I"), V248 = c("P", "P"), V249 = c("A", "A"), V250 = c("-", 
    "G"), V251 = c("-", "T"), V252 = c("-", "I"), V253 = c("-", 
    "F"), V254 = c("-", "F"), V255 = c("-", "L"), V256 = c("-", 
    "V"), V257 = c("-", "N"), V258 = c("-", "P"), V259 = c("-", 
    "N"), V260 = c("-", "D"), V261 = c("-", "N"), V262 = c("-", 
    "E"), V263 = c("-", "N"), V264 = c("-", "L"), V265 = c("-", 
    "R"), V266 = c("-", "I"), V267 = c("-", "-"), V268 = c("-", 
    "-"), V269 = c("-", "-"), V270 = c("-", "-"), V271 = c("-", 
    "-"), V272 = c("-", "-"), V273 = c("-", "-"), V274 = c("-", 
    "-"), V275 = c("-", "-"), V276 = c("-", "-"), V277 = c("-", 
    "-"), V278 = c("-", "-"), V279 = c("-", "-"), V280 = c("-", 
    "-"), V281 = c("-", "-"), V282 = c("-", "-"), V283 = c("-", 
    "-"), V284 = c("-", "-"), V285 = c("-", "-"), V286 = c("-", 
    "-"), V287 = c("-", "-"), V288 = c("-", "-"), V289 = c("-", 
    "-"), V290 = c("-", "-"), V291 = c("I", "I"), V292 = c("V", 
    "K"), V293 = c("L", "I"), V294 = c("S", "A"), V295 = c("K", 
    "T"), V296 = c("D", "P"), V297 = c("-", "I"), V298 = c("-", 
    "N"), V299 = c("-", "N"), V300 = c("-", "P"), V301 = c("-", 
    "H"), V302 = c("-", "R"), V303 = c("-", "F"), V304 = c("L", 
    "Q"), V305 = c("N", "D"), V306 = c("P", "F"), V307 = c("F", 
    "F"), V308 = c("L", "L"), V309 = c("-", "-"), V310 = c("-", 
    "-"), V311 = c("-", "-"), V312 = c("-", "-"), V313 = c("-", 
    "-"), V314 = c("-", "-"), V315 = c("-", "-"), V316 = c("-", 
    "-"), V317 = c("-", "-"), V318 = c("-", "-"), V319 = c("-", 
    "-"), V320 = c("-", "-"), V321 = c("-", "-"), V322 = c("-", 
    "S"), V323 = c("-", "S"), V324 = c("-", "T"), V325 = c("-", 
    "E"), V326 = c("-", "A"), V327 = c("Q", "Q"), V328 = c("-", 
    "Q"), V329 = c("E", "S"), V330 = c("L", "Y"), V331 = c("L", 
    "L"), V332 = c("D", "Q"), V333 = c("Q", "G"), V334 = c("E", 
    "-"), V335 = c("P", "-"), V336 = c("A", "F"), V337 = c("C", 
    "S"), V338 = c("-", "-"), V339 = c("-", "-"), V340 = c("-", 
    "-"), V341 = c("-", "-"), V342 = c("-", "-"), V343 = c("-", 
    "-"), V344 = c("-", "-"), V345 = c("-", "-"), V346 = c("-", 
    "-"), V347 = c("-", "-"), V348 = c("-", "-"), V349 = c("-", 
    "-"), V350 = c("-", "-"), V351 = c("-", "-"), V352 = c("-", 
    "-"), V353 = c("-", "-"), V354 = c("-", "-"), V355 = c("-", 
    "-"), V356 = c("-", "-"), V357 = c("-", "-"), V358 = c("-", 
    "-"), V359 = c("-", "-"), V360 = c("-", "-"), V361 = c("-", 
    "-"), V362 = c("-", "-"), V363 = c("-", "-"), V364 = c("-", 
    "-"), V365 = c("-", "-"), V366 = c("-", "-"), V367 = c("-", 
    "-"), V368 = c("-", "-"), V369 = c("-", "-"), V370 = c("-", 
    "-"), V371 = c("-", "-"), V372 = c("-", "-"), V373 = c("E", 
    "-"), V374 = c("H", "-"), V375 = c("D", "-"), V376 = c("I", 
    "-"), V377 = c("G", "K"), V378 = c("T", "N"), V379 = c("C", 
    "V"), V380 = c("Y", "L"), V381 = c("G", "E"), V382 = c("-", 
    "A"), V383 = c("-", "S"), V384 = c("-", "F"), V385 = c("-", 
    "D"), V386 = c("-", "S"), V387 = c("-", "E"), V388 = c("-", 
    "F"), V389 = c("-", "K"), V390 = c("-", "E"), V391 = c("-", 
    "I"), V392 = c("-", "N"), V393 = c("-", "R"), V394 = c("-", 
    "V"), V395 = c("-", "L"), V396 = c("-", "F"), V397 = c("-", 
    "G"), V398 = c("-", "E"), V399 = c("-", "E"), V400 = c("-", 
    "G"), V401 = c("-", "Q"), V402 = c("-", "Q"), V403 = c("-", 
    "Q"), V404 = c("-", "Q"), V405 = c("-", "G"), V406 = c("D", 
    "E"), V407 = c("A", "E"), V408 = c("-", "S"), V409 = c("-", 
    "Q"), V410 = c("-", "Q"), V411 = c("-", "E"), V412 = c("-", 
    "G"), V413 = c("-", "V"), V414 = c("-", "I"), V415 = c("-", 
    "V"), V416 = c("-", "E"), V417 = c("-", "L"), V418 = c("-", 
    "E"), V419 = c("-", "R"), V420 = c("-", "E"), V421 = c("-", 
    "Q"), V422 = c("-", "I"), V423 = c("-", "R"), V424 = c("-", 
    "E"), V425 = c("-", "L"), V426 = c("-", "I"), V427 = c("-", 
    "K"), V428 = c("-", "H"), V429 = c("-", "A"), V430 = c("-", 
    "-"), V431 = c("-", "-"), V432 = c("-", "-"), V433 = c("-", 
    "-"), V434 = c("-", "-"), V435 = c("-", "-"), V436 = c("-", 
    "-"), V437 = c("-", "-"), V438 = c("-", "-"), V439 = c("-", 
    "-"), V440 = c("-", "-"), V441 = c("-", "-"), V442 = c("-", 
    "-"), V443 = c("-", "-"), V444 = c("-", "-"), V445 = c("-", 
    "-"), V446 = c("-", "-"), V447 = c("-", "-"), V448 = c("-", 
    "-"), V449 = c("-", "-"), V450 = c("-", "-"), V451 = c("-", 
    "-"), V452 = c("-", "-"), V453 = c("-", "-"), V454 = c("-", 
    "-"), V455 = c("-", "-"), V456 = c("-", "-"), V457 = c("-", 
    "-"), V458 = c("-", "-"), V459 = c("-", "-"), V460 = c("-", 
    "-"), V461 = c("-", "-"), V462 = c("-", "-"), V463 = c("-", 
    "-"), V464 = c("-", "-"), V465 = c("-", "-"), V466 = c("-", 
    "-"), V467 = c("-", "-"), V468 = c("-", "-"), V469 = c("-", 
    "-"), V470 = c("-", "-"), V471 = c("P", "K"), V472 = c("C", 
    "S"), V473 = c("-", "S"), V474 = c("-", "S"), V475 = c("-", 
    "R"), V476 = c("-", "R"), V477 = c("-", "S"), V478 = c("I", 
    "L"), V479 = c("S", "S"), V480 = c("-", "-"), V481 = c("-", 
    "-"), V482 = c("-", "-"), V483 = c("-", "-"), V484 = c("-", 
    "-"), V485 = c("-", "-"), V486 = c("-", "-"), V487 = c("-", 
    "-"), V488 = c("-", "-"), V489 = c("-", "-"), V490 = c("-", 
    "-"), V491 = c("-", "-"), V492 = c("-", "-"), V493 = c("-", 
    "-"), V494 = c("-", "-"), V495 = c("-", "-"), V496 = c("-", 
    "-"), V497 = c("-", "-"), V498 = c("-", "-"), V499 = c("-", 
    "-"), V500 = c("-", "-"), V501 = c("-", "-"), V502 = c("-", 
    "-"), V503 = c("-", "-"), V504 = c("G", "S"), V505 = c("P", 
    "Q"), V506 = c("D", "-"), V507 = c("A", "-"), V508 = c("W", 
    "-"), V509 = c("N", "-"), V510 = c("H", "-"), V511 = c("S", 
    "D"), V512 = c("G", "E"), V513 = c("F", "P"), V514 = c("Q", 
    "F"), V515 = c("C", "N"), V516 = c("-", "L"), V517 = c("-", 
    "R"), V518 = c("-", "N"), V519 = c("-", "R"), V520 = c("Q", 
    "K"), V521 = c("-", "P"), V522 = c("-", "-"), V523 = c("-", 
    "-"), V524 = c("-", "-"), V525 = c("-", "-"), V526 = c("-", 
    "-"), V527 = c("-", "-"), V528 = c("-", "-"), V529 = c("-", 
    "-"), V530 = c("V", "I"), V531 = c("C", "Y"), V532 = c("-", 
    "-"), V533 = c("-", "-"), V534 = c("-", "S"), V535 = c("-", 
    "N"), V536 = c("-", "-"), V537 = c("-", "-"), V538 = c("-", 
    "-"), V539 = c("-", "-"), V540 = c("-", "-"), V541 = c("-", 
    "-"), V542 = c("-", "-"), V543 = c("-", "-"), V544 = c("-", 
    "-"), V545 = c("-", "-"), V546 = c("-", "-"), V547 = c("-", 
    "-"), V548 = c("-", "-"), V549 = c("-", "-"), V550 = c("-", 
    "-"), V551 = c("-", "-"), V552 = c("-", "-"), V553 = c("G", 
    "K"), V554 = c("L", "F"), V555 = c("V", "-"), V556 = c("K", 
    "G"), V557 = c("S", "R"), V558 = c("W", "W"), V559 = c("N", 
    "Y"), V560 = c("L", "E"), V561 = c("-", "I"), V562 = c("-", 
    "T"), V563 = c("-", "P"), V564 = c("-", "E"), V565 = c("-", 
    "K"), V566 = c("-", "N"), V567 = c("-", "P"), V568 = c("-", 
    "-"), V569 = c("-", "-"), V570 = c("-", "-"), V571 = c("-", 
    "-"), V572 = c("-", "-"), V573 = c("-", "-"), V574 = c("-", 
    "-"), V575 = c("-", "-"), V576 = c("-", "-"), V577 = c("-", 
    "-"), V578 = c("-", "-"), V579 = c("-", "-"), V580 = c("V", 
    "Q"), V581 = c("G", "-"), V582 = c("D", "-"), V583 = c("F", 
    "-"), V584 = c("V", "-"), V585 = c("V", "-"), V586 = c("Y", 
    "-"), V587 = c("R", "-"), V588 = c("Q", "-"), V589 = c("E", 
    "-"), V590 = c("-", "-"), V591 = c("-", "-"), V592 = c("-", 
    "-"), V593 = c("-", "-"), V594 = c("-", "-"), V595 = c("-", 
    "-"), V596 = c("-", "-"), V597 = c("-", "-"), V598 = c("-", 
    "-"), V599 = c("-", "-"), V600 = c("-", "-")), class = "data.frame", row.names = c("UniRef90_A0A1V4QIJ3", 
"UniRef90_A0A0L9V5F8"))

Answer 1

Update

It seems that part of the desired behavior is to write the sequences in the alignment separately. I am not sure that I understand why it is necessary to write them separately. Generally it is inadvisable to write many small files rather than one big file, based purely on issues of performance; you are likely to hit the I/O bound on performance very quickly, and that will be much slower.

One solution that has been suggested previously for this kind of problem is to write the whole alignment to a single file, and then post-process that filed in a second step to extract the sequences of interest. This could be as trivial as a samtools faidx call from the shell, or you could work with it in seqinr as suggested in the previous answer.

Of course, it seems like it would be simpler for most purposes to just have the big alignment file and use e.g. samtools indexing / faidx / biopython / whatever to extract the sequences of interest. But it seems that that is specifically not desired in this case.

Original answer

I would strongly suggest using the seqinr package, which is optimized for solving exactly these problems. See e.g. this similar question.

You will be able to read in an alignment (or whatever), cast it to as.matrix.alignment, do whatever your analysis is, then cast it back to as.alignment, which can then be passed to write.fasta to write the files.

Whenever possible it is preferable to work with such libraries, which handle these utility functions well, fast, and easy.